diff --git a/.gitignore b/.gitignore
index 97f8f388..fe23b548 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,10 +5,9 @@ build/
 .idea/
 .DS_Store
 *~
-pyscripts/__src__.py
 a.out
 pyscripts/__src__.py
 dist/uedge-8.0.0-py3.7-macosx-10.9-x86_64.egg
 uedge.egg-info
-pyscripts/__src__.py
 *.egg
+*.c
diff --git a/a.out b/a.out
new file mode 100755
index 00000000..1c8e93d1
Binary files /dev/null and b/a.out differ
diff --git a/aph/aph.v b/aph/aph.v
index c6960b02..207e62ae 100755
--- a/aph/aph.v
+++ b/aph/aph.v
@@ -1,7 +1,7 @@
 aph   # Atomic physics (hydrogenic)
 
 ***** Physical_constants:
-ev	real	/1.6022e-19/   # 1 electron volt in Joules
+ev_aph	real	/1.6022e-19/   # 1 electron volt in Joules
 m_prot  real    /1.67e-27/     # proton mass
 
 ***** Data_input:
@@ -15,7 +15,7 @@ aphdir	character*120 # name of directory containing data files
 data_directory	character*120 # another dirname containing data files. This is to be be passed in
 
 ***** Ionization_energy:
-erad	real [eV] /25./ # tot elec engy loss/ioniz (rad+binding) if istabon=0
+erad	real [eV] /25./ +input # tot elec engy loss/ioniz (rad+binding) if istabon=0
 
 ***** Rtdata:
 # hydrogenic rate table data from ADPAK via Braams' rate code
@@ -145,23 +145,23 @@ readehr2(fname:string)	subroutine
 
 ***** Aphwrk:
 # working arrays for 2-d spline interpolation
-nxdata  integer
-nydata  integer
-xdata(1:nxdata)             _real
-ydata(1:nydata)             _real
-fdata(1:nxdata,1:nydata)    _real
-ldf                          integer
-iflag                        integer
-kxords  integer /4/               # order of spline fit versus log(te)
-                                  # kxords=4 (default) is cubic interpolation
-kyords  integer /4/               # order of spline fit versus log10(ne)
-                                  # kyords=4 (default) is cubic interpolation
-xknots(1:nxdata+kxords)     _real
-yknots(1:nydata+kyords)     _real
-workh(1:nxdata*nydata+2*kxords*(nxdata+1)) _real # work array
-rsacoef(1:nxdata,1:nydata)  _real # spline coeff's for ionization
-rracoef(1:nxdata,1:nydata)  _real # spline coeff's for recombination
-rqacoef(1:nxdata,1:nydata)  _real # spline coeff's for line emission
+nxdata_aph  integer
+nydata_aph  integer
+xdata_aph(1:nxdata_aph)             _real
+ydata_aph(1:nydata_aph)             _real
+fdata_aph(1:nxdata_aph,1:nydata_aph)    _real
+ldf_aph                          integer
+iflag_aph                        integer
+kxords_aph  integer /4/               # order of spline fit versus log(te)
+                                  # kxords_aph=4 (default) is cubic interpolation
+kyords_aph  integer /4/               # order of spline fit versus log10(ne)
+                                  # kyords_aph=4 (default) is cubic interpolation
+xknots_aph(1:nxdata_aph+kxords_aph)     _real
+yknots_aph(1:nydata_aph+kyords_aph)     _real
+workh(1:nxdata_aph*nydata_aph+2*kxords_aph*(nxdata_aph+1)) _real # work array
+rsacoef(1:nxdata_aph,1:nydata_aph)  _real # spline coeff's for ionization
+rracoef(1:nxdata_aph,1:nydata_aph)  _real # spline coeff's for recombination
+rqacoef(1:nxdata_aph,1:nydata_aph)  _real # spline coeff's for line emission
 
 ***** Subs:
 # Subroutines that can be called from the parser
diff --git a/aph/aphrates.m b/aph/aphrates.m
index 33b581a2..abd76397 100755
--- a/aph/aphrates.m
+++ b/aph/aphrates.m
@@ -27,7 +27,7 @@ real function erl1 (te, ne, tau)
 c----------------------------------------------------------------------c
       if (istabon .le. 7) then   # various older models
 
-         erl1 = (rqa(te,ne,0)-13.6*ev*rsa(te,ne,0.,0))*ne
+         erl1 = (rqa(te,ne,0)-13.6*ev_aph*rsa(te,ne,0.,0))*ne
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 8 .or. istabon .eq. 9) then # linear interpolation
@@ -35,7 +35,7 @@ real function erl1 (te, ne, tau)
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -63,7 +63,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -98,7 +98,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          endif
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -174,7 +174,7 @@ real function erl2 (te, ne, tau)
 c----------------------------------------------------------------------c
       if (istabon .le. 7) then   # various older models
 
-	 erl2 = (13.6*ev+1.5*te)*ne*rra(te,ne,0.,1)
+	 erl2 = (13.6*ev_aph+1.5*te)*ne*rra(te,ne,0.,1)
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 8 .or. istabon .eq. 9) then # linear interpolation
@@ -182,7 +182,7 @@ real function erl2 (te, ne, tau)
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -210,7 +210,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -245,7 +245,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          endif
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -329,7 +329,7 @@ real function rcx (t0, n0, k)
          iti = 0
          ini = 0
 c     compute abscissae --
-         rlti = log(t0/ev)
+         rlti = log(t0/ev_aph)
          rlni = max(htln(0),min(htln(htnn),log(n0)))
 c     find iti --
  51      if (iti .lt. htnt-1) then
@@ -370,7 +370,7 @@ real function rcx (t0, n0, k)
 c			use DEGAS table look-up
 
 c     compute abscissa --
-         zloge=log(t0/ev)
+         zloge=log(t0/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
 c     table index for interpolation --
          je=int((rle-rlemin)/delekpt) + 1
@@ -394,7 +394,7 @@ call mcrates(n0,t0,t0,za,zamax,zn,kdum,kdum,rcxcopy)
 c----------------------------------------------------------------------c
       else     #     use analytic model (hydrogen) for all other istabon
 
-         a = 3*t0 / (10*ev)
+         a = 3*t0 / (10*ev_aph)
          rcx = 1.7e-14 * a**0.333
          if (issgvcxc.eq.1) rcx = sgvcxc # use fixed sig-v 
          if (issgvcxc.eq.2) rcx = sgvcxc*sqrt(t0/m_prot) # fixed sig
@@ -443,8 +443,8 @@ real function rqa (te, ne, k)
 c----------------------------------------------------------------------c
       if (istabon .eq. 0) then   # use analytic model (hydrogen) with
 c                                  # constant energy loss per ionization
-         a = te / (10*ev)
-         rqa = erad * ev * 3.0e-14 * a*a / (3.0 + a*a)
+         a = te / (10*ev_aph)
+         rqa = erad * ev_aph * 3.0e-14 * a*a / (3.0 + a*a)
 
 c----------------------------------------------------------------------c
       elseif ((istabon .eq. 1) .or. (istabon .eq. 2)) then
@@ -454,7 +454,7 @@ real function rqa (te, ne, k)
          ite = 0
          ine = 0
 c     compute abscissae --
-         rlte = log(te/ev)
+         rlte = log(te/ev_aph)
          rlne = max(htln(0),min(htln(htnn),log(ne)))
 c     find ite --
  51      if (ite .lt. htnt-1) then
@@ -488,7 +488,7 @@ real function rqa (te, ne, k)
 c     compute electron energy loss rate parameter --
          t0 = (1-fxne)*htlqa(ite,ine,k) + fxne*htlqa(ite,ine+1,k)
          t1 = (1-fxne)*htlqa(ite+1,ine,k) + fxne*htlqa(ite+1,ine+1,k)
-         rqa = ev*exp((1-fxte)*t0+fxte*t1)
+         rqa = ev_aph*exp((1-fxte)*t0+fxte*t1)
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 3) then
@@ -497,7 +497,7 @@ real function rqa (te, ne, k)
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -518,14 +518,14 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          w2=w21+fjd*(w22-w21)
          w = w1 + fje*(w2-w1)
 c     electron energy loss rate parameter --
-         rqa = ev * w * rsa(te,ne,0.,k)
+         rqa = ev_aph * w * rsa(te,ne,0.,k)
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 4) then
 c			use POST93 table look-up
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -546,16 +546,16 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          w2=w21+fjd*(w22-w21)
          w = w1 + fje*(w2-w1)
 c     electron energy loss rate parameter --
-         rqa = w + 13.6 * ev * rsa(te,ne,0.,k)
+         rqa = w + 13.6 * ev_aph * rsa(te,ne,0.,k)
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 5) then
 c			use spline fit to POST93 table data
-c      xuse=min(max(xdata(1),log(te/ev)),xdata(nxdata))
-c      yuse=min(max(ydata(1),log10(ne)),ydata(nydata))
+c      xuse=min(max(xdata_aph(1),log(te/ev_aph)),xdata_aph(nxdata_aph))
+c      yuse=min(max(ydata_aph(1),log10(ne)),ydata_aph(nydata_aph))
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -563,23 +563,23 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
       xuse=rle
       yuse=rld
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_aph
+      nycoef=nydata_aph
 
-      vlogw = B2VAhL(xuse, yuse, 0, 0, xknots, yknots, nxcoef,
-     .          nycoef, kxords, kyords, rqacoef, ldf, workh, iflag)
+      vlogw = B2VAhL(xuse, yuse, 0, 0, xknots_aph, yknots_aph, nxcoef,
+     .          nycoef, kxords_aph, kyords_aph, rqacoef, ldf_aph, workh, iflag_aph)
       w=10**vlogw
 c     electron energy loss rate parameter --
-         rqa = w + 13.6 * ev * rsa(te,ne,0.,k)
+         rqa = w + 13.6 * ev_aph * rsa(te,ne,0.,k)
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 6) then
 c			use spline fit to POST93 table data
-c      xuse=min(max(xdata(1),log(te/ev)),xdata(nxdata))
-c      yuse=min(max(ydata(1),log10(ne)),ydata(nydata))
+c      xuse=min(max(xdata_aph(1),log(te/ev_aph)),xdata_aph(nxdata_aph))
+c      yuse=min(max(ydata_aph(1),log10(ne)),ydata_aph(nydata_aph))
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -587,22 +587,22 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
       xuse=rle
       yuse=rld
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_aph
+      nycoef=nydata_aph
 
       tsval = gettime(sec4)
-      w = B2VAhL(xuse, yuse, 0, 0, xknots, yknots, nxcoef, nycoef,
-     .          kxords, kyords, rqacoef, ldf, workh, iflag)
+      w = B2VAhL(xuse, yuse, 0, 0, xknots_aph, yknots_aph, nxcoef, nycoef,
+     .          kxords_aph, kyords_aph, rqacoef, ldf_aph, workh, iflag_aph)
       totb2val = totb2val + gettime(sec4) - tsval
 c     electron energy loss rate parameter --
-         rqa = w + 13.6 * ev * rsa(te,ne,0.,k)
+         rqa = w + 13.6 * ev_aph * rsa(te,ne,0.,k)
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 7) then
 c                       use polynomial fit from Bob Campbell -  8/93
-c     Note that the 13.6 * ev * rsa(te,ne,k) is omitted here as Campbell
+c     Note that the 13.6 * ev_aph * rsa(te,ne,k) is omitted here as Campbell
 c     has already added it in
-         rqa = svradp(te/ev,ne)
+         rqa = svradp(te/ev_aph,ne)
 
 c----------------------------------------------------------------------c
       elseif (istabon .gt. 7) then	# write error message 
@@ -662,7 +662,7 @@ real function rra (te, ne, tau, k)
          ite = 0
          ine = 0
 c     compute abscissae --
-         rlte = log(te/ev)
+         rlte = log(te/ev_aph)
          rlne = max(htln(0),min(htln(htnn),log(ne)))
 c     find ite --
  51      if (ite .lt. htnt-1) then
@@ -706,7 +706,7 @@ real function rra (te, ne, tau, k)
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -730,11 +730,11 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 5) then
 c			use spline fit to POST93 table data
-c      xuse=min(max(xdata(1),log(te/ev)),xdata(nxdata))
-c      yuse=min(max(ydata(1),log10(ne)),ydata(nydata))
+c      xuse=min(max(xdata_aph(1),log(te/ev_aph)),xdata_aph(nxdata_aph))
+c      yuse=min(max(ydata_aph(1),log10(ne)),ydata_aph(nydata_aph))
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -742,21 +742,21 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
       xuse=rle
       yuse=rld
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_aph
+      nycoef=nydata_aph
 
-      vlog10rra = B2VAhL(xuse, yuse, 0, 0, xknots, yknots, nxcoef,
-     .          nycoef, kxords, kyords, rracoef, ldf, workh, iflag)
+      vlog10rra = B2VAhL(xuse, yuse, 0, 0, xknots_aph, yknots_aph, nxcoef,
+     .          nycoef, kxords_aph, kyords_aph, rracoef, ldf_aph, workh, iflag_aph)
       rra=10**vlog10rra
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 6) then
 c			use spline fit to POST93 table data
-c      xuse=min(max(xdata(1),log(te/ev)),xdata(nxdata))
-c      yuse=min(max(ydata(1),log10(ne)),ydata(nydata))
+c      xuse=min(max(xdata_aph(1),log(te/ev_aph)),xdata_aph(nxdata_aph))
+c      yuse=min(max(ydata_aph(1),log10(ne)),ydata_aph(nydata_aph))
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -764,24 +764,24 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
       xuse=rle
       yuse=rld
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_aph
+      nycoef=nydata_aph
 
       tsval = gettime(sec4)
-      rra = B2VAhL(xuse, yuse, 0, 0, xknots, yknots, nxcoef, nycoef,
-     .          kxords, kyords, rracoef, ldf, workh, iflag)
+      rra = B2VAhL(xuse, yuse, 0, 0, xknots_aph, yknots_aph, nxcoef, nycoef,
+     .          kxords_aph, kyords_aph, rracoef, ldf_aph, workh, iflag_aph)
       totb2val = totb2val + gettime(sec4) - tsval
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 7) then
 c                       use polynomial fit from Bob Campbell -  8/93
-         rra = srecf(te/ev,ne)
+         rra = srecf(te/ev_aph,ne)
 
 c----------------------------------------------------------------------c
       elseif ((istabon>9 .and. istabon<14) .or. istabon .eq. 17) then 
 c     log-log interp on Stotler DEGAS2 tables
          jr = 1
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -816,7 +816,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          endif
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -909,7 +909,7 @@ real function rsa (te, ne, tau, k)
 
 c----------------------------------------------------------------------c
       if (istabon .eq. 0) then   # use analytic model (hydrogen)
-         a = te / (10*ev)
+         a = te / (10*ev_aph)
          rsa = 3.0e-14 * a*a / (3.0 + a*a)
 
 c----------------------------------------------------------------------c
@@ -920,7 +920,7 @@ real function rsa (te, ne, tau, k)
          ite = 0
          ine = 0
 c     compute abscissae --
-         rlte = log(te/ev)
+         rlte = log(te/ev_aph)
          rlne = max(htln(0),min(htln(htnn),log(ne)))
 c     find ite --
  51      if (ite .lt. htnt-1) then
@@ -964,7 +964,7 @@ real function rsa (te, ne, tau, k)
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -988,11 +988,11 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 5) then
 c			use spline fit to POST93 table data
-c      xuse=min(max(xdata(1),log(te/ev)),xdata(nxdata))
-c      yuse=min(max(ydata(1),log10(ne)),ydata(nydata))
+c      xuse=min(max(xdata_aph(1),log(te/ev_aph)),xdata_aph(nxdata_aph))
+c      yuse=min(max(ydata_aph(1),log10(ne)),ydata_aph(nydata_aph))
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -1000,21 +1000,21 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
       xuse=rle
       yuse=rld
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_aph
+      nycoef=nydata_aph
 
-      vlog10rsa = B2VAhL(xuse, yuse, 0, 0, xknots, yknots, nxcoef,
-     .          nycoef, kxords, kyords, rsacoef, ldf, workh, iflag)
+      vlog10rsa = B2VAhL(xuse, yuse, 0, 0, xknots_aph, yknots_aph, nxcoef,
+     .          nycoef, kxords_aph, kyords_aph, rsacoef, ldf_aph, workh, iflag_aph)
       rsa=10**vlog10rsa
 
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 6) then
 c			use spline fit to POST93 table data
-c      xuse=min(max(xdata(1),log(te/ev)),xdata(nxdata))
-c      yuse=min(max(ydata(1),log10(ne)),ydata(nydata))
+c      xuse=min(max(xdata_aph(1),log(te/ev_aph)),xdata_aph(nxdata_aph))
+c      yuse=min(max(ydata_aph(1),log10(ne)),ydata_aph(nydata_aph))
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -1022,17 +1022,17 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
       xuse=rle
       yuse=rld
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_aph
+      nycoef=nydata_aph
 
       tsval = gettime(sec4)
-      rsa = B2VAhL(xuse, yuse, 0, 0, xknots, yknots, nxcoef, nycoef,
-     .          kxords, kyords, rsacoef, ldf, workh, iflag)
+      rsa = B2VAhL(xuse, yuse, 0, 0, xknots_aph, yknots_aph, nxcoef, nycoef,
+     .          kxords_aph, kyords_aph, rsacoef, ldf_aph, workh, iflag_aph)
       totb2val = totb2val + gettime(sec4) - tsval      
 c----------------------------------------------------------------------c
       elseif (istabon .eq. 7) then
 c                       use polynomial fit from Bob Campbell -  8/93
-         rsa = sionf(te/ev,ne)
+         rsa = sionf(te/ev_aph,ne)
 
 c----------------------------------------------------------------------c
       elseif ((istabon>9 .and. istabon<14) .or. istabon .eq. 17) then 
@@ -1041,7 +1041,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          jr = 1
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -1076,7 +1076,7 @@ c     fractional parts of intervals (je,je+1) and (jd,jd+1) --
          endif
 
 c     compute abscissae --
-         zloge=log(te/ev)
+         zloge=log(te/ev_aph)
          rle=max(rlemin, min(zloge,rlemax))
          zlogd=log10(ne)
          rld=max(rldmin, min(zlogd,rldmax))
@@ -1328,7 +1328,7 @@ real function svdiss (te)
       b7 =  2.159670289222e-04
       b8 = -4.928545325189e-06   
 
-      logt = log (te/ev)
+      logt = log (te/ev_aph)
       logsv = b0+logt*(b1+logt*(b2+logt*(b3+logt*(b4
      .          +logt*(b5+logt*(b6+logt*(b7+logt*b8)))))))
       svdiss = (1e-6)*exp(logsv)
diff --git a/aph/aphread.m b/aph/aphread.m
index 54a12c58..a9507070 100755
--- a/aph/aphread.m
+++ b/aph/aphread.m
@@ -753,8 +753,8 @@ c     charge exchange rate (cm**3/sec):
 c     (data from POST 93 tables)
 
 c     Allocate arrays for spline fitting --
-      nxdata=mpe		# temperature
-      nydata=mpd		# density
+      nxdata_aph=mpe		# temperature
+      nydata_aph=mpd		# density
       call gchange("Aphwrk",0)
 
       call splined1
@@ -774,61 +774,61 @@ call gchange("Aphwrk",0)
       integer i,j
  
 c     Define data arrays --
-      do i=1,nxdata
-        xdata(i)=ekpt(i)
+      do i=1,nxdata_aph
+        xdata_aph(i)=ekpt(i)
       enddo
-      do j=1,nydata
-        ydata(j)=dkpt(j)
+      do j=1,nydata_aph
+        ydata_aph(j)=dkpt(j)
       enddo
-      ldf=nxdata
+      ldf_aph=nxdata_aph
 
 c     Define the order of the spline fit
-c     kxords=4		# cubic in x=log(temperature)
-c     kyords=4		# cubic in y=log10(density)
+c     kxords_aph=4		# cubic in x=log(temperature)
+c     kyords_aph=4		# cubic in y=log10(density)
 
 c     Compute the coefficients --
 c     first, for ionization:
-      do i=1,nxdata
-        do j=1,nydata
+      do i=1,nxdata_aph
+        do j=1,nydata_aph
            if (istabon .eq. 5) then
-             fdata(i,j)=log10( wsveh(i,j,1) )
+             fdata_aph(i,j)=log10( wsveh(i,j,1) )
            elseif (istabon .eq. 6) then
-             fdata(i,j)=wsveh(i,j,1)
+             fdata_aph(i,j)=wsveh(i,j,1)
            endif
         enddo
       enddo
-      iflag = 1
-      call s2copy (nxdata,nydata,fdata,1,nxdata,rsacoef,1,nxdata)
-      call B2INhT (xdata, nxdata, ydata, nydata, kxords, kyords,
-     .            xknots, yknots, rsacoef, ldf, workh, iflag)
+      iflag_aph = 1
+      call s2copy (nxdata_aph,nydata_aph,fdata_aph,1,nxdata_aph,rsacoef,1,nxdata_aph)
+      call B2INhT (xdata_aph, nxdata_aph, ydata_aph, nydata_aph, kxords_aph, kyords_aph,
+     .            xknots_aph, yknots_aph, rsacoef, ldf_aph, workh, iflag_aph)
 c     next, for recombination:
-      do i=1,nxdata
-        do j=1,nydata
+      do i=1,nxdata_aph
+        do j=1,nydata_aph
            if (istabon .eq. 5) then
-             fdata(i,j)=log10( wsveh0(i,j,1) )
+             fdata_aph(i,j)=log10( wsveh0(i,j,1) )
            elseif (istabon .eq. 6) then
-             fdata(i,j)=wsveh0(i,j,1)
+             fdata_aph(i,j)=wsveh0(i,j,1)
            endif
         enddo
       enddo
-      iflag = 1
-      call s2copy (nxdata,nydata,fdata,1,nxdata,rracoef,1,nxdata)
-      call B2INhT (xdata, nxdata, ydata, nydata, kxords, kyords,
-     .            xknots, yknots, rracoef, ldf, workh, iflag)
+      iflag_aph = 1
+      call s2copy (nxdata_aph,nydata_aph,fdata_aph,1,nxdata_aph,rracoef,1,nxdata_aph)
+      call B2INhT (xdata_aph, nxdata_aph, ydata_aph, nydata_aph, kxords_aph, kyords_aph,
+     .            xknots_aph, yknots_aph, rracoef, ldf_aph, workh, iflag_aph)
 c     next, for hydrogen line radiation:
-      do i=1,nxdata
-        do j=1,nydata
+      do i=1,nxdata_aph
+        do j=1,nydata_aph
            if (istabon .eq. 5) then
-             fdata(i,j)=log10( wlemiss(i,j) )
+             fdata_aph(i,j)=log10( wlemiss(i,j) )
            elseif (istabon .eq. 6) then
-             fdata(i,j)=wlemiss(i,j)
+             fdata_aph(i,j)=wlemiss(i,j)
            endif
         enddo
       enddo
-      iflag = 1
-      call s2copy (nxdata,nydata,fdata,1,nxdata,rqacoef,1,nxdata)
-      call B2INhT (xdata, nxdata, ydata, nydata, kxords, kyords,
-     .            xknots, yknots, rqacoef, ldf, workh, iflag)
+      iflag_aph = 1
+      call s2copy (nxdata_aph,nydata_aph,fdata_aph,1,nxdata_aph,rqacoef,1,nxdata_aph)
+      call B2INhT (xdata_aph, nxdata_aph, ydata_aph, nydata_aph, kxords_aph, kyords_aph,
+     .            xknots_aph, yknots_aph, rqacoef, ldf_aph, workh, iflag_aph)
       return
       end
 
diff --git a/api/api.v b/api/api.v
index 44566d1c..d22d6bcb 100755
--- a/api/api.v
+++ b/api/api.v
@@ -44,7 +44,7 @@ getprad(nx,ny,ngsp,te,ne:real,ng:real,afrac,atau,
 ***** Impurity_transport:
 # variable specifying radial transport rate of impurities
 dnimp		real	/1./	[m**2/s]
-methimp         integer /33/   # specifies interp. for finite diff. for (y,x)
+methimp         integer /33/   +input # specifies interp. for finite diff. for (y,x)
                                # 66 is log interp., 77 inverse interp.,
                                # otherwise linear interp.
 csexpn		real    /0./   # exponent for reducing impurity || vel from
@@ -142,14 +142,14 @@ z2datm(nt,nr,nn)	_real			# average Z**2
 
 ***** Imslwrk:
 # working arrays for 3-d spline interpolation
-nxdata	integer
-nydata	integer
+nxdata_api	integer
+nydata_api	integer
 nzdata	integer
-xdata(1:nxdata)	_real
-ydata(1:nydata)	_real
+xdata_api(1:nxdata_api)	_real
+ydata_api(1:nydata_api)	_real
 zdata(1:nzdata)	_real
-fdata(1:nxdata,1:nydata,1:nzdata)	_real
-ldf	integer			# first dimension of 3-d data array
+fdata_api(1:nxdata_api,1:nydata_api,1:nzdata)	_real
+ldf_api	integer			# first dimension of 3-d data array
 mdf	integer			# second dimension of 3-d data array
 iflagi	integer			# input/output flag for 3-d spline routines
 nwork2	integer			# size of array work2
@@ -158,18 +158,18 @@ nwork3	integer			# size of array work3
 work3(nwork3)	_real		# work array for B3INT
 iworki(10)	integer		# work array for B3VAL
 icont		integer	/0/	# input flag for B3VAL
-kxords	integer	/4/	# order of spline fit versus x
-#	kxords=4 (default) is cubic interpolation
-kyords	integer	/4/	# order of spline fit versus y
-#	kyords=4 (default) is cubic interpolation
+kxords_api	integer	/4/	# order of spline fit versus x
+#	kxords_api=4 (default) is cubic interpolation
+kyords_api	integer	/4/	# order of spline fit versus y
+#	kyords_api=4 (default) is cubic interpolation
 kzords	integer	/4/	# order of spline fit versus z
 #	kzords=4 (default) is cubic interpolation
-xknots(1:nxdata+kxords)	_real
-yknots(1:nydata+kyords)	_real
+xknots_api(1:nxdata_api+kxords_api)	_real
+yknots_api(1:nydata_api+kyords_api)	_real
 zknots(1:nzdata+kzords)	_real
-emcoef(1:nxdata,1:nydata,1:nzdata)	_real	# spline coeff's for emissivity 
-z1coef(1:nxdata,1:nydata,1:nzdata)	_real	# spline coeff's for average-Z
-z2coef(1:nxdata,1:nydata,1:nzdata)	_real	# spline coeff's for average-Z**2
+emcoef(1:nxdata_api,1:nydata_api,1:nzdata)	_real	# spline coeff's for emissivity 
+z1coef(1:nxdata_api,1:nydata_api,1:nzdata)	_real	# spline coeff's for average-Z
+z2coef(1:nxdata_api,1:nydata_api,1:nzdata)	_real	# spline coeff's for average-Z**2
 
 ***** P93fcn:
 # setup and evaluation routines for spline representation of data on impurity
@@ -232,7 +232,7 @@ z2avgbs(te:real,nratio:real,ntau:real)	real function
  mntau(MXMISO*MXMISO)		real	# 
  usol(KXA*MXNZCH*MXMISO)	real	# 
  sbar(KXA*MXMISO1)		real	# 
- zi(MXMISO*MXNZCH)		real	# 
+ zi_api(MXMISO*MXNZCH)		real	# 
 
 ***** Cyield:
 # Variables used for DIVIMP physical sputtering models
diff --git a/api/apip93.m b/api/apip93.m
index 6e77d379..d4ae720c 100755
--- a/api/apip93.m
+++ b/api/apip93.m
@@ -91,7 +91,7 @@ subroutine readpost1 (nget)
       subroutine splinem
       implicit none
 Use(P93dat)    # nt,nr,nn
-Use(Imslwrk)   # nxdata,nydata,nzdata
+Use(Imslwrk)   # nxdata_api,nydata_api,nzdata
       external gallot, splinem1
 
 c     Construct 3-dimensional B-spline representation for impurity
@@ -99,12 +99,12 @@ subroutine readpost1 (nget)
 c     n*tau (data from POST '93 tables)
 
 c     Allocate arrays for spline fitting --
-      nxdata=nt		# temperature
-      nydata=nr		# density ratio
+      nxdata_api=nt		# temperature
+      nydata_api=nr		# density ratio
       nzdata=nn		# n*tau
-      nwork2 = kyords*kzords + 3*max(kxords,kyords,kzords) + kzords + 2
-      nwork3 = nxdata*nydata*nzdata + 2*max( kxords*(nxdata+1),
-     &           kyords*(nydata+1), kzords*(nzdata+1) )
+      nwork2 = kyords_api*kzords + 3*max(kxords_api,kyords_api,kzords) + kzords + 2
+      nwork3 = nxdata_api*nydata_api*nzdata + 2*max( kxords_api*(nxdata_api+1),
+     &           kyords_api*(nydata_api+1), kzords*(nzdata+1) )
       call gallot("Imslwrk",0)
 
       call splinem1
@@ -117,69 +117,69 @@ call gallot("Imslwrk",0)
       subroutine splinem1
       implicit none
 Use(P93dat)    # tdatm,rdatm,ndatm,emdatm,z1datm,z2datm
-Use(Imslwrk)   # nxdata,nydata,nzdata,xdata,ydata,zdata,fdata,ldf,mdf,
-               # kxords,kyords,kzords,xknots,yknots,zknots,emcoef,
+Use(Imslwrk)   # nxdata_api,nydata_api,nzdata,xdata_api,ydata_api,zdata,fdata_api,ldf_api,mdf,
+               # kxords_api,kyords_api,kzords,xknots_api,yknots_api,zknots,emcoef,
                # z1coef,z2coef
       integer i,j,k
       external B3INT
 
 c     Define data arrays --
-      do i=1,nxdata
-        xdata(i)=log10( tdatm(i,1,1) )
+      do i=1,nxdata_api
+        xdata_api(i)=log10( tdatm(i,1,1) )
       enddo
-      do j=1,nydata
-        ydata(j)=log10( rdatm(1,j,1) )
+      do j=1,nydata_api
+        ydata_api(j)=log10( rdatm(1,j,1) )
       enddo
       do k=1,nzdata
         zdata(k)=log10( ndatm(1,1,k) )
       enddo
 
 c     Define the order of the spline fit
-c      kxords=4		# cubic in x=log10(temperature)
-c      kyords=4		# cubic in y=log10(density ratio)
+c      kxords_api=4		# cubic in x=log10(temperature)
+c      kyords_api=4		# cubic in y=log10(density ratio)
 c      kzords=4		# cubic in z=log10(n*tau)
 
-      ldf=nxdata
-      mdf=nydata
+      ldf_api=nxdata_api
+      mdf=nydata_api
       iflagi = 1	# let B3INT choose knots
 
 c     Compute the coefficients --
 c     first, for emissivity:
-      do i=1,nxdata
-        do j=1,nydata
+      do i=1,nxdata_api
+        do j=1,nydata_api
           do k=1,nzdata
-            fdata(i,j,k)=log10( emdatm(i,j,k) )
-            emcoef(i,j,k)=fdata(i,j,k)
+            fdata_api(i,j,k)=log10( emdatm(i,j,k) )
+            emcoef(i,j,k)=fdata_api(i,j,k)
           enddo
         enddo
       enddo
-      call B3INT (xdata, nxdata, ydata, nydata, zdata, nzdata,
-     &            kxords, kyords, kzords, xknots, yknots, zknots,
-     &            emcoef, ldf, mdf, work3, iflagi)
+      call B3INT (xdata_api, nxdata_api, ydata_api, nydata_api, zdata, nzdata,
+     &            kxords_api, kyords_api, kzords, xknots_api, yknots_api, zknots,
+     &            emcoef, ldf_api, mdf, work3, iflagi)
 c     next, for average Z:
-      do i=1,nxdata
-        do j=1,nydata
+      do i=1,nxdata_api
+        do j=1,nydata_api
           do k=1,nzdata
-            fdata(i,j,k)=z1datm(i,j,k)
-            z1coef(i,j,k)=fdata(i,j,k)
+            fdata_api(i,j,k)=z1datm(i,j,k)
+            z1coef(i,j,k)=fdata_api(i,j,k)
           enddo
         enddo
       enddo
-      call B3INT (xdata, nxdata, ydata, nydata, zdata, nzdata,
-     &            kxords, kyords, kzords, xknots, yknots, zknots,
-     &            z1coef, ldf, mdf, work3, iflagi)
+      call B3INT (xdata_api, nxdata_api, ydata_api, nydata_api, zdata, nzdata,
+     &            kxords_api, kyords_api, kzords, xknots_api, yknots_api, zknots,
+     &            z1coef, ldf_api, mdf, work3, iflagi)
 c     next, for average Z**2:
-      do i=1,nxdata
-        do j=1,nydata
+      do i=1,nxdata_api
+        do j=1,nydata_api
           do k=1,nzdata
-            fdata(i,j,k)=z2datm(i,j,k)
-            z2coef(i,j,k)=fdata(i,j,k)
+            fdata_api(i,j,k)=z2datm(i,j,k)
+            z2coef(i,j,k)=fdata_api(i,j,k)
           enddo
         enddo
       enddo
-      call B3INT (xdata, nxdata, ydata, nydata, zdata, nzdata,
-     &            kxords, kyords, kzords, xknots, yknots, zknots,
-     &            z2coef, ldf, mdf, work3, iflagi)
+      call B3INT (xdata_api, nxdata_api, ydata_api, nydata_api, zdata, nzdata,
+     &            kxords_api, kyords_api, kzords, xknots_api, yknots_api, zknots,
+     &            z2coef, ldf_api, mdf, work3, iflagi)
 
       return
       end
@@ -189,8 +189,8 @@ call B3INT (xdata, nxdata, ydata, nydata, zdata, nzdata,
       real function emissbs (vte,vnr,vnt)
       implicit none
       real vnt,vnr,vte
-Use(Imslwrk)   # nxdata,nydata,nzdata,xdata,ydata,zdata,
-               # kxords,kyords,kzords,xknots,yknots,zknots,emcoef
+Use(Imslwrk)   # nxdata_api,nydata_api,nzdata,xdata_api,ydata_api,zdata,
+               # kxords_api,kyords_api,kzords,xknots_api,yknots_api,zknots,emcoef
 
       integer nxcoef,nycoef,nzcoef
       real vlogw,w,xuse,yuse,zuse
@@ -204,18 +204,18 @@ real function emissbs (vte,vnr,vnt)
 c     		vnr = ng/ne density ratio
 c     		vnt = ne*tau [sec/m**3].
 
-      xuse=min(max(xdata(1),log10(vte)),xdata(nxdata))
-      yuse=min(max(ydata(1),log10(vnr)),ydata(nydata))
+      xuse=min(max(xdata_api(1),log10(vte)),xdata_api(nxdata_api))
+      yuse=min(max(ydata_api(1),log10(vnr)),ydata_api(nydata_api))
       zuse=min(max(zdata(1),log10(vnt)),zdata(nzdata))
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_api
+      nycoef=nydata_api
       nzcoef=nzdata
 
       icont = 0
-      vlogw=B3VAL (xuse, yuse, zuse, 0, 0, 0, xknots, yknots, zknots,
-     &             nxcoef, nycoef, nzcoef, kxords, kyords, kzords, 
-     &             emcoef, ldf, mdf, icont, iworki, work2, iflagi)
+      vlogw=B3VAL (xuse, yuse, zuse, 0, 0, 0, xknots_api, yknots_api, zknots,
+     &             nxcoef, nycoef, nzcoef, kxords_api, kyords_api, kzords, 
+     &             emcoef, ldf_api, mdf, icont, iworki, work2, iflagi)
       w=10**vlogw
       emissbs=w
 
@@ -227,8 +227,8 @@ real function emissbs (vte,vnr,vnt)
       real function z1avgbs (vte,vnr,vnt)
       implicit none
       real vnt,vnr,vte
-Use(Imslwrk)   # nxdata,nydata,nzdata,xdata,ydata,zdata,
-               # kxords,kyords,kzords,xknots,yknots,zknots,z1coef
+Use(Imslwrk)   # nxdata_api,nydata_api,nzdata,xdata_api,ydata_api,zdata,
+               # kxords_api,kyords_api,kzords,xknots_api,yknots_api,zknots,z1coef
 
       integer nxcoef,nycoef,nzcoef
       real vz1,xuse,yuse,zuse
@@ -242,18 +242,18 @@ real function z1avgbs (vte,vnr,vnt)
 c     		vnr = ng/ne density ratio
 c     		vnt = ne*tau [sec/m**3].
 
-      xuse=min(max(xdata(1),log10(vte)),xdata(nxdata))
-      yuse=min(max(ydata(1),log10(vnr)),ydata(nydata))
+      xuse=min(max(xdata_api(1),log10(vte)),xdata_api(nxdata_api))
+      yuse=min(max(ydata_api(1),log10(vnr)),ydata_api(nydata_api))
       zuse=min(max(zdata(1),log10(vnt)),zdata(nzdata))
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_api
+      nycoef=nydata_api
       nzcoef=nzdata
 
       icont = 0
-      vz1=B3VAL (xuse, yuse, zuse, 0, 0, 0, xknots, yknots, zknots,
-     &             nxcoef, nycoef, nzcoef, kxords, kyords, kzords, 
-     &             z1coef, ldf, mdf, icont, iworki, work2, iflagi)
+      vz1=B3VAL (xuse, yuse, zuse, 0, 0, 0, xknots_api, yknots_api, zknots,
+     &             nxcoef, nycoef, nzcoef, kxords_api, kyords_api, kzords, 
+     &             z1coef, ldf_api, mdf, icont, iworki, work2, iflagi)
       z1avgbs=vz1
 
       return
@@ -264,8 +264,8 @@ real function z1avgbs (vte,vnr,vnt)
       real function z2avgbs (vte,vnr,vnt)
       implicit none
       real vnt,vnr,vte
-Use(Imslwrk)   # nxdata,nydata,nzdata,xdata,ydata,zdata,
-               # kxords,kyords,kzords,xknots,yknots,zknots,z2coef
+Use(Imslwrk)   # nxdata_api,nydata_api,nzdata,xdata_api,ydata_api,zdata,
+               # kxords_api,kyords_api,kzords,xknots_api,yknots_api,zknots,z2coef
 
       integer nxcoef,nycoef,nzcoef
       real vz2,xuse,yuse,zuse
@@ -279,18 +279,18 @@ real function z2avgbs (vte,vnr,vnt)
 c     		vnr = ng/ne density ratio
 c     		vnt = ne*tau [sec/m**3].
 
-      xuse=min(max(xdata(1),log10(vte)),xdata(nxdata))
-      yuse=min(max(ydata(1),log10(vnr)),ydata(nydata))
+      xuse=min(max(xdata_api(1),log10(vte)),xdata_api(nxdata_api))
+      yuse=min(max(ydata_api(1),log10(vnr)),ydata_api(nydata_api))
       zuse=min(max(zdata(1),log10(vnt)),zdata(nzdata))
 
-      nxcoef=nxdata
-      nycoef=nydata
+      nxcoef=nxdata_api
+      nycoef=nydata_api
       nzcoef=nzdata
 
       icont = 0
-      vz2=B3VAL (xuse, yuse, zuse, 0, 0, 0, xknots, yknots, zknots,
-     &             nxcoef, nycoef, nzcoef, kxords, kyords, kzords, 
-     &             z2coef, ldf, mdf, icont, iworki, work2, iflagi)
+      vz2=B3VAL (xuse, yuse, zuse, 0, 0, 0, xknots_api, yknots_api, zknots,
+     &             nxcoef, nycoef, nzcoef, kxords_api, kyords_api, kzords, 
+     &             z2coef, ldf_api, mdf, icont, iworki, work2, iflagi)
       z2avgbs=vz2
 
       return
diff --git a/api/fmombal.m b/api/fmombal.m
index 2970b841..9fefab1d 100755
--- a/api/fmombal.m
+++ b/api/fmombal.m
@@ -2,14 +2,14 @@
 c!include "../sptodp.h"
 c!include "api.h"
 !	SEE FMOMBAL SUBROUTINE FOR INPUT PARAMETER SPECIFICATIONS
-	subroutine coulfric(amu,denz2,dloglam,mntau,zi,capm,capn,
+	subroutine coulfric(amu,denz2,dloglam,mntau,zi_api,capm,capn,
      >	ela,elab,tempa)
   	implicit real (a-h,o-z), integer (i-n)
 	Use(Reduced_ion_constants)
 	real capm(KXA,miso,KXA,miso),denz2(miso),
      >		 capn(KXA,KXA,miso,miso),mntau(miso,miso),
      >		amu(miso),tempa(miso),
-     >		ela(*),elab(*),zi(miso,nzch)
+     >		ela(*),elab(*),zi_api(miso,nzch)
 c
 c	COMPUTES COULOMB COLLISION FRICTION TERMS
 c	ELA AND ELAB, WHERE THE FRICTION FORCE IS
@@ -206,24 +206,24 @@ integer natomic(misotope)
           amat(i)=zero
         enddo
 
-c****	Setup zi, mass-density, Z*e*density arrays
-	call setden(amu,den,denmass,denz,denz2,zi)
+c****	Setup zi_api, mass-density, Z*e*density arrays
+	call setden(amu,den,denmass,denz,denz2,zi_api)
 
 c****	Setup force arrays (gradp, gradt stuff)
 	call setforce(den,denz,denmass,epar,gradp,gradt,
      >	tempa,uneut,qneut,umass,fmomenta,nuion)
 
 c*****	Compute Coulomb friction coefficients la, lab
-	call coulfric(amu,denz2,dloglam,mntau,zi,capm,capn,
+	call coulfric(amu,denz2,dloglam,mntau,zi_api,capm,capn,
      >	ela,elab,tempa)
 
 c*****	Compute response matrices for inversion of momentum equations
 c*****	in charge-state space
-	call zrespond(den,denmass,zi,ela,nuion,nurec,uresp,
+	call zrespond(den,denmass,zi_api,ela,nuion,nurec,uresp,
      >	usave,caplams,fmomenta,ldir)
 
 c*****	Solve average-ion equations in mass-isotope space
-	call mrespond(elab,zi,den,denmass,uresp,sbar,
+	call mrespond(elab,zi_api,den,denmass,uresp,sbar,
      >	KXA*(miso+1),amat,nurec,umass,ldir)
 
 c*****	Compute individual ion flows (for all charge states)
@@ -240,7 +240,7 @@ call mzrespond(elab,uresp,sbar,caplam,caplams,usol,
 c	COMPUTE FRICTION FORCES
 c	
 	call getfrict(friction,fricc,caplam,denmass,ela,nuion,
-     .  nurec,usol,zi)
+     .  nurec,usol,zi_api)
 
 c ... End timing impurity calculations.
         if (istimingon .eq. 1 .and. misotope .gt. 1)
@@ -251,26 +251,26 @@ call getfrict(friction,fricc,caplam,denmass,ela,nuion,
 c---- End of subroutine fmombal ----------------------------------------
 c-----------------------------------------------------------------------
 	subroutine getfrict(friction,fricc,caplam,denmass,ela,
-     >	nuion,nurec,usol,zi)
+     >	nuion,nurec,usol,zi_api)
   	implicit real (a-h,o-z), integer (i-n)
 	Use(Reduced_ion_constants)
 	real friction(miso,nzch), usol(KXA,nzch,miso), 
      .       fricc(miso,nzch,5)
 	real nuion(miso,0:nzch), nurec(miso,nzch)
 	real denmass(miso,0:nzch), caplam(KXA,miso),
-     >	ela(3,3,miso), zi(miso,nzch)
+     >	ela(3,3,miso), zi_api(miso,nzch)
 	m = 1		!ONLY FRICTION FORCE
 	do misa = 1,miso
 	nzmax = natom(misa)
 	  do nz = 1,nzmax
 	  friction(misa,nz) =
-     >	  zi(misa,nz) * ( ela(m,1,misa)*usol(1,nz,misa)
+     >	  zi_api(misa,nz) * ( ela(m,1,misa)*usol(1,nz,misa)
      >	  + ela(m,2,misa)*usol(2,nz,misa)
      >	  + ela(m,3,misa)*usol(3,nz,misa) + caplam(m,misa) )
-            fricc(misa,nz,1) = zi(misa,nz)*ela(m,1,misa)*usol(1,nz,misa)
-            fricc(misa,nz,2) = zi(misa,nz)*ela(m,2,misa)*usol(2,nz,misa)
-            fricc(misa,nz,3) = zi(misa,nz)*ela(m,3,misa)*usol(3,nz,misa)
-            fricc(misa,nz,4) = zi(misa,nz)*caplam(m,misa)
+            fricc(misa,nz,1) = zi_api(misa,nz)*ela(m,1,misa)*usol(1,nz,misa)
+            fricc(misa,nz,2) = zi_api(misa,nz)*ela(m,2,misa)*usol(2,nz,misa)
+            fricc(misa,nz,3) = zi_api(misa,nz)*ela(m,3,misa)*usol(3,nz,misa)
+            fricc(misa,nz,4) = zi_api(misa,nz)*caplam(m,misa)
 	  friction(misa,nz) = friction(misa,nz)
      >	  - denmass(misa,nz)*usol(m,nz,misa)*
      >	  (nuion(misa,nz) + nurec(misa,nz))*al32(m)
@@ -316,7 +316,7 @@ implicit real (a-h,o-z), integer (i-n)
 	one = 1.0e0
 c*****	Calculate pi0 for greatest accuracy.
 	pi0=acos(-one)
-c*****	Set zero for initializing arrays.
+c*****	Set zero for initializi_aping arrays.
 	zero=0.e0
 c*****	Integer constants
 	ilam1 = 1
@@ -352,14 +352,14 @@ integer natomic(misotope)
 	end
 c---- End of subroutine initmombal -------------------------------------
 c-----------------------------------------------------------------------
-	subroutine mrespond(elab,zi,den,denmass,uresp,sbar,
+	subroutine mrespond(elab,zi_api,den,denmass,uresp,sbar,
      >	nmat,amat,nurec,umass,ldir)
   	implicit real (a-h,o-z), integer (i-n)
 	Use(Reduced_ion_constants)
         integer nmat
 	real elab(KXA,miso,KXA*miso),uresp(KXA,nzch,miso,NBA),
      >	sbar(KXA,miso+1), sbar0(KXA*(MXMISO1)), ubar0(KXA*(MXMISO1)),
-     >	zi(miso,*),amat(nmat,nmat),denmass(miso,0:nzch)
+     >	zi_api(miso,*),amat(nmat,nmat),denmass(miso,0:nzch)
 	real den(miso,0:nzch), nurec(miso,nzch)
 	real usum(MXNZCH), bmat(KXA*(MXMISO1)*KXA*(MXMISO1))
 	integer nrow(KXA*(MXMISO1)), z1
@@ -427,9 +427,9 @@ c	AND U(1,1,alpha) MUST BE EXPRESSED IN TERMS OF AI, UBAR
 	  do 10 m = 1,KXA
 	    if( (misa.ne.mise) .or. (m.ne.mflow) )then
 	      sbar(m,misa) =
-     >	      sdot(nz,zi(misa,1),miso,uresp(m,z1,misa,iforc),KXA)
+     >	      sdot(nz,zi_api(misa,1),miso,uresp(m,z1,misa,iforc),KXA)
 	      amat(m+i,1+j) =
-     >	      -sdot(nz,zi(misa,1),miso,uresp(m,z1,misa,iacci),KXA)
+     >	      -sdot(nz,zi_api(misa,1),miso,uresp(m,z1,misa,iacci),KXA)
 	    endif
 	  do 10 mpmisb = 1,KXA*miso
 	    do nzb = 1,nz
@@ -438,7 +438,7 @@ c	AND U(1,1,alpha) MUST BE EXPRESSED IN TERMS OF AI, UBAR
      >	              + uresp(m,nzb,misa,ilam3)*elab(ilam3,misa,mpmisb)
 	    enddo
 	    if( (misa.ne.mise) .or. (m.ne.mflow) )
-     >	    amat(m+i,mpmisb) = sdot(nz,zi(misa,z1),miso,usum,1)
+     >	    amat(m+i,mpmisb) = sdot(nz,zi_api(misa,z1),miso,usum,1)
 c
 c	PERFORM SUMS OVER MISA (ISOTOPE MASS A)
 c
@@ -673,7 +673,7 @@ real amu(miso), tempa(miso)
       end
 c---- End of subroutine neomn ------------------------------------------
 c-----------------------------------------------------------------------
-	subroutine printit(amu,den,epar,zi,ela,
+	subroutine printit(amu,den,epar,zi_api,ela,
      >  caplam,sbar,usol,fmom,denmass,nuion,nurec,
      >	gradp,gradt,parcurrent,xirl,tempa,uneut,umass)
   	implicit real (a-h,o-z), integer (i-n)
@@ -683,7 +683,7 @@ real den(miso,0:nzch), caplam(KXA,miso)
 	real denmass(miso,0:nzch)
 	real nuion(miso,0:nzch), nurec(miso,nzch),
      >	gradp(miso,*), gradt(miso,*), ela(3,3,miso),
-     >	       zi(miso,nzch), fmom(KXA,nzch,miso), amu(miso),
+     >	       zi_api(miso,nzch), fmom(KXA,nzch,miso), amu(miso),
      >	       tempa(miso), uneut(miso)
 	
 c*****	Print out average-ion quantities
@@ -710,7 +710,7 @@ real nuion(miso,0:nzch), nurec(miso,nzch),
 	nzmax = natom(misa)
 	do 55 nz = 1,nzmax
 	force = fmom(m,nz,misa)
-	friction = zi(misa,nz) * ( ela(m,1,misa)*usol(1,nz,misa)
+	friction = zi_api(misa,nz) * ( ela(m,1,misa)*usol(1,nz,misa)
      >	+ ela(m,2,misa)*usol(2,nz,misa)
      >	+ ela(m,3,misa)*usol(3,nz,misa) + caplam(m,misa) )
 	friction = friction - denmass(misa,nz)*usol(m,nz,misa)*
@@ -724,7 +724,7 @@ real nuion(miso,0:nzch), nurec(miso,nzch),
 	  sumflow = sumflow + denmass(misa,nz)*usol(1,nz,misa)
 	  sumaflow= sumaflow+ denmass(misa,nz)*abs(usol(1,nz,misa))
 	  write(*,550)nz,usol(m,nz,misa),force,friction,
-     >	  den(misa,nz),zi(misa,nz),nuion(misa,nz),nurec(misa,nz)
+     >	  den(misa,nz),zi_api(misa,nz),nuion(misa,nz),nurec(misa,nz)
 	else if( m.eq.2 )then
 	  pres = den(misa,nz)*tempa(misa)
 	  write(*,550)nz,-2.5*usol(m,nz,misa)*pres,
@@ -756,12 +756,12 @@ real nuion(miso,0:nzch), nurec(miso,nzch),
 	end
 c---- End of subroutine printit ----------------------------------------
 c-----------------------------------------------------------------------
-	subroutine setden(amu,den,denmass,denz,denz2,zi)
+	subroutine setden(amu,den,denmass,denz,denz2,zi_api)
   	implicit real (a-h,o-z), integer (i-n)
 	Use(Reduced_ion_constants)
 	real amu(miso), denz2(miso)
 	real den(miso,0:nzch), denmass(miso,0:nzch), denz(miso,*)
-	real zi(miso,*)
+	real zi_api(miso,*)
 c*****	Sum over isotopes for electron density-isotope 1.
 	do misa = 2,miso
 	  do nza = 1,natom(misa)
@@ -776,8 +776,8 @@ real zi(miso,*)
 	  denz2(misa)=zero
 	  do nza = 1,natom(misa)
 	    denmass(misa,nza) = bmass*den(misa,nza)
-	    zi(misa,nza) = den(misa,nza)*real(nza)**2
-	    denz2(misa)=denz2(misa) + zi(misa,nza)
+	    zi_api(misa,nza) = den(misa,nza)*real(nza)**2
+	    denz2(misa)=denz2(misa) + zi_api(misa,nza)
 	    totmass = totmass + denmass(misa,nza)
 	  enddo
 	enddo
@@ -785,16 +785,16 @@ real zi(miso,*)
 	do misa = 2,miso
 	  denmass(misa,0) = amu(misa)*promas*den(misa,0)
 	enddo
-c*****	Provide pedestal for zi to avoid matrix inversion singularity
-	ziped = 1.E-4
+c*****	Provide pedestal for zi_api to avoid matrix inversion singularity
+	zi_apiped = 1.E-4
 	do misa=1,miso
 	  zisum = zero
 	  do nza=1,natom(misa)
-	    zi(misa,nza)=zi(misa,nza)/denz2(misa) + ziped
-	    zisum = zisum + zi(misa,nza)
+	    zi_api(misa,nza)=zi_api(misa,nza)/denz2(misa) + zi_apiped
+	    zisum = zisum + zi_api(misa,nza)
 	  enddo
-	  do nza = 1,natom(misa)	!zi normed to 1
-	    zi(misa,nza) = zi(misa,nza)/zisum
+	  do nza = 1,natom(misa)	!zi_api normed to 1
+	    zi_api(misa,nza) = zi_api(misa,nza)/zisum
 	  enddo
 	enddo
 	return
@@ -1045,14 +1045,14 @@ call scopy(k2,a(nrow(l)+k+1),1,a(nrow(l)+1),1)
 	end
 c---- End of subroutine uinvm2 -----------------------------------------
 c-----------------------------------------------------------------------
-	subroutine zrespond(den,denmass,zi,ela,nuion,nurec,
+	subroutine zrespond(den,denmass,zi_api,ela,nuion,nurec,
      >	uresp,usave,caplams,fmom,ldir)
   	implicit real (a-h,o-z), integer (i-n)
 	Use(Reduced_ion_constants)
 	parameter( NSIZE = 2*KXA*KXA*MXNZCH )
 	real zmat(KNX,MXMISO), source(KXA*MXNZCH,MXMISO)
 	real amat(KNX), asource(KXA*MXNZCH*NBA)
-	real den(miso,0:nzch), zi(miso,nzch), ela(KXA,KXA,miso)
+	real den(miso,0:nzch), zi_api(miso,nzch), ela(KXA,KXA,miso)
 	real nuion(miso,0:nzch), nurec(miso,nzch)
 	real uresp(KXA,nzch,miso,NBA), usave(KXA,nzch,miso)
 	real fmom(KXA,nzch,miso),denmass(miso,0:nzch)
@@ -1126,7 +1126,7 @@ c	SAME (SEE SUBROUTINE ZSOURCE FOR DETAILS)
           asource(i)=zero
         enddo
 
-	call zsource(asource,zi,den,fmom(1,1,misa),denmass,misa,nz)
+	call zsource(asource,zi_api,den,fmom(1,1,misa),denmass,misa,nz)
 	nforc = nkz*(iforc-1)
 	nacci = nkz*(iacci-1)
 	if( ldir.le.1 )then
@@ -1156,11 +1156,11 @@ call zsource(asource,zi,den,fmom(1,1,misa),denmass,misa,nz)
 c
 c	LOWER DIAGONAL ELEMENTS (IONIZATION FROM LOWER CHARGE STATE)
 c
-	ozi = al32(m)/zi(misa,jz)
+	ozi_api = al32(m)/zi_api(misa,jz)
 	if (jz.gt.1)then
 	  jp = jz-1
 	  if( (m.eq.mp) )then
-	  amat(index) = ozi*denmass(misa,jp)*nuion(misa,jp)
+	  amat(index) = ozi_api*denmass(misa,jp)*nuion(misa,jp)
 	  if( ldir.le.1 )
      >	  asource(is) = asource(is) - amat(index)*usave(mp,jp,misa)
 	  endif
@@ -1172,7 +1172,7 @@ c	LOWER DIAGONAL ELEMENTS (IONIZATION FROM LOWER CHARGE STATE)
 	amat(index) = ela(m,mp,misa)
 	if( (m.eq.mp) )
      >	amat(index) = amat(index) - denmass(misa,jz)*
-     >	( nuion(misa,jz) + nurec(misa,jz) )*ozi
+     >	( nuion(misa,jz) + nurec(misa,jz) )*ozi_api
 	if( ldir.le.1 )
      >	asource(is) = asource(is) - amat(index)*usave(mp,jz,misa)
 c
@@ -1182,7 +1182,7 @@ c	UPPER DIAGONAL ELEMENTS (RECOMBINATION FROM HIGHER CHARGE STATE)
 	  index = index + KXA
 	  jp = jz+1
 	  if( (m.eq.mp) )then
-	  amat(index) = ozi*denmass(misa,jp)*nurec(misa,jp)
+	  amat(index) = ozi_api*denmass(misa,jp)*nurec(misa,jp)
 	  if( ldir.le.1 )
      >	  asource(is) = asource(is) - amat(index)*usave(mp,jp,misa)
 	  endif
@@ -1227,20 +1227,20 @@ call scopy(nkz,xsol(noff),1,uresp(1,1,misa,ntype),1)
 	end
 c---- End of subroutine zrespond ---------------------------------------
 c-----------------------------------------------------------------------
-	subroutine zsource(source,zi,den,fmom,denmass,misa,nz)
+	subroutine zsource(source,zi_api,den,fmom,denmass,misa,nz)
   	implicit real (a-h,o-z), integer (i-n)
 	Use(Reduced_ion_constants)
-	real zi(miso,*), den(miso,0:nz), source(KXA,nz,NBA), fmom(KXA,*)
+	real zi_api(miso,*), den(miso,0:nz), source(KXA,nz,NBA), fmom(KXA,*)
 	real denmass(miso,0:nz)
 	do 20 jz= 1,nz
 	do 20 m = 1,KXA
 	if( m.eq.1 )then
 	  source(m,jz,ilam1) = one
-	  source(m,jz,iacci) = denmass(misa,jz) * anorm / zi(misa,jz)
+	  source(m,jz,iacci) = denmass(misa,jz) * anorm / zi_api(misa,jz)
 	else if( (m.eq.ilam2) .or. (m.eq.ilam3) )then
 	  source(m,jz,m) = one
 	endif
-	source(m,jz,iforc) = fmom(m,jz)/zi(misa,jz)
+	source(m,jz,iforc) = fmom(m,jz)/zi_api(misa,jz)
  20	continue
 	return
 	end
diff --git a/bbb/bbb.v b/bbb/bbb.v
index 27211be0..34309f35 100755
--- a/bbb/bbb.v
+++ b/bbb/bbb.v
@@ -21,93 +21,97 @@ numvarbwpad     integer    /1/  # add to numvar for bandwidth calc;safety param
 
 ***** UEpar:
 #  Parameters and switches for the simulation
-csfaclb(nispmx,nxptmx)  real /ndcsmx*1./  #frac of cs used for Bohm sheath b.c.
-csfacrb(nispmx,nxptmx)  real /ndcsmx*1./  #frac of cs used for Bohm sheath b.c.
-csfacti   real            /1./  #Bohm speed = sqrt((te+csfacti*ti)/mi)
-cslim     real            /1./  #frac of cs used for limiter Bohm sheath b.c.
-dcslim    real            /0./  #reduce sonic flow at limiter by the factor
+csfaclb(nispmx,nxptmx)  real /ndcsmx*1./  +input #frac of cs used for Bohm sheath b.c.
+csfacrb(nispmx,nxptmx)  real /ndcsmx*1./  +input #frac of cs used for Bohm sheath b.c.
+csfacti   real            /1./  +input #Bohm speed = sqrt((te+csfacti*ti)/mi)
+cslim     real            /1./  +input #frac of cs used for limiter Bohm sheath b.c.
+dcslim    real            /0./  +input 
+                                #reduce sonic flow at limiter by the factor
                                 #cslim*[1-exp(-(iy-iy_lims+1)/dcslim)]
-islnlamcon integer        /0/   #=0, loglambda=Braginskii;if=1,loglambda=lnlam
-lnlam     real            /12./ #Coulomb log;shouldn't be constant
-methe     integer         /33/  #elec. eng. eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
-methu     integer         /33/  #ion mom. eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
-methn     integer         /33/  #ion cont. eqn: 22-harmonic average, 33-uw
-methi     integer         /33/  #ion eng. eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
-methg     integer         /33/  #neut. gas eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
+islnlamcon integer        /0/   +input #=0, loglambda=Braginskii;if=1,loglambda=lnlam
+lnlam     real            /12./ +input #Coulomb log;shouldn't be constant
+methe     integer         /33/  +input #elec. eng. eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
+methu     integer         /33/  +input #ion mom. eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
+methn     integer         /33/  +input #ion cont. eqn: 22-harmonic average, 33-uw
+methi     integer         /33/  +input #ion eng. eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
+methg     integer         /33/  +input 
+                                #neut. gas eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
                                 #66 nonorth. log intrp, 77 nonorth. 1/ng intrp
-methp     integer         /33/  #potential eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
-isgxvon   integer         /0/   #=0 uses gx in fmix; =1 for harmonic ave of gxf
-ishavisy  integer         /1/   #=1 uses harmonic ave for conxi up
-cfaccony  real            /1./  #scales conxi for up
-isvylog   real            /0/   #=0 for vy~(1/n)dn/dy; =1 for vy~d(log(n))/dy
-isintlog  integer         /0/   #nonog logrithm interp for remaining terms
-concap    integer         /0/   #=1 fixes Te and Ti to afix for thermal cond.
-convis    integer         /0/   #=1 fixes Te to afix for ion viscosity
-cniatol   real            /1./  #multiplier for atol for ni
-cngatol   real            /1./  #multiplier for atol for ng
-cupatol   real            /1./  #multiplier for atol for up
-cteatol   real            /1./  #multiplier for atol for te
-ctiatol   real            /1./  #multiplier for atol for ti
-cphiatol  real            /1./  #multiplier for atol for phi
-tolbf     real            /1./  #multiplier for atol&rtol for the boundary eqns
-tadj      real            /10./ #reduces time step by 1/tadj if iopts=1
-icnuiz    integer         /0/   #=1 constant ioniz. freq., cnuiz; =2 freezes
-icnucx    integer         /0/   #=0, var nucx;=1 const. nucx=cnucx;
+methp     integer         /33/  +input #potential eqn: 22-cd, 33-uw, 44-hyb, 55-p-law
+isgxvon   integer         /0/   +input #=0 uses gx in fmix; =1 for harmonic ave of gxf
+ishavisy  integer         /1/   +input #=1 uses harmonic ave for conxi up
+cfaccony  real            /1./  +input #scales conxi for up
+isvylog   real            /0/   +input #=0 for vy~(1/n)dn/dy; =1 for vy~d(log(n))/dy
+isintlog  integer         /0/   +input #nonog logrithm interp for remaining terms
+concap    integer         /0/   +input #=1 fixes Te and Ti to afix for thermal cond.
+convis    integer         /0/   +input #=1 fixes Te to afix for ion viscosity
+cniatol   real            /1./  +input #multiplier for atol for ni
+cngatol   real            /1./  +input #multiplier for atol for ng
+cupatol   real            /1./  +input #multiplier for atol for up
+cteatol   real            /1./  +input #multiplier for atol for te
+ctiatol   real            /1./  +input #multiplier for atol for ti
+cphiatol  real            /1./  +input #multiplier for atol for phi
+tolbf     real            /1./  +input #multiplier for atol&rtol for the boundary eqns
+tadj      real            /10./ +input #reduces time step by 1/tadj if iopts=1
+icnuiz    integer         /0/   +input #=1 constant ioniz. freq., cnuiz; =2 freezes
+icnucx    integer         /0/   +input 
+                                #=0, var nucx;=1 const. nucx=cnucx;
                                 # =2, use sigcx, so nucx~(Tg)**.5
-cnuiz     real [1/s]      /5.e+4/ #constant ioniz. freq. for icnuiz=1
-cnucx     real [1/s]      /1.e+0/ #constant charge exhange freq. for icnucx=1
-isrecmon  integer         /0/  +restart
+cnuiz     real [1/s]      /5.e+4/ +input #constant ioniz. freq. for icnuiz=1
+cnucx     real [1/s]      /1.e+0/ +input #constant charge exhange freq. for icnucx=1
+isrecmon  integer         /0/  +input 
 				 #flag to turn-on recombination (yes=1); use
 				 #cfrecom to turn-off recomb after isrecmon was on
-cfrecom   real            /1./ +restart
+cfrecom   real            /1./ +input 
                                   #scale factor multiplying recombination freq.
-igas      integer         /0/     #=1 invokes local rate eqn. for ng
-ngbackg(ngspmx) real [1/m**3] /ngspmx*1.e14/ + restart
+igas      integer         /0/     +input #=1 invokes local rate eqn. for ng
+ngbackg(ngspmx) real [1/m**3] /ngspmx*1.e14/ +input 
                                   #background gas density
-ingb      integer         /2/     #background gas source=nuiz*ngbackg*
+ingb      integer         /2/     +input 
+                                  #background gas source=nuiz*ngbackg*
                                   #                  (.9+.1*(ngbackg/ng)**ingb)
-inflbg    integer         /4/     #expon to force flalfg large near ng~ngback
-				  #ex:flalfgx,y*(1.+(cflgb*ngbackg/ng)**inflbg)
-cflbg     real            /10./   #scaling fac for flalfgx,y using inflbg
-facngbackg2ngs(ngspmx) real /ngspmx*1.e-8/ 
+inflbg    integer         /4/     +input 
+                                  #expon to force flalfg large near ng~ngback
+                				  #ex:flalfgx,y*(1.+(cflgb*ngbackg/ng)**inflbg)
+cflbg     real            /10./   +input #scaling fac for flalfgx,y using inflbg
+facngbackg2ngs(ngspmx) real /ngspmx*1.e-8/ +input 
                                   #fraction of ngbackg add to initial ngs
-nzbackg(nispmx) real [1/m**3] /nispmx*1.e9/ #background impurity density
-inzb      integer         /2/     #background impurity source=nuiz*nzbackg*
+nzbackg(nispmx) real [1/m**3] /nispmx*1.e9/ +input #background impurity density
+inzb      integer         /2/     +input
+                                  #background impurity source=nuiz*nzbackg*
                                   #                 (.9+.1*(nzbackg/nzi)**ingb)
-facnzbackg2nis(nispmx) real /nispmx*1.e-8/ 
+facnzbackg2nis(nispmx) real /nispmx*1.e-8/ +input 
                                   #fraction of nzbackg add to initial nis
-upclng(nispmx) real [m/s] /nispmx*1.e8/ 
+upclng(nispmx) real [m/s] /nispmx*1.e8/ +input 
                                   #max ion vel at beginning of iteration
-facupclng2ups(nispmx) real /nispmx*1.e-8/ 
+facupclng2ups(nispmx) real /nispmx*1.e-8/ +input 
                                   #fraction of upclng subtract from initial ups
-tebg      real [eV]    /1.e-20/   #backgrd elec eng sor to limit te~tebg
-tibg      real [eV]    /1.e-20/   #backgrd ion eng sor to limit te~tebg
-iteb      integer         /2/     #exponent of (tebg*ev/te)**iteb for bkg sor
-temin     real [eV]      /0.03/   #min value of te allow; if less, reset to
-temin2    real [eV]      /0.03/   #soft floor with te=sqrt[te**2+(temin2*ev)**2]
-pwrbkg_c  real [W/m**3]  /1.e3/   #const background factor in pwrebkg express
-pwribkg_c real [W/m**3]  /1.e3/   #const background factor in pwribkg express
-cfwjdotelim real         /1./     #factor scaling reduction of wjdote if te<tebg
-nlimix(nispmx) real  /nispmx*0./  #factor to prevent ion density pump out in x
-nlimiy(nispmx) real  /nispmx*0./  #factor to prevent ion density pump out in y
-nlimgx	  real            /0./    #factor to prevent ion density pump out in x
-nlimgy	  real            /0./    #factor to prevent ion density pump out in y
-is1D_gbx  integer         /0/     #=1 turns on 1-D gas-box model
-xgbx      real [m]        /.25/   #poloidal location of 1-D gas box
-ixgb      integer         /0/     #poloidal index of xgbx 1-D gas box (calc)
-agdc      real            /1./    #exp. decay factor ng from gas-box edge
-pcolwid   real [m]        /0./    #width of plasma column for 1-D gas-box model
-eion      real [eV]       /5./    #energy that ionized ion is born with
-ediss     real [eV]       /10./ +restart
+tebg      real [eV]    /1.e-20/   +input #backgrd elec eng sor to limit te~tebg
+tibg      real [eV]    /1.e-20/   +input #backgrd ion eng sor to limit te~tebg
+iteb      integer         /2/     +input #exponent of (tebg*ev/te)**iteb for bkg sor
+temin     real [eV]      /0.03/   +input #min value of te allow; if less, reset to
+temin2    real [eV]      /0.03/   +input #soft floor with te=sqrt[te**2+(temin2*ev)**2]
+pwrbkg_c  real [W/m**3]  /1.e3/   +input #const background factor in pwrebkg express
+pwribkg_c real [W/m**3]  /1.e3/   +input #const background factor in pwribkg express
+cfwjdotelim real         /1./     +input #factor scaling reduction of wjdote if te<tebg
+nlimix(nispmx) real  /nispmx*0./  +input #factor to prevent ion density pump out in x
+nlimiy(nispmx) real  /nispmx*0./  +input #factor to prevent ion density pump out in y
+nlimgx	  real            /0./    +input #factor to prevent ion density pump out in x
+nlimgy	  real            /0./    +input #factor to prevent ion density pump out in y
+is1D_gbx  integer         /0/     +input #=1 turns on 1-D gas-box model
+xgbx      real [m]        /.25/   +input #poloidal location of 1-D gas box
+ixgb      integer         /0/     +input #poloidal index of xgbx 1-D gas box (calc)
+agdc      real            /1./    +input #exp. decay factor ng from gas-box edge
+pcolwid   real [m]        /0./    +input #width of plasma column for 1-D gas-box model
+eion      real [eV]       /5./    +input #energy that ionized ion is born with
+ediss     real [eV]       /10./   +input
                                   #elec eng lost by mol. dissoc; should = 2*eion
-ebind     real [eV]     /13.6/ +restart
+ebind     real [eV]     /13.6/    +input 
                                   #binding energy carried by hydrogen ion
-tfcx      real [eV]    /1.e-20/   #NO LONGER USED; instead see tgas
-tfcy      real [eV]    /1.e-20/   #NO LONGER USED; instead see tgas
-afix      real [e]        /50./   #Te,i for fixed cond.(concap), visc.(convis)
-coef      real            /0.96/  #factor for ion viscosity: was 1.92 ???
-ce        real            /3.16/  #factor for electron thermal conductivity
-ci        real            /3.9/   #factor for ion thermal conductivity
+afix      real [e]        /50./   +input #Te,i for fixed cond.(concap), visc.(convis)
+coef      real            /0.96/  +input #factor for ion viscosity: was 1.92 ???
+ce        real            /3.16/  +input #factor for electron thermal conductivity
+ci        real            /3.9/   +input #factor for ion thermal conductivity
                 #The zeff dependence of ce has been explicitly added in zcoef,
                 #thus ce should always be left as 3.16 even if zeff is not 1,
                 #provided zeff is less than or equal to 4.
@@ -128,12 +132,12 @@ fxe       real
 fxi       real
 zcoef     real          #factor (calc) give zeff dependence of elec thermal c.
 coef1     real          #factor (calc) for energy equipartion rate
-cnurn     real    /1./  #scales nurlx rate for ion continuity eqn.
-cnuru     real    /1./  #scales nurlx rate for ion mom. eqn.
-cnure     real    /1./  #scales nurlx rate for elec. eng. eqn.
-cnuri     real    /1./  #scales nurlx rate for ion eng. eqn.
-cnurg     real    /1./  #scales nurlx rate for gas eqn.
-cnurp     real    /1./  #scales nurlx rate for potential eqn.
+cnurn     real    /1./  +input #scales nurlx rate for ion continuity eqn.
+cnuru     real    /1./  +input #scales nurlx rate for ion mom. eqn.
+cnure     real    /1./  +input #scales nurlx rate for elec. eng. eqn.
+cnuri     real    /1./  +input #scales nurlx rate for ion eng. eqn.
+cnurg     real    /1./  +input #scales nurlx rate for gas eqn.
+cnurp     real    /1./  +input #scales nurlx rate for potential eqn.
 nurlxn    real
 nurlxu    real
 nurlxe    real
@@ -141,80 +145,85 @@ nurlxi    real
 nurlxg    real
 nurlxp    real
 label     character*72 #code name and run time, date, and machine
-rnewpot   real    /0./ #mixture of fqy=(1-rnewpot)*fqy_old+rnewpot*fqy_new
-r0slab	  real [m]/1e-20/ #effect. major radius for isnewpot j_r calc in slab
-ishymol   integer  /0/ #=1 turns on hydr. mol; requires nhgsp=2
-te_s_dis  real     /5./ #Te shift of ioniz curve to approx dissociation curve
-isfqpave  integer  /0/ #=0 for lin interp for fqp terms; =1 for simple ave.
-svrpkg    character*8 /"nksol"/ #use solver pkg daspk,vodpk,nksol,newton
+rnewpot   real    /0./      +input #mixture of fqy=(1-rnewpot)*fqy_old+rnewpot*fqy_new
+r0slab	  real [m]/1e-20/   +input #effect. major radius for isnewpot j_r calc in slab
+ishymol   integer  /0/      +input #=1 turns on hydr. mol; requires nhgsp=2
+te_s_dis  real     /5./     +input #Te shift of ioniz curve to approx dissociation curve
+isfqpave  integer  /0/      +input #=0 for lin interp for fqp terms; =1 for simple ave.
+svrpkg    character*8 /"nksol"/ +input #use solver pkg daspk,vodpk,nksol,newton
                                 #reset to newton if inewton=1
-petscoptfile  character*80 /""/ #specify options file for petsc code
-petscopts     character*2048 /""/ #specify options for petsc code
-isgpye    integer  /0/ #change -vy*dP/dy eng. terms; =1 for old B2; =2 for Knoll
+petscoptfile  character*80 /""/     +input #specify options file for petsc code
+petscopts     character*2048 /""/   +input #specify options for petsc code
+isgpye    integer  /0/ +input #change -vy*dP/dy eng. terms; =1 for old B2; =2 for Knoll
 iigsp     integer      # Ion index for neutrals when isupgon=1 (zi(iigsp)=0)
-fnnuiz    real    /1./ #fraction of new nuiz used for Jacobian
-itrap_negni integer /1/ #flag to trap negative ni condition
-itrap_negt integer /1/ #flag to trap negative Te,i condition
-itrap_negng integer /1/ #flag to trap negative ng condition
-isybdryog integer  /0/ #=1 sets fx0, fmx stencil to orthog values at iy=0 & ny
-isybdrywd integer  /0/ #=1 vy diffusion-only for iy=0 & ny if matwalli,o=1
-isxmpog   integer  /0/ #=1 sets fy0, fmy stencil to orthog values at ix=nxc-1
-                       # and ix=nxc+1 for geometry='dnbot'
-iexclnxc1 integer  /0/ #if=0; include nxc+1 for fee,iytotc if geometry=dnbot;
-                       #if=1; exclude nxc+1 for fee,iytotc
-ineudif   integer  /2/ #=1 gas sub. neudif uses ng, tg for gas vel & fngx->fnix
-		       #=2 gas sub. neudifgp uses pg for gas vel & fngx->fnix
-		       #=3 gas sub. neudifl use log_ng, tg for gas vel
+fnnuiz    real    /1./  +solver #fraction of new nuiz used for Jacobian
+itrap_negni integer /1/ +solver #flag to trap negative ni condition
+itrap_negt integer /1/  +solver #flag to trap negative Te,i condition
+itrap_negng integer /1/ +solver #flag to trap negative ng condition
+isybdryog integer  /0/  +input #=1 sets fx0, fmx stencil to orthog values at iy=0 & ny
+isybdrywd integer  /0/  +input #=1 vy diffusion-only for iy=0 & ny if matwalli,o=1
+isxmpog   integer  /0/  +input 
+                        #=1 sets fy0, fmy stencil to orthog values at ix=nxc-1
+                        # and ix=nxc+1 for geometry='dnbot'
+iexclnxc1 integer  /0/  +input 
+                        #if=0; include nxc+1 for fee,iytotc if geometry=dnbot;
+                        #if=1; exclude nxc+1 for fee,iytotc
+ineudif   integer  /2/  +input 
+                #=1 gas sub. neudif uses ng, tg for gas vel & fngx->fnix
+		        #=2 gas sub. neudifgp uses pg for gas vel & fngx->fnix
+		        #=3 gas sub. neudifl use log_ng, tg for gas vel
 		       #otherwise, old case has ug=ui (strong cx coupling)
-thetar    real    /0./ #rotate (R,Z) coordinates by angle theta (degrees)
-isbcwdt   integer /0/  #include dtreal in B.C. if isbcwdt=1
-ishosor   integer /0/  #if=1, integrate hydr. sources over cell; full RHS only
-iseesorave real   /0./ #cell ave factor; 0 ctr only; 1 5 pt ave elec eng sors
-ispsorave real    /0./ #cell ave factor; 0 ctr only; 1 5 pt ave of psorg,psor,etc.
-fsprd     real /.0625 / #fraction of eng. sor. spread to each of 4 neighbors
-issyvxpt0 integer /0/  #if=1, set syv=0 around x-point; ambig. rad. mom. flux
-isrrvave  integer /0/  #if=0, rrv from vertex B's; if=1, rrv=0.5*(rr_1+rr_2);
-                       #if=2, average of cases 0 and 1
-rr_fac    real    /1./ #scale factor to multiple rr and rrv
-rrmin     real    /0./ #min rr used in calc of u_tor & fqy for potential calc.
-isdtsfscal integer /0/ #if=1, dt is included in sfscal Jac scaling factor
-frfqpn    real    /1./ #frac. of new fqp at ix=0,nx using grad at ix=1,nx-1
-cffqpsat  real    /1./ #factor by which fqp can exceed fqpsatlb,rb (sat. cur)
-isplflxl  integer /0/  #=0, flalfe,i not active at ix=0 & nx;=1 active all ix
-isplflxlv integer /0/  #=0, flalfv not active at ix=0 & nx;=1 active all ix
-isplflxlgx integer /0/ #=0, flalfgx not active at ix=0 & nx;=1 active all ix
-isplflxlgxy integer /0/ #=0, flalfgxy not active at ix=0 & nx;=1 active all ix
-iswflxlgy   integer /0/ #=0, flalfgy not active at iy=0 & ny;=1 active all iy
-isplflxlvgx integer /0/ #=0, flalfvgx not active at ix=0 & nx;=1 active all ix
-isplflxlvgxy integer /0/ #=0, flalfvgxy not active at ix=0 & nx;=1 active all ix
-iswflxlvgy  integer /1/ #=0, flalfvgy not active at iy=0 & ny;=1 active all iy
-isplflxltgx integer /0/ #=0, flalfvgx not active at ix=0 & nx;=1 active all ix
-isplflxltgxy integer /0/ #=0, flalfvgxy not active at ix=0 & nx;=1 active all ix
-iswflxltgy  integer /1/ #=0, flalfvgy not active at iy=0 & ny;=1 active all iy
-flalfipl  real /1.e20/ #ion therm flux lim factor on plates when isplflxl=0
-flalfepl  real /1.e20/ #elec therm flux lim factor on plates when isplflxl=0
-isfeexpl0 integer  /0/ #if=1, feex cannot be out of inner/outer plates
-isfeixpl0 integer  /0/ #if=1, feix cannot be out of inner/outer plates
-isofric   integer /0/  #If =1, use old (B2) interspecies up drag expression
-del_te_ro real /1e10/  #te width in eV of tanh which turns off pwrze below 1 eV
+thetar    real    /0./  +input #rotate (R,Z) coordinates by angle theta (degrees)
+isbcwdt   integer /0/   +solver #include dtreal in B.C. if isbcwdt=1
+ishosor   integer /0/   +input #if=1, integrate hydr. sources over cell; full RHS only
+iseesorave real   /0./  +input #cell ave factor; 0 ctr only; 1 5 pt ave elec eng sors
+ispsorave real    /0./  +input #cell ave factor; 0 ctr only; 1 5 pt ave of psorg,psor,etc.
+fsprd     real /.0625 / +input #fraction of eng. sor. spread to each of 4 neighbors
+issyvxpt0 integer /0/   +input #if=1, set syv=0 around x-point; ambig. rad. mom. flux
+isrrvave  integer /0/   +input 
+                        #if=0, rrv from vertex B's; 
+                        #if=1, rrv=0.5*(rr_1+rr_2);
+                        #if=2, average of cases 0 and 1
+rr_fac    real    /1./ +input #scale factor to multiple rr and rrv
+rrmin     real    /0./ +input #min rr used in calc of u_tor & fqy for potential calc.
+isdtsfscal integer /0/ +input #if=1, dt is included in sfscal Jac scaling factor
+frfqpn    real    /1./ +input #frac. of new fqp at ix=0,nx using grad at ix=1,nx-1
+cffqpsat  real    /1./ +input #factor by which fqp can exceed fqpsatlb,rb (sat. cur)
+isplflxl  integer /0/  +input #=0, flalfe,i not active at ix=0 & nx;=1 active all ix
+isplflxlv integer /0/  +input #=0, flalfv not active at ix=0 & nx;=1 active all ix
+isplflxlgx integer /0/ +input #=0, flalfgx not active at ix=0 & nx;=1 active all ix
+isplflxlgxy integer /0/ +input #=0, flalfgxy not active at ix=0 & nx;=1 active all ix
+iswflxlgy   integer /0/ +input #=0, flalfgy not active at iy=0 & ny;=1 active all iy
+isplflxlvgx integer /0/ +input #=0, flalfvgx not active at ix=0 & nx;=1 active all ix
+isplflxlvgxy integer /0/ +input #=0, flalfvgxy not active at ix=0 & nx;=1 active all ix
+iswflxlvgy  integer /1/ +input #=0, flalfvgy not active at iy=0 & ny;=1 active all iy
+isplflxltgx integer /0/ +input #=0, flalfvgx not active at ix=0 & nx;=1 active all ix
+isplflxltgxy integer /0/ +input #=0, flalfvgxy not active at ix=0 & nx;=1 active all ix
+iswflxltgy  integer /1/ +input #=0, flalfvgy not active at iy=0 & ny;=1 active all iy
+flalfipl  real /1.e20/ +input #ion therm flux lim factor on plates when isplflxl=0
+flalfepl  real /1.e20/ +input #elec therm flux lim factor on plates when isplflxl=0
+isfeexpl0 integer  /0/ +input #if=1, feex cannot be out of inner/outer plates
+isfeixpl0 integer  /0/ +input #if=1, feix cannot be out of inner/outer plates
+isofric   integer /0/  +input #If =1, use old (B2) interspecies up drag expression
+del_te_ro real /1e10/  +input #te width in eV of tanh which turns off pwrze below 1 eV
 iskaboom  integer /0/  #=1 turns on ijmgetmr "k" or "kaboom" stopping option
-isnglf	  integer /0/  #=1 gives ng=nglfix at ix=0
-nglfix    real  /1e15/ #value of ng at ix=0 if isnglf=1
-isngrf	  integer /0/  #=1 gives ng=nglfix at ix=nx+1
-ngrfix    real  /1e19/ #value of ng at ix=nx+1 if isnglf=1
-isnion(nispmx) integer  /nispmx*1/   #user:turns on (=1) ion continuity eqn.
-isupon(nispmx) integer  /nispmx*1/   #user:turns on (=1) parallel vel. eqn.
-isup1up2       integer   /0/         #=1 sets up2=rup21*up1
-rup21          real      /1./        #rup21=up2/up1 if isup1up2
-isupgon(ngspmx) integer /ngspmx*0/   #user:=1 for par neutral vel. eqn.; index igsp
-isteon      integer  /1/             #user:turns on (=1) electron energy eqn.
-istion      integer  /1/             #user:turns on (=1) ion enegy eqn.
-isngon(ngspmx) integer  /6*1/        #user:turns on (=1) neutral eqn.; index igsp
-istgon(ngspmx) integer  /6*0/        #user:turns on (=1) gas enegy eqn.
-isphion     integer  /0/             #user:turns on (=1) potential eqn.
-isphiofft integer  /0/ #user:=1 leaves old cur. on & ex=-d(phis)/dx; must be used
+isnglf	  integer /0/  +input #=1 gives ng=nglfix at ix=0
+nglfix    real  /1e15/ +input #value of ng at ix=0 if isnglf=1
+isngrf	  integer /0/  +input #=1 gives ng=nglfix at ix=nx+1
+ngrfix    real  /1e19/ +input #value of ng at ix=nx+1 if isnglf=1
+isnion(nispmx) integer  /nispmx*1/   +input #user:turns on (=1) ion continuity eqn.
+isupon(nispmx) integer  /nispmx*1/   +input #user:turns on (=1) parallel vel. eqn.
+isup1up2       integer   /0/         +input #=1 sets up2=rup21*up1
+rup21          real      /1./        +input #rup21=up2/up1 if isup1up2
+isupgon(ngspmx) integer /ngspmx*0/   +input #user:=1 for par neutral vel. eqn.; index igsp
+isteon      integer  /1/             +input #user:turns on (=1) electron energy eqn.
+istion      integer  /1/             +input #user:turns on (=1) ion enegy eqn.
+isngon(ngspmx) integer  /6*1/        +input #user:turns on (=1) neutral eqn.; index igsp
+istgon(ngspmx) integer  /6*0/        +input #user:turns on (=1) gas enegy eqn.
+isphion     integer  /0/             +input #user:turns on (=1) potential eqn.
+isphiofft integer  /0/ +input #user:=1 leaves old cur. on & ex=-d(phis)/dx; must be used
                        #with isphion=0
-isnewpot  integer  /0/ #user:turns on (=1) new potential; J_r from tor. mom. bal.
+isnewpot  integer  /0/ +input #user:turns on (=1) new potential; J_r from tor. mom. bal.
                        #=-2 sets phi constant on core boundary with
                        #total core current = icoreelec
 isnionxy(0:nx+1,0:ny+1,nisp)  _integer   #calc:=1 for ni eqn on; =0 for eqn off
@@ -238,13 +247,15 @@ fdttixy(0:nx+1,0:ny+1)      _real /0./ #user:=1 for ti eqn off; =0 for eqn on
 fdtngxy(0:nx+1,0:ny+1,ngsp) _real /0./ #user:=1 for ng eqn off; =0 for eqn on
 fdttgxy(0:nx+1,0:ny+1,ngsp) _real /0./ #user:=1 for tg eqn off; =0 for eqn on
 fdtphixy(0:nx+1,0:ny+1)     _real /0./ #user:=1 for phi eqn off; =0 for eqn on
-isugfm1side               integer /0/  #=0, use pol ave gas vels in par up eqn
-                                       #=1, use 1-sided vals for domain decomp
-isnupdot1sd               integer /0/  #=0, use 2-pt ndot for (n*up)_dot;
-  				       #=1, use 1-sided n_dot for (n*up)_dot
-isphicore0		  integer /0/  #=1 sets phi=phi_mp in core if isphion=1
-is_z0_imp_const           integer /0/  #=0 use hydr Keilhacker;=1 z0_imp_const
-z0_imp_const              real    /1./ #z0 in therm force if is_z0_imp_const=1
+isugfm1side               integer /0/   +input 
+                                        #=0, use pol ave gas vels in par up eqn
+                                        #=1, use 1-sided vals for domain decomp
+isnupdot1sd               integer /0/   +input 
+                                        #=0, use 2-pt ndot for (n*up)_dot;
+                                        #=1, use 1-sided n_dot for (n*up)_dot
+isphicore0		  integer /0/  +input #=1 sets phi=phi_mp in core if isphion=1
+is_z0_imp_const           integer /0/  +input #=0 use hydr Keilhacker;=1 z0_imp_const
+z0_imp_const              real    /1./ +input #z0 in therm force if is_z0_imp_const=1
 					
 ***** Model_choice restart:
 #Flags for choosing one or another calculation of a part of the model
@@ -252,181 +263,187 @@ iondenseqn	character*8	/"llnl"/	# ion continuity equation
 
 ***** Coefeq restart:
 #Coefficients for the different terms in the fluid equations.
-cnfx      real      /1./    #X-flux coef for conv. in n-eq.
-cnfy      real      /1./    #Y-flux coef for conv. in n-eq.
-cnsor     real      /1./    #Coef for particle src. in n-eq.
-cfneut    real      /1./    #Coef for fluid neutrals contrib's to resid's
-cfnidh    real      /1./    #Coef for neutral-ion drift heating
-cfupcx    real      /1./    #Coef for nucx*(up_ion - up_gas) momentum coupling
-cfticx    real      /1./    #Coef for nucx*(up_ion-up_gas)**2 heating in Ti Eq
-cfupimpg  real      /0./    #Coef for impur up Cx/elast drag on up=0 imp gas
-cftiimpg  real      /0./    #Coef for Ti cooling CX/elast loss to cold imp gas
-cmneut    real      /0./    #Coef for Monte Carlo neutrals contrib's to resid's
-cnflux(ngspmx) real /ngspmx*1./ #coef for particle flux in n-eq. (resco)
-chradi    real      /1./    #Coef for hyd. ioniz. rad. loss in elec. eng. eq.
-chradr    real      /1./    #Coef for hyd. recomb. rad. loss in elec. eng. eq.
-chioniz   real      /1./    #Coef for hydrogen ionization in elec. eng. eq.
-ifxnsgi   integer   /0/	    #=1 sets ne for <sig*v>_i to cne_sgvi
-cne_sgvi  real [1/m**3] /1.e18/ #ne for <sig*v>_i if ifxnsgi=1
-ctsor     real      /1./    #Coef for eng. src. in Ti eq. 0.5*mi*up**2*psor
-ceisor    real      /1./    #scale fac for ion energy source term (nu_i & eion)
-ccoldsor  real      /0./    #scale fac for ion eng loss from cold cx
-cngfx(ngspmx)  real /ngspmx*1./#scale fac for flux from grad_x T_g in gas eqn.
-cngfy(ngspmx)  real /ngspmx*1./#scale fac for flux from grad_y T_g in gas eqn.
-cngmom(nispmx) real /nispmx*0./#mom. cx-loss coeff for diffusve-neut hydr only
-cmwall(nispmx) real /nispmx*0./#mom. wall-loss coeff for diff-neut hydr only
-cngtgx(ngspmx) real /ngspmx*0./#X-flux coef for gas comp. of Ti eqn.
-cngtgy(ngspmx) real /ngspmx*0./#Y-flux coef for gas comp. of Ti eqn.
-sxgsol    real      /1./    #stretches x-coord. for gas in sol & core regions
-sxgpr     real      /1./    #stretches x-coord. for gas in private flux region
-xstscal   real  [m] /1./    #scale-length with stretch-coord decays from plates
-rld2dxg(ngspmx) real /ngspmx*0./ #ratio of gas decay-length to dx via artificial diff.
-rld2dyg(ngspmx) real /ngspmx*0./ #ratio of gas decay-length to dy via artificial diff.
-cngflox(ngspmx) real /ngspmx*0./ #fac for x-flux from convection in ng-eqn.
-cngfloy(ngspmx) real /ngspmx*1./ #fac for y-flux from convection in ng-eqn.
-cngniflox(nispmx,ngspmx) real /nispmxngspmx*0./ #fac for rel ion-neut x-vel in ng-eqn
-cngnifloy(nispmx,ngspmx) real /nispmxngspmx*0./ #fac for rel ion-neut y-vel in ng-eqn
-cngsor          real    /1./     #Coef for part. src. in ng-eq.
-cdifg(ngspmx)   real /ngspmx*1./ #scale factor for gas diffusion coeff.
-lgmax(ngspmx)   real /ngspmx*1.e20/ #max gas scale length for calc particle D_g
-lgtmax(ngspmx)  real /ngspmx*1.e20/ #max gas scale length for calc. thermal D_g
-lgvmax          real   /1.e20/   #max gas scale length for calc. viscous D_g
-rtg2ti(ngspmx)  real /ngspmx*1./ #ratio of gas temp to ion temp
-tgas(ngspmx) real [eV] /ngspmx*1./ #value of tg if istgcon=1
-cmfx      real      /1./    #X-flux coef for conv. in up-eq.
-cmfy      real      /1./    #Y-flux coef for conv. in up-eq.
-cpgx      real      /1./    #Coef for Grad(p) in up-eq.
-cfvisx    real      /1./    #Coef. for x-visc. in ti-eq.
-cfvisy    real      /1./    #Coef. for y-visc. in ti-eq.
-cfanomvisxg real    /0./    #Coef. for neut x-visc ~travis(2)
-cfanomvisyg real    /0./    #Coef. for neut y-visc ~travis(2)
-cfvisxn   real      /1./    #Coef. for neutral x-visc. in up(,,iispg) eqn
-cfvisxy(1:nispmx) real /nispmx*1./    #Coef. mult fmixy(ifld)
-isvisxn_old integer /0/     #=1 uses sigcx,rrfac=1; =0 uses kelhihg, rrfac=rr**2
-cfvxnrr   real      /1./    #=1 gives rr**2 in visx gas; =0 gives old 1 factor
-cfvisyn   real      /1./    #Coef. for neutral y-visc. in up(,,iispg) eqn
-cfvcsx(1:nispmx) real /nispmx*1./  #Coefs for x-visc. in ti-eq. with ismcnon>0
-cfvcsy(1:nispmx) real /nispmx*1./  #Coefs for y-visc. in ti-eq. with ismcnon>0
-isvhyha   integer   /0/     #switch (=1) for harmonic y-ave of up in visc heat
-upvhflr   real      /1.e2/  #min denom for up harmc ave (isvhyha=1); visc heat
-vboost    real      /1./    #previously scaled eqp; no longer in use
-cvgp      real      /1./    #Coef for v.Grad(p) ion/elec eng. terms
-cvgpg     real      /1./    #Coef for v.Grad(pg) gas eng. terms
-cfvgpx(1:nispmx) real /nispmx*1./ #Coefs for x components of v.grad(p) in ti-eq
-cfvgpy(1:nispmx) real /nispmx*1./ #Coefs for y components of v.grad(p) in ti-eq
-cfbgt     real      /0./    #Coef for the B x Grad(T) terms.
-cfjhf     real      /1./    #Coef for convective cur (fqp) heat flow
-jhswitch  integer   /0/     #Coef for the Joule-heating terms
-oldseec   integer   /1/     #Switch for Joule-heating bugfix
-override  integer   /0/     #Switch to manually override checks on old models
-cf2ef     real      /0./    #Coef for ExB drift in 2-direction
-cfyef     real      /0./    #Coef for ExB drift in y-direction
-cftef     real      /0./    #Coef for ExB drift in toroidal direction
-cf2bf     real      /0./    #Coef for Grad B drift in 2-direction
-cfybf     real      /0./    #Coef for Grad B drift in y-direction
-cfcbti    real      /0./    #Coef for adding fnixcb & fniycb to Ti eqn.
-cfcurv	  real      /1./    #Coef for curvature part of Grad_B drift
-cfgradb   real      /1./    #Coef for p_perp part of Grad_B drift	
-cfq2bf    real      /0./    #Coef for Grad_B current in 2-direction
-cfqybf    real      /0./    #Coef for Grad_B current in y-direction
-cfqyn     real      /0./    #Coef for cx coll. rad current in y-direction
-cfqym     real      /1./    #Coef for spatial inertial rad current in y-dir.
-cfqydt    real      /0./    #Coef for time-dep inertial rad current in y-dir.
-cf2dd     real      /0./    #Coef for diamagnetic drift in 2-direction
-cfydd     real      /0./    #Coef for diamagnetic drift in y-direction
-cftdd     real      /0./    #Coef for diamagnetic drift in toroidal direction
-cfrd      real      /0./    #Coef for resistive cross-field drift
-cfvisxneov real     /0./    #Coef for v-driven parallel viscosity
-cfvisxneoq real     /0./    #Coef for q-driven parallel viscosity
-cfvycr    real      /0./    #Coef for thermal force class. vel. vycr
-cfvycf    real      /0./    #Coef for visc. force class. vel. vycf
-cfvyavis  real      /0./    #Coef for vy from anom perp viscosity 
-cfjve     real      /0./    #Coef for J-contribution to ve.
-cfjp2     real      /0./    #Coef for B x gradP terms in div(J) eqn
-cfjpy     real      /0./    #Coef for B x gradP terms in div(J) eqn
-isnfmiy   integer   /0/     #diff fmiy for symmetry for vel. cells touching x-pt.
-cfnfmiy   real      /1./    #Coef for new fmiy for vel. cells touching x-pt.
-cnimp	  real	    /1./    #Coef for impurity radiation loss
-fac2sp    real  [ ] /1./    #factor to test 2-species model; for
+cnfx      real      /1./    +input #X-flux coef for conv. in n-eq.
+cnfy      real      /1./    +input #Y-flux coef for conv. in n-eq.
+cnsor     real      /1./    +input #Coef for particle src. in n-eq.
+cfneut    real      /1./    +input #Coef for fluid neutrals contrib's to resid's
+cfnidh    real      /1./    +input #Coef for neutral-ion drift heating
+cfupcx    real      /1./    +input #Coef for nucx*(up_ion - up_gas) momentum coupling
+cfticx    real      /1./    +input #Coef for nucx*(up_ion-up_gas)**2 heating in Ti Eq
+cfupimpg  real      /0./    +input #Coef for impur up Cx/elast drag on up=0 imp gas
+cftiimpg  real      /0./    +input #Coef for Ti cooling CX/elast loss to cold imp gas
+cmneut    real      /0./    +input #Coef for Monte Carlo neutrals contrib's to resid's
+cnflux(ngspmx) real /ngspmx*1./ +input #coef for particle flux in n-eq. (resco)
+chradi    real      /1./    +input #Coef for hyd. ioniz. rad. loss in elec. eng. eq.
+chradr    real      /1./    +input #Coef for hyd. recomb. rad. loss in elec. eng. eq.
+chioniz   real      /1./    +input #Coef for hydrogen ionization in elec. eng. eq.
+ifxnsgi   integer   /0/	    +input #=1 sets ne for <sig*v>_i to cne_sgvi
+cne_sgvi  real [1/m**3] /1.e18/ +input #ne for <sig*v>_i if ifxnsgi=1
+ctsor     real      /1./    +input #Coef for eng. src. in Ti eq. 0.5*mi*up**2*psor
+ceisor    real      /1./    +input #scale fac for ion energy source term (nu_i & eion)
+ccoldsor  real      /0./    +input #scale fac for ion eng loss from cold cx
+cngfx(ngspmx)  real /ngspmx*1./+input #scale fac for flux from grad_x T_g in gas eqn.
+cngfy(ngspmx)  real /ngspmx*1./+input #scale fac for flux from grad_y T_g in gas eqn.
+cngmom(nispmx) real /nispmx*0./+input #mom. cx-loss coeff for diffusve-neut hydr only
+cmwall(nispmx) real /nispmx*0./+input #mom. wall-loss coeff for diff-neut hydr only
+cngtgx(ngspmx) real /ngspmx*0./+input #X-flux coef for gas comp. of Ti eqn.
+cngtgy(ngspmx) real /ngspmx*0./+input #Y-flux coef for gas comp. of Ti eqn.
+sxgsol    real      /1./    +input #stretches x-coord. for gas in sol & core regions
+sxgpr     real      /1./    +input #stretches x-coord. for gas in private flux region
+xstscal   real  [m] /1./    +input #scale-length with stretch-coord decays from plates
+rld2dxg(ngspmx) real /ngspmx*0./ +input #ratio of gas decay-length to dx via artificial diff.
+rld2dyg(ngspmx) real /ngspmx*0./ +input #ratio of gas decay-length to dy via artificial diff.
+cngflox(ngspmx) real /ngspmx*0./ +input #fac for x-flux from convection in ng-eqn.
+cngfloy(ngspmx) real /ngspmx*1./ +input #fac for y-flux from convection in ng-eqn.
+cngniflox(nispmx,ngspmx) real /nispmxngspmx*0./ +input #fac for rel ion-neut x-vel in ng-eqn
+cngnifloy(nispmx,ngspmx) real /nispmxngspmx*0./ +input #fac for rel ion-neut y-vel in ng-eqn
+cngsor          real    /1./     +input #Coef for part. src. in ng-eq.
+cdifg(ngspmx)   real /ngspmx*1./ +input #scale factor for gas diffusion coeff.
+lgmax(ngspmx)   real /ngspmx*1.e20/ +input #max gas scale length for calc particle D_g
+lgtmax(ngspmx)  real /ngspmx*1.e20/ +input #max gas scale length for calc. thermal D_g
+lgvmax          real   /1.e20/   +input #max gas scale length for calc. viscous D_g
+rtg2ti(ngspmx)  real /ngspmx*1./ +input #ratio of gas temp to ion temp
+tgas(ngspmx) real [eV] /ngspmx*1./ +input #value of tg if istgcon=1
+cmfx      real      /1./    +input #X-flux coef for conv. in up-eq.
+cmfy      real      /1./    +input #Y-flux coef for conv. in up-eq.
+cpgx      real      /1./    +input #Coef for Grad(p) in up-eq.
+cfvisx    real      /1./    +input #Coef. for x-visc. in ti-eq.
+cfvisy    real      /1./    +input #Coef. for y-visc. in ti-eq.
+cfanomvisxg real    /0./    +input #Coef. for neut x-visc ~travis(2)
+cfanomvisyg real    /0./    +input #Coef. for neut y-visc ~travis(2)
+cfvisxn   real      /1./    +input #Coef. for neutral x-visc. in up(,,iispg) eqn
+cfvisxy(1:nispmx) real /nispmx*1./    +input #Coef. mult fmixy(ifld)
+isvisxn_old integer /0/     +input #=1 uses sigcx,rrfac=1; =0 uses kelhihg, rrfac=rr**2
+cfvxnrr   real      /1./    +input #=1 gives rr**2 in visx gas; =0 gives old 1 factor
+cfvisyn   real      /1./    +input #Coef. for neutral y-visc. in up(,,iispg) eqn
+cfvcsx(1:nispmx) real /nispmx*1./  +input #Coefs for x-visc. in ti-eq. with ismcnon>0
+cfvcsy(1:nispmx) real /nispmx*1./  +input #Coefs for y-visc. in ti-eq. with ismcnon>0
+isvhyha   integer   /0/     +input #switch (=1) for harmonic y-ave of up in visc heat
+upvhflr   real      /1.e2/  +input #min denom for up harmc ave (isvhyha=1); visc heat
+vboost    real      /1./    +input #previously scaled eqp; no longer in use
+cvgp      real      /1./    +input #Coef for v.Grad(p) ion/elec eng. terms
+cvgpg     real      /1./    +input #Coef for v.Grad(pg) gas eng. terms
+cfvgpx(1:nispmx) real /nispmx*1./ +input #Coefs for x components of v.grad(p) in ti-eq
+cfvgpy(1:nispmx) real /nispmx*1./ +input #Coefs for y components of v.grad(p) in ti-eq
+cfvgpgx(1:ngspmx) real /ngspmx*0./ +input # Coefs for v*grad(pg) term (poloidal component) for Tg if isupgon=0.
+cfvgpgy(1:ngspmx) real /ngspmx*0./ +input # Coefs for v*grad(pg) term (poloidal component) for Tg if isupgon=0.
+cfbgt     real      /0./    +input #Coef for the B x Grad(T) terms.
+cfjhf     real      /1./    +input #Coef for convective cur (fqp) heat flow
+jhswitch  integer   /0/     +input #Coef for the Joule-heating terms
+oldseec   integer   /1/     +input #Switch for Joule-heating bugfix
+override  integer   /0/     +input #Switch to manually override checks on old models
+cf2ef     real      /0./    +input #Coef for ExB drift in 2-direction
+cfyef     real      /0./    +input #Coef for ExB drift in y-direction
+cftef     real      /0./    +input #Coef for ExB drift in toroidal direction
+cf2bf     real      /0./    +input #Coef for Grad B drift in 2-direction
+cfybf     real      /0./    +input #Coef for Grad B drift in y-direction
+cfcbti    real      /0./    +input #Coef for adding fnixcb & fniycb to Ti eqn.
+cfcurv	  real      /1./    +input #Coef for curvature part of Grad_B drift
+cfgradb   real      /1./    +input #Coef for p_perp part of Grad_B drift	
+cfq2bf    real      /0./    +input #Coef for Grad_B current in 2-direction
+cfqybf    real      /0./    +input #Coef for Grad_B current in y-direction
+cfqyn     real      /0./    +input #Coef for cx coll. rad current in y-direction
+cfqym     real      /1./    +input #Coef for spatial inertial rad current in y-dir.
+cfqydt    real      /0./    +input #Coef for time-dep inertial rad current in y-dir.
+cf2dd     real      /0./    +input #Coef for diamagnetic drift in 2-direction
+cfydd     real      /0./    +input #Coef for diamagnetic drift in y-direction
+cftdd     real      /0./    +input #Coef for diamagnetic drift in toroidal direction
+cfrd      real      /0./    +input #Coef for resistive cross-field drift
+cfvisxneov real     /0./    +input #Coef for v-driven parallel viscosity
+cfvisxneoq real     /0./    +input #Coef for q-driven parallel viscosity
+cfvycr    real      /0./    +input #Coef for thermal force class. vel. vycr
+cfvycf    real      /0./    +input #Coef for visc. force class. vel. vycf
+cfvyavis  real      /0./    +input #Coef for vy from anom perp viscosity 
+cfjve     real      /0./    +input #Coef for J-contribution to ve.
+cfjp2     real      /0./    +input #Coef for B x gradP terms in div(J) eqn
+cfjpy     real      /0./    +input #Coef for B x gradP terms in div(J) eqn
+isnfmiy   integer   /0/     +input #diff fmiy for symmetry for vel. cells touching x-pt.
+cfnfmiy   real      /1./    +input #Coef for new fmiy for vel. cells touching x-pt.
+cnimp	  real	    /1./    +input #Coef for impurity radiation loss
+fac2sp    real  [ ] /1./    +input #factor to test 2-species model; for
                             #equal densities, set fac2sp=2
-$$$cfw(1:10) real   /0.1,9*1./ #Coeff's for the parallel neutral momentum eq.
+$$$cfw(1:10) real   /0.1,9*1./ +input #Coeff's for the parallel neutral momentum eq.
 $$$                            #cfw(1)*(the local sound speed) is the parallel
 $$$                            #neutral velocity out of the plate (bound. con.)
-cftnm     real  [ ] /0./    #Coef for neutral cx in toroidal mom. eq for fqy
-cfupjr    real  [ ] /0./    #coef to include u_par in Jr calc.
-cfcximp1  real  [ ] /1./    #coef multi. kcxrz for imp(+1)+D(0)->imp(0)+D(+1)
-cfcximp2  real  [ ] /1./    #coef mult. kcxrz;imp(+p)+D(0)->imp(p-1)+D(+1),p>1
-cfnetap   real  [ ] /1./    #coef mult. netap*fqp term in frice express.
-fcdif     real  [ ] /1./    #coef mult all constant anomal diff coef
-cfmsor    real  [ ] /1./    #coef mult msor and msorxr in up eqn.
-cpiup(nispmx) real /nispmx*1./ #mult. press. grad term in up eqn
-cfloyi    real  [ ] /2.5/   #coef mult ion radial convective energy flow
-cfloye    real  [ ] /2.5/   #coef mult elec radial convective energy flow
-cfcvte	  real  [ ] /1.0/   #coef mult elec poloidal convect(~5/2) energy flow
-cfcvti	  real  [ ] /1.0/   #coef mult ion & neut pol convect(~5/2) energy flow
-cfcvtg	  real  [ ] /1.0/   #coef mult gas pol convect(~5/2) energy flow
-cfloxiplt real  [ ] /.0/    #coef mult neutral convect engy from plates
-cfloygwall real [ ] /.0/    #coef mult neutral convect engy from walls
-cftgdiss(ngspmx)  real  [ ] /ngspmx*1./ # coef mult tg*nu_diss eng loss
-exjbdry   real  [ ] /10./   #exponent pwr to limit fqp < fqpsat at plates
-cfgpijr   real  [ ] /1./    #scalar factor for grad_Pi term in fqya
-iszeffcon integer   /0/     #if =1, zeff=zeffcon
-zeffcon   real      /1./    #value of zeff if iszeffcon=1
-alftng    real      /0./    #neutral thermal force coeff; careful of sign
-
-cfqya     real      /1./    #Coef for anomalous current in y-direction (new model)
-cfqyao    real      /1./    #Coef for anomalous current in y-direction (old model)
-cfqyae    real      /1./    #Coef for anomalous electron current in y-direction
-cfqyai    real      /0./    #Coef for anomalous ion current in y-direction
-cfhcxgc(ngspmx) real /ngspmx*0./ # Coef constant pol heat conduct (chixg_use)
-cfhcygc(ngspmx) real /ngspmx*0./ # Coef constant rad heat conduct (chiyg_use)
-cftgcond  real      /1./    #Coef for gas thermal cond (usually molecules)
-cftgeqp  real       /1.5/   #Coef for gas thermal equipartion (usually molecules)
+cftnm     real  [ ] /0./    +input #Coef for neutral cx in toroidal mom. eq for fqy
+cfupjr    real  [ ] /0./    +input #coef to include u_par in Jr calc.
+cfcximp1  real  [ ] /1./    +input #coef multi. kcxrz for imp(+1)+D(0)->imp(0)+D(+1)
+cfcximp2  real  [ ] /1./    +input #coef mult. kcxrz;imp(+p)+D(0)->imp(p-1)+D(+1),p>1
+cfnetap   real  [ ] /1./    +input #coef mult. netap*fqp term in frice express.
+fcdif     real  [ ] /1./    +input #coef mult all constant anomal diff coef
+cfmsor    real  [ ] /1./    +input #coef mult msor and msorxr in up eqn.
+cpiup(nispmx) real /nispmx*1./ +input #mult. press. grad term in up eqn
+cfloyi    real  [ ] /2.5/   +input #coef mult ion radial convective energy flow
+cfloye    real  [ ] /2.5/   +input #coef mult elec radial convective energy flow
+cfcvte	  real  [ ] /1.0/   +input #coef mult elec poloidal convect(~5/2) energy flow
+cfcvti	  real  [ ] /1.0/   +input #coef mult ion & neut pol convect(~5/2) energy flow
+cfcvtg	  real  [ ] /1.0/   +input #coef mult gas pol convect(~5/2) energy flow
+cfloxiplt real  [ ] /.0/    +input #coef mult neutral convect engy from plates
+cfloygwall real [ ] /.0/    +input #coef mult neutral convect engy from walls
+cftgdiss(ngspmx)  real  [ ] /ngspmx*1./ +input # coef mult tg*nu_diss eng loss
+exjbdry   real  [ ] /10./   +input #exponent pwr to limit fqp < fqpsat at plates
+cfgpijr   real  [ ] /1./    +input #scalar factor for grad_Pi term in fqya
+iszeffcon integer   /0/     +input #if =1, zeff=zeffcon
+zeffcon   real      /1./    +input #value of zeff if iszeffcon=1
+alftng    real      /0./    +input #neutral thermal force coeff; careful of sign
+
+cfqya     real      /1./    +input #Coef for anomalous current in y-direction (new model)
+cfqyao    real      /1./    +input #Coef for anomalous current in y-direction (old model)
+cfqyae    real      /1./    +input #Coef for anomalous electron current in y-direction
+cfqyai    real      /0./    +input #Coef for anomalous ion current in y-direction
+cfhcxgc(ngspmx) real /ngspmx*0./ +input # Coef constant pol heat conduct (chixg_use)
+cfhcygc(ngspmx) real /ngspmx*0./ +input # Coef constant rad heat conduct (chiyg_use)
+cftgcond  real      /1./    +input #Coef for gas thermal cond (usually molecules)
+cftgeqp  real       /1.5/   +input #Coef for gas thermal equipartion (usually molecules)
  
 
 ***** Bcond restart:
 #Variables for setting the boundary conditions.
-ibctepl   integer	/1/	#Switch for ix=0 energy flux bc's
+ibctepl   integer	/1/	+input 
+                #Switch for ix=0 energy flux bc's
 				#=0, fixed te (see tepltl)
 				#=1, standard sheath transmission b.c.
 				#=2, zero poloidal gradients for te
-ibctipl	  integer       /1/     # Same as ibctepl, with te --> ti
-ibctepr   integer	/1/	#Switch for ix=nx+1 energy flux bc's
+ibctipl	  integer       /1/     +input # Same as ibctepl, with te --> ti
+ibctepr   integer	/1/	+input 
+                #Switch for ix=nx+1 energy flux bc's
 				#=0, fixed te (see tepltr)
 				#=1, standard sheath transmission b.c.
 				#=2, zero poloidal gradients for te
-ibctipr   integer       /1/	# Same as ibctepr, with te --> ti
-isphilbc	integer	/0/     #Switch for ix=0 b.c. on phi
+ibctipr   integer       /1/	+input # Same as ibctepr, with te --> ti
+isphilbc	integer	/0/     +input 
+                #Switch for ix=0 b.c. on phi
 				#=0, phi = phi0l + kappal * te
 				#=1, phi = phi0l
-isphirbc	integer	/0/     #Switch for ix=nx+1 b.c. on phi
+isphirbc	integer	/0/     +input 
+                #Switch for ix=nx+1 b.c. on phi
 				#=0, phi = phi0r + kappar * te
 				#=1, phi = phi0r
-iphibcc 	integer /3/	#core BC at iy=1 when isnewpot=1;iy=0 
+iphibcc 	integer /3/	+input #core BC at iy=1 when isnewpot=1;iy=0 
                                 #=1, d^2(ey)/dy^2=0
                                 #=2, te=constant & ey(ixmp,0)=eycore
                                 #=3, phi=constant & ey(ixmp,0)=eycore
                                 #>3 or < 1 now unavailable, previously
 				#dphi(ix,1)=dphi_iy1,isutcore ctrls ix=ixmp
-iphibcwi        integer /0/     #=0, d(ey)/dy=0
+iphibcwi        integer /0/   +input #=0, d(ey)/dy=0
 				#=1, phi(ix,0) = phintewi*te(ix,0)/ev
 				#=3, d(phi)/dy/phi = 1/lyphi(1)
 				#=4, phi(ix,0)=phiwi(ix) in PF region
-iphibcwo        integer /0/     #=0, d(ey)/dy=0
+iphibcwo        integer /0/    +input  #=0, d(ey)/dy=0
 				#=1, phi(ix,ny+1) = phintewi*te(ix,ny+1)/ev
 				#=3, d(phi)/dy/phi = 1/lyphi(2)
 				#=4, phi(ix,ny+1)=phiwo(ix)
-phiwi(0:nx+1) _real [eV] #/(nx+2)*0./
+phiwi(0:nx+1) _real [eV] +input #/(nx+2)*0./
                                 #PF wall phi profile if iphicwi=4;user set
-phiwo(0:nx+1) _real [eV] #/(nx+2)*0./
+phiwo(0:nx+1) _real [eV] +input #/(nx+2)*0./
                                 #outer wall phi profile if iphicwo=4;user set
-phintewi        real /3./	#phi/te on inner wall if iphibcwi=1
-phintewo        real /3./	#phi/te on outer wall if iphibcwo=1
-ncore(nispmx)  real [m**-3]/nispmx*7.e19/ #core ion dens if isnicore=1
-upcore(nispmx) real [m/s]  /nispmx*0./    #core ion parall vel. if isupcore=0
-ngcore(ngspmx) real [m**-3]/ngspmx*1.e15/ #core gas dens if isngcore=1
-tgcore(ngspmx) real [eV]  /ngspmx*100./   #core gas temp if istgcore=1
-isnicore(nispmx)  integer   /1,30*0/      #switch for ion-density core B.C.
+phintewi        real /3./	+input #phi/te on inner wall if iphibcwi=1
+phintewo        real /3./	+input #phi/te on outer wall if iphibcwo=1
+ncore(nispmx)  real [m**-3]/nispmx*7.e19/ +input #core ion dens if isnicore=1
+upcore(nispmx) real [m/s]  /nispmx*0./    +input #core ion parall vel. if isupcore=0
+ngcore(ngspmx) real [m**-3]/ngspmx*1.e15/ +input #core gas dens if isngcore=1
+tgcore(ngspmx) real [eV]  /ngspmx*100./   +input #core gas temp if istgcore=1
+isnicore(nispmx)  integer   /1,30*0/      +input #switch for ion-density core B.C.
 				    #=1, set uniform, fixed density, ncore
 				    #=0, set flux to curcore/sy locally in ix
 				    #=2, set flux & ni over range
@@ -434,13 +451,13 @@ isnicore(nispmx)  integer   /1,30*0/      #switch for ion-density core B.C.
 				    #=4, use impur. source terms (impur only)
 				    #=5, set d(ni)/dy=-ni/lynicore at midp &
                                     #    ni constant poloidally
-isupcore(nispmx) integer /nispmx*0/ #=0 sets up=upcore on core bdry
+isupcore(nispmx) integer /nispmx*0/ +input #=0 sets up=upcore on core bdry
 				    #=1 sets d(up)/dy=0 on the core bdry
 				    #=2 sets d^2(up)/dy^2 = 0
  				    #=3 sets fmiy = 0
 			   	    #=4 sets tor. ang mom flux = lzflux & n*up/R=const
 			   	    #=5 sets ave tor vel = utorave & n*up/R=const
-isngcore(ngspmx) integer /ngspmx*0/ #switch for neutral-density core B.C.
+isngcore(ngspmx) integer /ngspmx*0/ +input #switch for neutral-density core B.C.
 				    #=0, set loc flux= -(1-albedoc)*ng*vtg/4
 				    #=1, set uniform, fixed density, ngcore
 				    #=2, not available
@@ -448,327 +465,339 @@ isngcore(ngspmx) integer /ngspmx*0/ #switch for neutral-density core B.C.
 				    #=anything else, set zero deriv which was
 				    #prev default inert hy
 				    # anything else same as =0
-istgcore(ngspmx) integer /ngspmx*1/ #switch for neutral-density core B.C.
+istgcore(ngspmx) integer /ngspmx*1/ +input #switch for neutral-density core B.C.
                                     #=0, set tg(ixcore,0,igsp)=ti(ixcore,0)
 				    #=1, set fixed temp tgcore(igsp)
 				    #if > 1, set zero grad; tg(,0,)=tg(,1,)
-curcore(1:nispmx) real [A] /0.,30*0./ #value of current from core if isnicore=0
-lzcore(1:nispmx)  real [kg/ms] /nispmx*0./ #tor. ang. mom dens core bdry; phi eqn
-lzflux(1:nispmx)  real [kg/s**2]/nispmx*0./ #tor. ang. mom dens flux core bdry; up eqn
-utorave(1:nispmx) real [m/s] /nispmx*0./ #ave tor ave vel = utorave; up eqn
-icoreelec real [A]   /0./    # electrical current from core
-eycore	  real [V/m] /0./    # rad E-field core BC is iphibcc=3
-cfniybbo  real       /0./    # factor to includ. vycb in fniy,feiy at iy=0 only
-cfniydbo  real       /0./    # factor to includ. vycp in fniy,feiy at iy=0 only
-cfeeybbo  real       /0./    # factor to includ. vycb in feey at iy=0 only
-cfeeydbo  real       /0./    # factor to includ. vycp in feey at iy=0 only
-cfeexdbo  real       /0./    # factor includ v2cde & BxgradTe in BC at ix=0,nx
-cfeixdbo  real       /0./    # factor includ v2cdi & BxgradTi in BC at ix=0,nx
-cfqybbo   real       /0./    # factor to includ. fqyb in core current B.C. only
-cfqydbo   real       /0./    # factor to includ. fqyd in core current B.C. only
-nfqya0core integer   /0/     # num iy core cells beyond iy=0 where force fqya=0
-nfqya0pf  integer    /1/     # num. iy pf cells beyond iy=0 where force fqya=0
-nfqya0ow  integer    /1/     # num iy outer wall cell below iy=ny+1 with fqya=0
-ixfixnc   integer    /1/     # ix where ni=ncore if isnicore=2 begins
-incixc	  integer    /0/     # ix range for ni=ncore from ixfixnc if isnicore=2
-tcoree    real [eV] /50./    #core elecron temp if iflcore=0
-tcorei    real [eV] /50./    #core ion temp if iflcore=0
-tedge     real [eV] /2./     #edge ion and elec. temp; used for te,iwalli,o
+curcore(1:nispmx) real [A] /0.,30*0./ +input #value of current from core if isnicore=0
+lzcore(1:nispmx)  real [kg/ms] /nispmx*0./ +input #tor. ang. mom dens core bdry; phi eqn
+lzflux(1:nispmx)  real [kg/s**2]/nispmx*0./ +input #tor. ang. mom dens flux core bdry; up eqn
+utorave(1:nispmx) real [m/s] /nispmx*0./ +input #ave tor ave vel = utorave; up eqn
+icoreelec real [A]   /0./    +input # electrical current from core
+eycore	  real [V/m] /0./    +input # rad E-field core BC is iphibcc=3
+cfniybbo  real       /0./    +input # factor to includ. vycb in fniy,feiy at iy=0 only
+cfniydbo  real       /0./    +input # factor to includ. vycp in fniy,feiy at iy=0 only
+cfeeybbo  real       /0./    +input # factor to includ. vycb in feey at iy=0 only
+cfeeydbo  real       /0./    +input # factor to includ. vycp in feey at iy=0 only
+cfeexdbo  real       /0./    +input # factor includ v2cde & BxgradTe in BC at ix=0,nx
+cfeixdbo  real       /0./    +input # factor includ v2cdi & BxgradTi in BC at ix=0,nx
+cfqybbo   real       /0./    +input # factor to includ. fqyb in core current B.C. only
+cfqydbo   real       /0./    +input # factor to includ. fqyd in core current B.C. only
+nfqya0core integer   /0/     +input # num iy core cells beyond iy=0 where force fqya=0
+nfqya0pf  integer    /1/     +input # num. iy pf cells beyond iy=0 where force fqya=0
+nfqya0ow  integer    /1/     +input # num iy outer wall cell below iy=ny+1 with fqya=0
+ixfixnc   integer    /1/     +input # ix where ni=ncore if isnicore=2 begins
+incixc	  integer    /0/     +input # ix range for ni=ncore from ixfixnc if isnicore=2
+tcoree    real [eV] /50./    +input #core elecron temp if iflcore=0
+tcorei    real [eV] /50./    +input #core ion temp if iflcore=0
+tedge     real [eV] /2./     +input #edge ion and elec. temp; used for te,iwalli,o
                              #arrays if last element zero (as in interpolation)
-tepltl    real [eV]  /2./    #left plate Te B.C. if ibctepl=0
-tipltl    real [eV]  /2./    #left plate Ti B.C. if ibctipl=0
-tepltr    real [eV]  /2./    #right plate Te B.C. if ibcteplr=0
-tipltr    real [eV]  /2./    #right plate Ti B.C. if ibctiplr=0
-tbmin     real [eV] /.1/     #min. wall & pf temp for extrap. b.c.(isextrt..)
-nbmin     real [m**-3] /1.e17/ #min. wall & pf den for extrap. b.c.(isextrn..)
-ngbmin    real [m**-3] /1.e10/ #min. core gas den for extrap. b.c.(isextrngc)
-istewc    integer    /1/     # switch for outer-wall BC on Te
+tepltl    real [eV]  /2./    +input #left plate Te B.C. if ibctepl=0
+tipltl    real [eV]  /2./    +input #left plate Ti B.C. if ibctipl=0
+tepltr    real [eV]  /2./    +input #right plate Te B.C. if ibcteplr=0
+tipltr    real [eV]  /2./    +input #right plate Ti B.C. if ibctiplr=0
+tbmin     real [eV] /.1/     +input #min. wall & pf temp for extrap. b.c.(isextrt..)
+nbmin     real [m**-3] /1.e17/ +input #min. wall & pf den for extrap. b.c.(isextrn..)
+ngbmin    real [m**-3] /1.e10/ +input #min. core gas den for extrap. b.c.(isextrngc)
+istewc    integer    /1/     +input # switch for outer-wall BC on Te
 			     # =0, set zero energy flux
 	 		     # =1, set fixed temp to tedge or tewallo
 			     # =2, use extrapolation BC
 			     # =3, set Te scale length to lyte
                              # =4, set feey = bceew*fniy*te
-istiwc    integer    /1/     #switch for outer-wall BC on Ti, see istewc detail
-istgwc(ngspmx) integer/ngspmx*0/    #switch for outer-wall BC on Tg(,0,igsp)
+istiwc    integer    /1/     +input #switch for outer-wall BC on Ti, see istewc detail
+istgwc(ngspmx) integer/ngspmx*0/    +input #switch for outer-wall BC on Tg(,0,igsp)
 	 		     # =0, set fixed temp to tgwall
 			     # =1, use extrapolation BC
 			     # =2, set Tg scale length to lytg(2,
 			     # =3, eng flux = 2Tg*Maxw-flux
                              # >3, report error in input
-istepfc   integer    /0/     # switch for priv.-flux BC on Te
+istepfc   integer    /0/    +input  # switch for priv.-flux BC on Te
 			     # =0, set zero energy flux
 	 		     # =1, set fixed temp to tedge or tewalli
 			     # =2, use extrapolation BC
 			     # =3, set Te scale length to lyte
                              # =4, set feey = bceew*fniy*te
-istipfc   integer    /0/     #switch for priv.-flux BC on Ti, see istewc detail
-istgpfc(ngspmx) integer/ngspmx*0/   #switch for PF BC on Tg(,0,igsp)
+istipfc   integer    /0/    +input  #switch for priv.-flux BC on Ti, see istewc detail
+istgpfc(ngspmx) integer/ngspmx*0/   +input #switch for PF BC on Tg(,0,igsp)
 	 		     # =0, set fixed temp to tgwall
 			     # =1, use extrapolation BC
 			     # =2, set Tg scale length to lytg(1,
 			     # =3, eng flux = 2Tg*Maxw-flux
                              # >2, report error in input
-tewalli(0:nx+1) _real [eV] #/(nx+2)*0./
+tewalli(0:nx+1) _real [eV] +input #/(nx+2)*0./
                              #inner wall Te for istepfc=1.; = tedge if not set
-tiwalli(0:nx+1) _real [eV] #/(nx+2)*0./
+tiwalli(0:nx+1) _real [eV] +input #/(nx+2)*0./
                              #inner wall Ti for istipfc=1.; = tedge if not set
-tewallo(0:nx+1) _real [eV] #/(nx+2)*0./
+tewallo(0:nx+1) _real [eV] +input #/(nx+2)*0./
                              #outer wall Te for istewc=1.; = tedge if not set
-tiwallo(0:nx+1) _real [eV] #/(nx+2)*0./
+tiwallo(0:nx+1) _real [eV] +input #/(nx+2)*0./
                              #outer wall Ti for istiwc=1.; = tedge if not set
-tgwall(ngspmx)   real [eV] /ngspmx*0.025/ #Wall gas temp BC
-lyte(1:2)  real /2*1e20/ [m] #decaying rad Te grad leng;(1,2) istepfc,wc=3
-isulytex        integer /0/  #if=0, lytex filled with lyte
+tgwall(ngspmx)   real [eV] /ngspmx*0.025/ +input #Wall gas temp BC
+lyte(1:2)  real /2*1e20/ [m] +input #decaying rad Te grad leng;(1,2) istepfc,wc=3
+isulytex        integer /0/  +input #if=0, lytex filled with lyte
                              #if=1, user values of lytex used
-lytex(2,0:nx+1)    _real [m] # pol dep radial te grad length if set < 1e5
+lytex(2,0:nx+1)    _real [m] +input # pol dep radial te grad length if set < 1e5
                              # istepfc,wc=3: 1:2=i:o, 2nd dim ix
-lyti(1:2)  real /2*1e20/ [m] #decaying rad Ti grad leng;(1,2) istipfc,wc=3
-lytg(1:2,ngspmx) real /12*1e20/ #rad tg scale length: PF (1,; Outer(2,
-isulytix        integer /0/  #if=0, lytix filled with lyti
+lyti(1:2)  real /2*1e20/ [m] +input #decaying rad Ti grad leng;(1,2) istipfc,wc=3
+lytg(1:2,ngspmx) real /12*1e20/ +input #rad tg scale length: PF (1,; Outer(2,
+isulytix        integer /0/  +input #if=0, lytix filled with lyti
                              #if=1, user values of lytex used
-lytix(2,0:nx+1)    _real [m] # pol dep radial ti grad length if set < 1e5
+lytix(2,0:nx+1)    _real [m] +input # pol dep radial ti grad length if set < 1e5
                              # istipfc,wc=3: 1:2=i:o, 2nd dim ix
-lyphi(1:2) real /2*1e20/ [m] #decaying rad phi grad leng;(1,2) iphibcwi,o=3
-isulyphix       integer /0/  #if=0, lyphix filled with lyphix
+lyphi(1:2) real /2*1e20/ [m] +input #decaying rad phi grad leng;(1,2) iphibcwi,o=3
+isulyphix       integer /0/  +input #if=0, lyphix filled with lyphix
                              #if=1, user values of lyphix used
-lyphix(2,0:nx+1)   _real [m] # pol dep radial phi grad length if set < 1e5
+lyphix(2,0:nx+1)   _real [m] +input # pol dep radial phi grad length if set < 1e5
                              # isphipfc,wc=3: 1:2=i:o, 2nd dim ix
-isextrnp  integer   /0/      #=1 sets extrap. b.c. at div. plate bound'y for ni
-isextrnpf integer   /0/      #=1 sets extrap. b.c. at p.f. bound'y for ni
-isextrtpf integer   /0/      #=1 sets extrap. b.c. at p.f. bound'y for Te & Ti
-isextrngc integer   /0/      #=1 sets extrap. b.c. on core bdry for ng
-isextrnw  integer   /0/      #=1 sets extrap. b.c. at outer wall for ni
-isextrtw  integer   /0/      #=1 sets extrap. b.c. at outer wall for Te & Ti
-iflcore   integer   /0/      #=0, core Te,i=tcoree,i; =1 core power=pcoree,i;
+isextrnp  integer   /0/      +input #=1 sets extrap. b.c. at div. plate bound'y for ni
+isextrnpf integer   /0/      +input #=1 sets extrap. b.c. at p.f. bound'y for ni
+isextrtpf integer   /0/      +input #=1 sets extrap. b.c. at p.f. bound'y for Te & Ti
+isextrngc integer   /0/      +input #=1 sets extrap. b.c. on core bdry for ng
+isextrnw  integer   /0/      +input #=1 sets extrap. b.c. at outer wall for ni
+isextrtw  integer   /0/      +input #=1 sets extrap. b.c. at outer wall for Te & Ti
+iflcore   integer   /0/      +input #=0, core Te,i=tcoree,i; =1 core power=pcoree,i;
 			     #=-1, core d(Te,i)/dy=0
-pcoree    real [W]  /4e4/    #electron power from core if iflcore=1
-pcorei    real [W]  /4e4/    #ion power from core if iflcore=1
-ifluxni   integer  /1/       #flag for setting iy=0,ny+1 dens flux to 0 (=1,yes)
-ckinfl    real    /1./       #includes kinetic viscosity in energy bound. cond.
-isupss(nispmx) integer /nispmx*0/ +restart
+pcoree    real [W]  /4e4/    +input #electron power from core if iflcore=1
+pcorei    real [W]  /4e4/    +input #ion power from core if iflcore=1
+ifluxni   integer  /1/       +input #flag for setting iy=0,ny+1 dens flux to 0 (=1,yes)
+ckinfl    real    /1./       +input #includes kinetic viscosity in energy bound. cond.
+isupss(nispmx) integer /nispmx*0/ +input
                              #=0, up=cs; =1, up>=1; =-1, dup/dx=0 at plates
-isbohmms  integer /0/        #=0 for single-species Bohm; =1 for multispecies B
-isnwconi(1:nispmx) integer /nispmx*0/
+isbohmms  integer /0/       +input  #=0 for single-species Bohm; =1 for multispecies B
+isnwconi(1:nispmx) integer /nispmx*0/ +input 
 		#switch for private-flux wall (iy=0) density B.C.
 		#=0, old case; if ifluxni=0, dn/dy=0; if ifluxni=1, fniy=0
 		#=1, fixed density to nwalli(ix) array
 		#=2, extrapolation B.C.
 		#=3, approx grad-length lyni, but limited by nwimin
-isnwcono(1:nispmx) integer /nispmx*0/
+isnwcono(1:nispmx) integer /nispmx*0/ +input 
 		#switch for outer wall (iy=ny+1) density B.C.
 		#=0, old case; if ifluxni=0, dn/dy=0; if ifluxni=1, fniy=0
 		#=1, fixed density to nwallo(ix) array
 		#=2, extrapolation B.C.
 		#=3, approx grad-length lyni, but limited by nwomin
-nwalli(0:nx+1) _real [m**-3] #inner wall dens set by isnwconi
-nwallo(0:nx+1) _real [m**-3] #outer wall dens set by isnwcono
-nwimin(nispmx)  real [m**-3] /nispmx*1e16/  # min inner wall dens if isnwconi=3
-nwomin(nispmx)  real [m**-3] /nispmx*1e16/  # min outer wall dens if isnwcono=3
-ncoremin(nispmx) real [m**-3] /nispmx*1e10/ # min ncore for isnicore=5
-lyni(2)         real [m]     /2*1e20/       #rad dens grad length -isnwconi,o=3
-isulynix        integer      /0/            #if=0, lynix filled with lyni
+nwalli(0:nx+1) _real [m**-3] +input #inner wall dens set by isnwconi
+nwallo(0:nx+1) _real [m**-3] +input #outer wall dens set by isnwcono
+nwimin(nispmx)  real [m**-3] /nispmx*1e16/  +input # min inner wall dens if isnwconi=3
+nwomin(nispmx)  real [m**-3] /nispmx*1e16/  +input # min outer wall dens if isnwcono=3
+ncoremin(nispmx) real [m**-3] /nispmx*1e10/ +input # min ncore for isnicore=5
+lyni(2)         real [m]     /2*1e20/       +input #rad dens grad length -isnwconi,o=3
+isulynix        integer      /0/            +input #if=0, lynix filled with lyni
 					    #if=1, user values of lynix used
-lynix(2,0:nx+1,nisp) _real [m] # pol dep radial dens grad length if set < 1e5
+lynix(2,0:nx+1,nisp) _real [m] +input # pol dep radial dens grad length if set < 1e5
 			         # isnwconi,o=3: 1:2=i:o, 2nd dim ix, 3rd spec
-lynicore(nispmx) real [m] /nispmx*1e20/     # ni core BC rad scale-length if
+lynicore(nispmx) real [m] /nispmx*1e20/     +input # ni core BC rad scale-length if
 					    # isnicore=5
-lyup(2) real    /2*1e20/     #radial up grad length if isupwi,o=3: 1:2=i:o
+lyup(2) real    /2*1e20/     +input #radial up grad length if isupwi,o=3: 1:2=i:o
 isulyupx        integer      /0/            #if=0, lyupx filled with lyup
 					    #if=1, user values of lynup used
-lyupx(2,0:nx+1,nusp) _real [m] # pol dep radial up grad length if set < 1e5
+lyupx(2,0:nx+1,nusp) _real [m] +input # pol dep radial up grad length if set < 1e5
 			       # isupwi,o=3: indices,1:2=i:o, 2nd dim ix, 3rd spec
-nwsor     integer    /1/     #number of sources on wall; must be < 10
-igasi(10) real [Amp] /10*0./ #Gas currents from inner wall (iy=0)
-igaso(10) real [Amp] /10*0./ #Gas currents from outer wall (iy=ny+1)
-igspsori(10) integer /10*1/  #index of gas species for inner wall sources
-igspsoro(10) integer /10*1/  #index of gas species for outer wall sources
-issorlb(10) integer  /10*1/  +restart
+nwsor     integer    /1/     +input #number of sources on wall; must be < 10
+igasi(10) real [Amp] /10*0./ +input #Gas currents from inner wall (iy=0)
+igaso(10) real [Amp] /10*0./ +input #Gas currents from outer wall (iy=ny+1)
+igspsori(10) integer /10*1/  +input #index of gas species for inner wall sources
+igspsoro(10) integer /10*1/  +input #index of gas species for outer wall sources
+issorlb(10) integer  /10*1/  +input
                              #flag for coord. origin of source.;=1, left plate;
                              #=0, right plate
-jxsori(10)  integer  /10*1/  # xgasi=0. is located at left boundary
+jxsori(10)  integer  /10*1/  +input # xgasi=0. is located at left boundary
                              # of mesh region jxsori
-jxsoro(10)  integer  /10*1/  # xgaso=0. is located at left boundary
+jxsoro(10)  integer  /10*1/  +input # xgaso=0. is located at left boundary
                              # of mesh region jxsoro
-xgasi(10) real [m]   /10*0./ +restart
+xgasi(10) real [m]   /10*0./ +input
                              #location of inner wall sources; if issorlb(i)=1,0
                              #measured from left plate, right plate
-xgaso(10) real [m]   /10*0./ +restart
+xgaso(10) real [m]   /10*0./ +input 
                              #location of outer wall sources; if issorlb(i)=1,0,
                              #measured from left plate, right plate
-wgasi(10)  real [m] /10*100./ +restart
+wgasi(10)  real [m] /10*100./+input 
                              #total cosine widths of inner wall gas sources
-wgaso(10)  real [m] /10*100./ +restart
+wgaso(10)  real [m] /10*100./+input 
                              #total cosine widths of outer wall gas sources
-albdsi(10) real [m] /10*1.0/ #albedos at inner gas source locations
-albdso(10) real [m] /10*1.0/ #albedos at outer gas source locations
-chemsputi(10,10)   /100*0/   #chem sputt coeff, priv flux surface, flux(i)=
+albdsi(10) real [m] /10*1.0/ +input #albedos at inner gas source locations
+albdso(10) real [m] /10*1.0/ +input #albedos at outer gas source locations
+chemsputi(10,10)   /100*0/   +input #chem sputt coeff, priv flux surface, flux(i)=
                              # sum(chemsputi(i,j)*ng(j)*vt*sy)
-chemsputo(10,10)   /100*0/   #chem sputt coeff, outer wall - see chemsputi def.
-matwsi(10) integer  /10*0/   #material wall at inner gas source locations
-matwso(10) integer  /10*0/   #material wall at outer gas source locations
-issori(10) integer  /10*0/   #starting ix cell index for inner source
-iesori(10) integer  /10*0/   #ending ix cell index for inner source
-issoro(10) integer  /10*0/   #starting ix cell index for outer source
-iesoro(10) integer  /10*0/   #ending ix cell index for outer source
-iwalli(10) real     /10*0./  #current from inner source region isor for coupling
-iwallo(10) real     /10*0./  #current from outer source region isor for coupling
-ncpli(10)  integer  /10*0/   #flag for coupling between inner srce isor & ncpli
-ncplo(10)  integer  /10*0/   #flag for coupling between outer srce isor & ncpli
-cplsori(10)  real   /10*0./  #coeff. giving coupling from inner isor to ncpli
-cplsoro(10)  real   /10*0./  #coeff. giving coupling from outer isor to ncpli
-iscpli(0:nx+1)      _integer #(=1) => ix pt involved in inner bndry coupling
-iscplo(0:nx+1)      _integer #(=1) => ix pt involved in outer bndry coupling
-fwsori(0:nx+1,10)    _real   #profile of inner wall source isor (missing igasi)
-fwsoro(0:nx+1,10)    _real   #profile of outer wall source isor (missing igasi)
-fngysi(0:nx+1,ngsp)  _real -restart
+chemsputo(10,10)   /100*0/   +input #chem sputt coeff, outer wall - see chemsputi def.
+matwsi(10) integer  /10*0/   +input #material wall at inner gas source locations
+matwso(10) integer  /10*0/   +input #material wall at outer gas source locations
+issori(10) integer  /10*0/   +input #starting ix cell index for inner source
+iesori(10) integer  /10*0/   +input #ending ix cell index for inner source
+issoro(10) integer  /10*0/   +input #starting ix cell index for outer source
+iesoro(10) integer  /10*0/   +input #ending ix cell index for outer source
+iwalli(10) real     /10*0./  +input #current from inner source region isor for coupling
+iwallo(10) real     /10*0./  +input #current from outer source region isor for coupling
+ncpli(10)  integer  /10*0/   +input #flag for coupling between inner srce isor & ncpli
+ncplo(10)  integer  /10*0/   +input #flag for coupling between outer srce isor & ncpli
+cplsori(10)  real   /10*0./  +input #coeff. giving coupling from inner isor to ncpli
+cplsoro(10)  real   /10*0./  +input #coeff. giving coupling from outer isor to ncpli
+iscpli(0:nx+1)      _integer +maybeinput #(=1) => ix pt involved in inner bndry coupling
+iscplo(0:nx+1)      _integer +maybeinput #(=1) => ix pt involved in outer bndry coupling
+fwsori(0:nx+1,10)    _real   +maybeinput #profile of inner wall source isor (missing igasi)
+fwsoro(0:nx+1,10)    _real   +maybeinput #profile of outer wall source isor (missing igasi)
+fngysi(0:nx+1,ngsp)  _real   +maybeinput
                              #gas input flux from igasi on inner wall (calc)
-fngyi_use(0:nx+1,ngsp) _real [1/m**3s] #user supplied gas input flux*area
-fngysig(0:nxg+1,ngsp) _real  #global value of fngysi if domain decomp (parll)
-fngyso(0:nx+1,ngsp)  _real -restart
+fngyi_use(0:nx+1,ngsp) _real [1/m**3s] +input #user supplied gas input flux*area
+fngysig(0:nxg+1,ngsp) _real  +maybeinput #global value of fngysi if domain decomp (parll)
+fngyso(0:nx+1,ngsp)  _real   +maybeinput 
                              #gas input flux from igaso on outer wall (calc)
-fngyo_use(0:nx+1,ngsp) _real [1/m**3s] #user supplied gas input flux*area
-fngysog(0:nxg+1,ngsp) _real  #global value of fngyso if domain-decomp (parll)
-albedoo(0:nx+1,ngsp) _real -restart
+fngyo_use(0:nx+1,ngsp) _real [1/m**3s] +input #user supplied gas input flux*area
+fngysog(0:nxg+1,ngsp) _real  +maybeinput #global value of fngyso if domain-decomp (parll)
+albedoo(0:nx+1,ngsp) _real   +input
                              #albedo outer iy=ny+1 surface for neutrals (calc)
-albedoog(0:nxg+1,ngsp) _real #global val albedoo if domain-decomp (parll)
-albedoi(0:nx+1,ngsp) _real -restart
+albedoog(0:nxg+1,ngsp) _real +maybeinput #global val albedoo if domain-decomp (parll)
+albedoi(0:nx+1,ngsp) _real   +input 
                              #albedo of inner iy=0 surface for neutrals (calc)
-albedoig(0:nxg+1,ngsp) _real #global val albedoi if domain-decomp (parll)
-matwallo(0:nx+1)     _integer -restart
+albedoig(0:nxg+1,ngsp) _real +maybeinput #global val albedoi if domain-decomp (parll)
+matwallo(0:nx+1)     _integer +maybeinput 
                              #flag (=1) denoting outer material side wall
-matwallog(0:nxg+1)  _integer #global val matwallo if domain-decomp (parll)
-matwalli(0:nx+1)    _integer -restart
+matwallog(0:nxg+1)  _integer +maybeinput #global val matwallo if domain-decomp (parll)
+matwalli(0:nx+1)    _integer +maybeinput 
                              #flag (=1) denoting inner material side wall (pf)
-matwallig(0:nxg+1)  _integer #global val matwalli if domain-decomp (parll)
-sinphi    real         /.1/     #sine of angle between side wall and flux surf.
-isfixlb(nxptmx) integer /nxptmx*0/#=1 fixes values left bndry;=2 for symm. pt.
-isfixrb(nxptmx) integer /nxptmx*0/#=2 for symmetry pt. at ix=nx+1
-nib(20)   real [m**-3]/20*5.e19/#left plate density for isfixlb=1
-upb(20)   real [m/s]  /20*1e2/  #left plate parallel velocity for isfixlb=1
-teb       real [eV]    /50./    #left plate electron temp for isfixlb=1
-tib       real [eV]    /50./    #left plate ion temp for isfixlb=1
-yylb0     real [m]     /0./     #radial shift in LHB profiles for isfixlb=1
-ywnii     real [m]     /.01/    #inner Gaussian radial width of nib
-ywnio     real [m]     /.04/    #outer Gaussian radial width of nib
-ywupi     real [m]     /.01/    #inner Gaussian radial width of upb
-ywupo     real [m]     /.04/    #outer Gaussian radial width of upb
-ywtei     real [m]     /.01/    #inner Gaussian radial width of teb
-ywteo     real [m]     /.04/    #outer Gaussian radial width of teb
-ywtii     real [m]     /.01/    #inner Gaussian radial width of tib
-ywtio     real [m]     /.04/    #outer Gaussian radial width of tib
-nibprof(0:ny+1) _real -restart  #radial profile of nib
-upbprof(0:ny+1) _real -restart  #radial profile of upb
-tebprof(0:ny+1) _real -restart  #radial profile of teb
-tibprof(0:ny+1) _real -restart  #radial profile of tib
-engbsr    real [ ]     /1./     #energy factor for backscattered neutrals to Ti
-epsbs     real [ ]     /1.e-5/  #small fac added (substracted) from Rbs (Rfc)
-isguardc  integer      /1/      #using guard cells? (=1 yes, =0 no)
-rlimiter  real [m]     /1.e20/  #position of limiter at ix=0 for isfixlb=2
-islimsor  integer      /0/      #=1 extends sources into limiter region
-isutcore  integer      /0/      #Used for ix=ixcore phi BC ONLY IF iphibcc > 3
+matwallig(0:nxg+1)  _integer +maybeinput #global val matwalli if domain-decomp (parll)
+sinphi    real         /.1/     +input #sine of angle between side wall and flux surf.
+isfixlb(nxptmx) integer /nxptmx*0/+input #=1 fixes values left bndry;=2 for symm. pt.
+isfixrb(nxptmx) integer /nxptmx*0/+input #=2 for symmetry pt. at ix=nx+1
+nib(20)   real [m**-3]/20*5.e19/+input #left plate density for isfixlb=1
+upb(20)   real [m/s]  /20*1e2/  +input #left plate parallel velocity for isfixlb=1
+teb       real [eV]    /50./    +input #left plate electron temp for isfixlb=1
+tib       real [eV]    /50./    +input #left plate ion temp for isfixlb=1
+yylb0     real [m]     /0./     +input #radial shift in LHB profiles for isfixlb=1
+ywnii     real [m]     /.01/    +input #inner Gaussian radial width of nib
+ywnio     real [m]     /.04/    +input #outer Gaussian radial width of nib
+ywupi     real [m]     /.01/    +input #inner Gaussian radial width of upb
+ywupo     real [m]     /.04/    +input #outer Gaussian radial width of upb
+ywtei     real [m]     /.01/    +input #inner Gaussian radial width of teb
+ywteo     real [m]     /.04/    +input #outer Gaussian radial width of teb
+ywtii     real [m]     /.01/    +input #inner Gaussian radial width of tib
+ywtio     real [m]     /.04/    +input #outer Gaussian radial width of tib
+nibprof(0:ny+1) _real           +input #radial profile of nib
+upbprof(0:ny+1) _real           +input #radial profile of upb
+tebprof(0:ny+1) _real           +input #radial profile of teb
+tibprof(0:ny+1) _real           +input #radial profile of tib
+engbsr    real [ ]     /1./     +input #energy factor for backscattered neutrals to Ti
+epsbs     real [ ]     /1.e-5/  +input #small fac added (substracted) from Rbs (Rfc)
+isguardc  integer      /1/      +input #using guard cells? (=1 yes, =0 no)
+rlimiter  real [m]     /1.e20/  +input #position of limiter at ix=0 for isfixlb=2
+islimsor  integer      /0/      +input #=1 extends sources into limiter region
+isutcore  integer      /0/      +input #Used for ix=ixcore phi BC ONLY IF iphibcc > 3
 				#=0, tor mom=lzcore on core;
-                                #=1, d<uz>/dy=0;
+                #=1, d<uz>/dy=0;
 				#>1, d^2(Ey)/dy^2=0 at outer midplane
-isupwi(nispmx) integer /nispmx*2/ #=0 sets up=0 on inner wall
-                                #=1 sets fmiy=0 (parallel mom-dens y-flux)
+isupwi(nispmx) integer /nispmx*2/ +input 
+                        #=0 sets up=0 on inner wall
+                        #=1 sets fmiy=0 (parallel mom-dens y-flux)
               			#=2 sets dup/dy=0 on inner wall
               			#=3 sets (1/up)dup/dy=1/lyup(1) scale length
-isupwo(nispmx) integer /nispmx*2/ #=0 sets up=0 on outer wall
-                                #=1 sets fmiy=0 (parallel mom-dens y-flux)
+isupwo(nispmx) integer /nispmx*2/ +input 
+                        #=0 sets up=0 on outer wall
+                        #=1 sets fmiy=0 (parallel mom-dens y-flux)
               			#=2 sets dup/dy=0 on outer wall
               			#=3 sets (1/up)dup/dy=1/lyup(2) scale length
-islbcn    integer      /2/	# b.c. for ni at limiter guard cells;
+islbcn    integer      /2/	+input 
+                # b.c. for ni at limiter guard cells;
 				# =0,1 set ni in 2 cells
 				# =2 set ni in 1 cell, fnix at interface
-islbcu    integer      /5/	# b.c. for up at limiter guard cells;
+islbcu    integer      /5/	+input 
+                # b.c. for up at limiter guard cells;
 				# =0,1 set up in 3 cells
 				# =2 set up in 2 cells, fmix at interface
 				# =3,4,6 set fmix at interface
 				# =5 set fmix-fmixy at interface
-islbce    integer      /2/	# b.c. for te at limiter guard cells;
+islbce    integer      /2/	+input 
+                # b.c. for te at limiter guard cells;
 				# =0,1 set te in 2 cells
 				# =2 set te in 1 cell, feex at interface
-islbci    integer      /2/	# b.c. for ti at limiter guard cells;
+islbci    integer      /2/	+input 
+                # b.c. for ti at limiter guard cells;
 				# =0,1 set ti in 2 cells
 				# =2 set ti in 1 cell, feix at interface
-islbcg    integer      /2/	# b.c. for ng at limiter guard cells;
+islbcg    integer      /2/	+input 
+                # b.c. for ng at limiter guard cells;
 				# =0,1 set ng in 2 cells
 				# =2 set ng in 1 cell, fngx at interface
-islbcp    integer      /2/	# b.c. for phi at limiter guard cells;
+islbcp    integer      /2/	+input 
+                # b.c. for phi at limiter guard cells;
 				# =0,1 set phi in 2 cells
 				# =2 set phi in 1 cell, fqx at interface
-isph_sput(ngspmx) integer /ngspmx*0/  #flag for plate sputtering;
+isph_sput(ngspmx) integer /ngspmx*0/  +input 
+                #flag for plate sputtering;
 				#0=old fixed case; 1=DIVIMP/JET phys sputt fits
 				#=2 adds h-ion chem sputt;=3 adds h-neut c_sput
-isi_sputw(ngspmx) integer /ngspmx*0/ #flag for outer wall ion-based sputter;
+isi_sputw(ngspmx) integer /ngspmx*0/ +input 
+                #flag for outer wall ion-based sputter;
 				#=0, no ion sputtering
 				#=1 adds phys ion sputt; =2 adds chem ion sputt
-isi_sputpf(ngspmx) integer /ngspmx*0/ #flag for priv flux ion-based sputter;
+isi_sputpf(ngspmx) integer /ngspmx*0/ +input 
+                #flag for priv flux ion-based sputter;
 				#=0, no ion sputtering
 				#=1 adds phys ion sputt; =2 adds chem ion sputt
 matt	  integer               #output flag from syld96 for sputt. target mat.
 matp	  integer               #output flag from syld96 for sputt. plasma
-cion      integer     /6/       #input to syld96; atom num. of sputt. target
-cizb      integer     /1/       #input to syld96; max charge state of plasma
-crmb	  real        /2./[AMU] #input to syld96; mass of plasma ions
-isch_sput(ngspmx) integer /ngspmx*0/ #chem sputt. opt; 0=old;
-			       #5=Roth,G-R; 6=Haasz97; 7=Haasz97+Davis at low E
-eincid    real         [eV]     #incident energy of ion or neut. for chem sputt
-t_wall    real       /300./ [K] #temp. of side wall; now use tvwallo,i
-t_plat    real       /300./ [K] #temp. of divertor plate; now use tvplatlb,rb
-tvwallo(0:nx+1) _real /300./ [K] #user outer wall temp if iswalltempc=0
-tvwalli(0:nx+1) _real /300./ [K] #user inner wall temp if iswalltempc=0
-tvplatlb(0:ny+1,nxptmx) _real /300./ [K] #user left plate temp if isplttempc=0
-tvplatrb(0:ny+1,nxptmx) _real /300./ [K] #user left plate temp if isplttempc=0
+cion      integer     /6/       +input #input to syld96; atom num. of sputt. target
+cizb      integer     /1/       +input #input to syld96; max charge state of plasma
+crmb	  real        /2./[AMU] +input #input to syld96; mass of plasma ions
+isch_sput(ngspmx) integer /ngspmx*0/ +input 
+                    #chem sputt. opt; 0=old;
+			        #5=Roth,G-R; 
+                    #6=Haasz97; 
+                    #7=Haasz97+Davis at low E
+eincid    real         [eV]     +input #incident energy of ion or neut. for chem sputt
+t_wall    real       /300./ [K] +input #temp. of side wall; now use tvwallo,i
+t_plat    real       /300./ [K] +input #temp. of divertor plate; now use tvplatlb,rb
+tvwallo(0:nx+1) _real /300./ [K] +input #user outer wall temp if iswalltempc=0
+tvwalli(0:nx+1) _real /300./ [K] +input #user inner wall temp if iswalltempc=0
+tvplatlb(0:ny+1,nxptmx) _real /300./ [K] +input #user left plate temp if isplttempc=0
+tvplatrb(0:ny+1,nxptmx) _real /300./ [K] +input #user left plate temp if isplttempc=0
 flux_in   real        [1/m**2s] #incident ion or neutral flux for chem sputt
 ychem     real                  #chem sputt. yield output from sputchem
 yld_carbi(0:nx+1) _real         #chem sputt. yield, inner wall if isch_sput=5,6
 yld_carbo(0:nx+1) _real         #chem sputt. yield, outer wall if isch_sput=5,6
-fchemywi            real   /1./ #deprecated var; use fchemygwi; no harm if=1
-fchemywo            real   /1./ #deprecated var; use fchemygwo; no harm if=1
-fchemygwi(ngspmx) _real   /1./ #fac mult pf wall gas chem yield if isch_sput>0
-fchemygwo(ngspmx) _real   /1./ #fac mult outer wall gas chem yield; isch_sput>0
-fchemyiwi(ngspmx) _real   /1./ #fac mult pf wall ion chem yield if isch_sput>0
-fchemyiwo(ngspmx) _real   /1./ #fac mult outer wall ion chem yield; isch_sput>0
-fphysyiwi(ngspmx) _real   /1./ #fac mult pf wall ion phys yield if isch_sput>0
-fphysyiwo(ngspmx) _real   /1./ #fac mult outer wall ion phys yield; isch_sput>0
-fchemylb(ngspmx,nxptmx) _real /1./ #fac*inner plt gas chem yield; isch_sput>0
-fchemyrb(ngspmx,nxptmx) _real /1./ #fac*outer plt gas chem yield; isch_sput>0
-fphysylb(ngspmx,nxptmx) _real /1./ #fac*inner plt ion phys sp yield;isch_sput>0
-fphysyrb(ngspmx,nxptmx) _real /1./ #fac*outer plt ion phys sp yield;isch_sput>0
-isexunif  integer      /0/      #=1 forces ex ~ uniform at div. plates
+fchemygwi(ngspmx) _real   /1./ +input #fac mult pf wall gas chem yield if isch_sput>0
+fchemygwo(ngspmx) _real   /1./ +input #fac mult outer wall gas chem yield; isch_sput>0
+fchemyiwi(ngspmx) _real   /1./ +input #fac mult pf wall ion chem yield if isch_sput>0
+fchemyiwo(ngspmx) _real   /1./ +input #fac mult outer wall ion chem yield; isch_sput>0
+fphysyiwi(ngspmx) _real   /1./ +input #fac mult pf wall ion phys yield if isch_sput>0
+fphysyiwo(ngspmx) _real   /1./ +input #fac mult outer wall ion phys yield; isch_sput>0
+fchemylb(ngspmx,nxptmx) _real /1./ +input #fac*inner plt gas chem yield; isch_sput>0
+fchemyrb(ngspmx,nxptmx) _real /1./ +input #fac*outer plt gas chem yield; isch_sput>0
+fphysylb(ngspmx,nxptmx) _real /1./ +input #fac*inner plt ion phys sp yield;isch_sput>0
+fphysyrb(ngspmx,nxptmx) _real /1./ +input #fac*outer plt ion phys sp yield;isch_sput>0
+isexunif  integer      /0/      +maybeinput #=1 forces ex ~ uniform at div. plates
 xcnearlb  logical    /FALSE/    #=TRUE if Jac'n "box" overlaps a left boundary
 xcnearrb  logical    /FALSE/    #=TRUE if Jac'n "box" overlaps a right boundary
 openbox   logical    /FALSE/    #=TRUE if Jac'n "box" is wide open
-kappa0	  real       /3.0/	#modified sheath drop (allows j>jsat) for kappa > kappa0
-kappamx   real       /10.0/	#maximum kappa value
+kappa0	  real       /3.0/	+maybeinput #modified sheath drop (allows j>jsat) for kappa > kappa0
+kappamx   real       /10.0/	+maybeinput #maximum kappa value
 fqpsatlb(0:ny+1,nxptmx)	_real	#ion saturation current at left boundary
 fqpsatrb(0:ny+1,nxptmx)	_real	#ion saturation current at right boundary
-cfueb		real	/1./	#scale factor for ueb in plate b.c.'s
-ikapmod   integer	/0/	#=1 for new kappa model; =0 for qpfac model
-fvapi(10) real		/10*0./	#scale factor for inner evap vapor source
-avapi(10) real		/10*1./	#linear coeff. for inner evap vapor source
-bvapi(10) real		/10*1./ #exponent coeff. for inner evap vapor source
-fvapo(10) real		/10*0./	#scale factor for outer evap vapor source
-avapo(10) real		/10*1./	#linear coeff. for outer evap vapor source
-bvapo(10) real		/10*1./ #exponent coeff. for outer evap vapor source
-tvapi(0:nx+1) _real [K]   	#inner wall temp for evap; input after alloc
-tvapo(0:nx+1) _real [K]   	#outer wall temp for evap; input after alloc
-cfvytanbc real          /1./    #factor for adding vytan to plate B.C.
-totfeexl(0:ny+1,nxpt) _real [W] #elec polod energy flux*area on "left" plate
-totfeexr(0:ny+1,nxpt) _real [W] #elec polod energy flux*area on "right" plate
-totfeixl(0:ny+1,nxpt) _real [W] #elec polod energy flux*area on "left" plate
-totfeixr(0:ny+1,nxpt) _real [W] #elec polod energy flux*area on "right" plate
-cgpl      real           /0./   #scale fac atom eng plate loss; experim.
-cgpld     real           /0./   #scale fac disso eng loss; experim.
-cgengpl   real		 /0./   #new scale fac atom eng plate loss; old cgpl
-cgengw    real           /0./   #new scale fac atom eng wall loss
-cgmompl   real           /1./   #scale fac atom par mom plate loss
-vgmomp    real     [m/s] /2.e3/ #vel used in exp factor of atom mom loss
-istglb(ngspmx) _integer  /0/    #=0 for tg=tgwall; =1 for extrap;=3, Maxw flux
-istgrb(ngspmx) _integer  /0/    #=0 for tg=tgwall; =1 for extrap;=3, Maxw flux
-cgengmpl  real		 /1./   #scale fac mol plate eng loss for Maxw
-cgengmw  real		 /1./   #scale fac mol wall eng loss for Maxw
+cfueb		real	/1./	+input #scale factor for ueb in plate b.c.'s
+ikapmod   integer	/0/	    +input #=1 for new kappa model; =0 for qpfac model
+fvapi(10) real		/10*0./	+input #scale factor for inner evap vapor source
+avapi(10) real		/10*1./	+input #linear coeff. for inner evap vapor source
+bvapi(10) real		/10*1./ +input #exponent coeff. for inner evap vapor source
+fvapo(10) real		/10*0./	+input #scale factor for outer evap vapor source
+avapo(10) real		/10*1./	+input #linear coeff. for outer evap vapor source
+bvapo(10) real		/10*1./ +input #exponent coeff. for outer evap vapor source
+tvapi(0:nx+1) _real [K]   	+input #inner wall temp for evap; input after alloc
+tvapo(0:nx+1) _real [K]   	+input #outer wall temp for evap; input after alloc
+cfvytanbc real          /1./    +input #factor for adding vytan to plate B.C.
+totfeexl(0:ny+1,nxpt) _real [W] +maybeinput #elec polod energy flux*area on "left" plate
+totfeexr(0:ny+1,nxpt) _real [W] +maybeinput #elec polod energy flux*area on "right" plate
+totfeixl(0:ny+1,nxpt) _real [W] +maybeinput #elec polod energy flux*area on "left" plate
+totfeixr(0:ny+1,nxpt) _real [W] +maybeinput #elec polod energy flux*area on "right" plate
+cgpl      real           /0./   +input #scale fac atom eng plate loss; experim.
+cgpld     real           /0./   +input #scale fac disso eng loss; experim.
+cgengpl   real		 /0./       +input #new scale fac atom eng plate loss; old cgpl
+cgengw    real           /0./   +input #new scale fac atom eng wall loss
+cgmompl   real           /1./   +input #scale fac atom par mom plate loss
+vgmomp    real     [m/s] /2.e3/ +input #vel used in exp factor of atom mom loss
+istglb(ngspmx) _integer  /0/    +input #=0 for tg=tgwall; =1 for extrap;=3, Maxw flux
+istgrb(ngspmx) _integer  /0/    +input #=0 for tg=tgwall; =1 for extrap;=3, Maxw flux
+cgengmpl  real		 /1./   +input #scale fac mol plate eng loss for Maxw
+cgengmw  real		 /1./   +input #scale fac mol wall eng loss for Maxw
 
 ***** Outpwall:
 # Arrays used to communicate wall fluxes to a wall simulation code
@@ -816,99 +845,101 @@ ue_pot_engh2p1yo(0:nx+1)         _real [J] #outer (PF) wall deut ion pot energy
 ***** Rccoef:
 #Variables for recycling coeff. profiles on divertor plates
 #Set for ngspmx gas species
-recylb(0:ny+1,ngspmx,nxptmx) _real     #tot inner plate recycling coeff. (calc)
+recylb(0:ny+1,ngspmx,nxptmx) _real     +input
+                       #tot inner plate recycling coeff. (calc)
 				       #if recylb > 0, recycling coeff
 				       #if in range [-1,0], acts as albedo
 				       #if in range (-2,-1), gives ng=nglfix
 				       #if recylb <= -2, gives ng(1)=ng(0)
-recyrb(0:ny+1,ngspmx,nxptmx) _real     #tot outer plate recycling coeff. (calc)
+recyrb(0:ny+1,ngspmx,nxptmx) _real     +input 
+                       #tot outer plate recycling coeff. (calc)
 				       #if recyrb > 0, recycling coeff
 				       #if in range [-1,0], acts as albedo
 				       #if in range (-2,-1), gives ng=ngrfix
 				       #if recyrb <= -2, gives ng(nx+1)=ng(nx)
-recylb_use(0:ny+1,ngspmx,nxptmx) _real #inner plate recycling coeff. user input
-recyrb_use(0:ny+1,ngspmx,nxptmx) _real #outer plate recycling coeff. user input
-recycp(ngspmx)   real       /.9,5*0./  #recycling coef at plates if ndatlb,rb=0
-recycflb(ngspmx,nxptmx) _real /1./     #extra factor for recycling at ix=0
-recycfrb(ngspmx,nxptmx) _real /1./     #extra factor for recycling at ix=nx+1
-recycm           real       /-0.9/     #mom recycling inertial gas; at plates
+recylb_use(0:ny+1,ngspmx,nxptmx) _real +input #inner plate recycling coeff. user input
+recyrb_use(0:ny+1,ngspmx,nxptmx) _real +input #outer plate recycling coeff. user input
+recycp(ngspmx)   real       /.9,5*0./  +input #recycling coef at plates if ndatlb,rb=0
+recycflb(ngspmx,nxptmx) _real /1./     +maybeinput #extra factor for recycling at ix=0
+recycfrb(ngspmx,nxptmx) _real /1./     +maybeinput #extra factor for recycling at ix=nx+1
+recycm           real       /-0.9/     +input #mom recycling inertial gas; at plates
                                        # =up(,,2)/up(,,1)=-recycm.
 				       #if recycm betwn -9.9 & -10.1 d(up)/dx=0
                                        #if recycm < -10.1, therm mom flux used
-recycmlb_use(0:ny+1,ngspmx,nxptmx) _real #inner plt mom-recycl coeff user input
-recycmrb_use(0:ny+1,ngspmx,nxptmx) _real #outer plt mom-recycl coeff user input
-recycmlb(0:ny+1,ngspmx,nxptmx) _real   #total inner plt mom recycling coeff
-recycmrb(0:ny+1,ngspmx,nxptmx) _real   #total outer plt mom recycling coeff
-recyce           real       /0./       #energy recycling/Rp for inertial gas
-recycl           real       /1./       #recycling coef. at a limiter (ix_lim)
-recycml          real       /0.1/      #momentum recycling/Rp for gas at limtr
-recycc(ngspmx)   real       /6*1./     #core recycling coeff. if isnicore=3
-albedoc(ngspmx)  real       /6*1./     #core neut albedo for isngcore=0
-albedolb(ngspmx,nxptmx) _real /1./       #albedo at inner plate if ndatlb=0
-albedorb(ngspmx,nxptmx) _real /1./       #albedo at outer plate if ndatrb=0
-ndatlb(ngspmx,nxptmx)    _integer   /0/  #number of recycp data pts on inner plt
-ndatrb(ngspmx,nxptmx)    _integer   /0/  #number of recycp data pts on outer plt
-ydatlb(ngspmx,50,nxptmx) _real [m]  /0./ #inner data pt location from sep.
-ydatrb(ngspmx,50,nxptmx) _real [m]  /0./ #outer data pt location from sep.
-rdatlb(ngspmx,50,nxptmx) _real      /0./ #inner recycp data for each ydatlb
-rdatrb(ngspmx,50,nxptmx) _real      /0./ #outer recycp data for each ydatrb
-alblb(0:ny+1,ngspmx,nxptmx) _real        #inner plate albedo; used if <1 (calc)
-albrb(0:ny+1,ngspmx,nxptmx) _real        #outer plate albedo; used if <1 (calc)
-albedo_by_user   integer            /0/  #if=1, user fills albedoo,i & albdlb,rb
-fngxslb(0:ny+1,ngspmx,nxptmx) _real [1/s]#inner plt liq vapor gas sour. if sputtlb>0
-fngxsrb(0:ny+1,ngspmx,nxptmx) _real [1/s]#outer plt liq vapor gas sour. if sputtlb>0
-fngxlb_use(0:ny+1,ngspmx,nxptmx) _real [1/s] #user external left plate source
-fngxrb_use(0:ny+1,ngspmx,nxptmx) _real [1/s] #user external left plate source
-adatlb(ngspmx,50,nxptmx) _real    /1./   #inner albdedo data for each ydati
-adatrb(ngspmx,50,nxptmx) _real    /1./   #outer albdedo data for each ydati
-recycw(ngspmx)   real     /ngspmx*1e-10/ #recycling coef. at side walls
-recypf_use(0:nx+1,ngspmx,nxptmx) _real   #priv flux recycling coef; user input
-recywall_use(0:nx+1,ngspmx)      _real   #outer wall recycling coef; user input
-recycwit(0:nx+1,ngspmx,nxptmx)   _real    #tot recyc coeff on PF wall
-recycwot(0:nx+1,ngspmx)         _real    #tot recyc coeff on outer wall
-isrefluxclip     integer       /1/       #=1 prohib outward gas for inward ion
-gamsec           real       /0./         #secondary elec emiss coeff on plates
-sputtr           real       /0./         #sputtering coef. at plates
-sputtlb(0:ny+1,ngspmx,nxptmx)    _real   #set sputt coef. inner plate (iy,igsp)
-sputtrb(0:ny+1,ngspmx,nxptmx)    _real   #set sputt coef. outer plate (iy,igsp)
-sputflxlb(0:ny+1,ngspmx,nxptmx)  _real   #calc sput flux inner plate (iy,igsp)
-sputflxrb(0:ny+1,ngspmx,nxptmx)  _real   #calc sput flux outer plate (iy,igsp)
-sputflxw(0:nx+1,ngspmx)          _real   #calc sput flux outer wall (ix,igsp)
-sputflxpf(0:nx+1,ngspmx)         _real   #calc sput flux PF wall (ix,igsp)
-ngplatlb(ngspmx,nxptmx)          _real   #ng on inner plate if sputti < -9.9
-ngplatrb(ngspmx,nxptmx)          _real   #ng on outer plate if sputto < -9.9
-ipsputt_s		integer /1/      #start dens-index phys sputt species
-ipsputt_e		integer /1/      #end dens-index of phys sputt species
-npltsor     integer    /1/               #number sources on plates; must be <= 10
-igaslb(10,nxptmx) _real [Amp] /0./     #Gas cur from left-hand plate(s) (ix=0)
-igasrb(10,nxptmx) _real [Amp] /0./     #Gas cur from right-hand plate(s) (ix=nx)
-igspsorlb(10,nxptmx) _integer /1/      #gas species index, left-hand plate sources
-igspsorrb(10,nxptmx) _integer /1/      #gas species index, right-hand plate sources
-ygaslb(10,nxptmx)  _real [m]  /0./     #loc of left-plate sources wrt strike pt
-ygasrb(10,nxptmx)  _real [m]  /0./     #loc of right-plate sources wrt strike pt
-wgaslb(10,nxptmx)  _real [m] /100./    #total cos width of left-plate gas sources
-wgasrb(10,nxptmx)  _real [m] /100./    #total cos  width of right-plate gas sources
-fvaplb(ngspmx,nxptmx) _real     /0./  #scale factor left-plate evap vapor source
-avaplb(ngspmx,nxptmx) _real [k**.5/(m**2s)] /1./ #lin coeff left-plate evapor sor
-bvaplb(ngspmx,nxptmx) _real [K] /1./  #expon. coeff. left-plate evap vapor source
-fvaprb(ngspmx,nxptmx) _real     /0./  #scale factor right-plate evap vapor source
-avaprb(ngspmx,nxptmx) _real [k**.5/(m**2s)] /1./ #lin coeff right-plate evapor sor
-bvaprb(ngspmx,nxptmx) _real [K] /1./  #expon coeff. right-plate evap vapor source
-tvaplb(0:ny+1,nxptmx)   _real [K]     #left-plate temp for evap; input after alloc
-tvaprb(0:ny+1,nxptmx)   _real [K]     #right-plate temp for evap; input after alloc
-isextpltmod            integer  /0/   #=1 use ext gas plate fluxes fngxextlb,rb
+recycmlb_use(0:ny+1,ngspmx,nxptmx) _real +maybeinput #inner plt mom-recycl coeff user input
+recycmrb_use(0:ny+1,ngspmx,nxptmx) _real +maybeinput #outer plt mom-recycl coeff user input
+recycmlb(0:ny+1,ngspmx,nxptmx) _real   +maybeinput #total inner plt mom recycling coeff
+recycmrb(0:ny+1,ngspmx,nxptmx) _real   +maybeinput #total outer plt mom recycling coeff
+recyce           real       /0./       +input #energy recycling/Rp for inertial gas
+recycl           real       /1./       +input #recycling coef. at a limiter (ix_lim)
+recycml          real       /0.1/      +input #momentum recycling/Rp for gas at limtr
+recycc(ngspmx)   real       /6*1./     +input #core recycling coeff. if isnicore=3
+albedoc(ngspmx)  real       /6*1./     +input #core neut albedo for isngcore=0
+albedolb(ngspmx,nxptmx) _real /1./       +input #albedo at inner plate if ndatlb=0
+albedorb(ngspmx,nxptmx) _real /1./       +input #albedo at outer plate if ndatrb=0
+ndatlb(ngspmx,nxptmx)    _integer   /0/  +maybeinput #number of recycp data pts on inner plt
+ndatrb(ngspmx,nxptmx)    _integer   /0/  +maybeinput #number of recycp data pts on outer plt
+ydatlb(ngspmx,50,nxptmx) _real [m]  /0./ +maybeinput #inner data pt location from sep.
+ydatrb(ngspmx,50,nxptmx) _real [m]  /0./ +maybeinput #outer data pt location from sep.
+rdatlb(ngspmx,50,nxptmx) _real      /0./ +maybeinput #inner recycp data for each ydatlb
+rdatrb(ngspmx,50,nxptmx) _real      /0./ +maybeinput #outer recycp data for each ydatrb
+alblb(0:ny+1,ngspmx,nxptmx) _real        +input #inner plate albedo; used if <1 (calc)
+albrb(0:ny+1,ngspmx,nxptmx) _real        +input #outer plate albedo; used if <1 (calc)
+albedo_by_user   integer            /0/  +input #if=1, user fills albedoo,i & albdlb,rb
+fngxslb(0:ny+1,ngspmx,nxptmx) _real [1/s]+input #inner plt liq vapor gas sour. if sputtlb>0
+fngxsrb(0:ny+1,ngspmx,nxptmx) _real [1/s]+input #outer plt liq vapor gas sour. if sputtlb>0
+fngxlb_use(0:ny+1,ngspmx,nxptmx) _real [1/s] +input #user external left plate source
+fngxrb_use(0:ny+1,ngspmx,nxptmx) _real [1/s] +input #user external left plate source
+adatlb(ngspmx,50,nxptmx) _real    /1./   +maybeinput #inner albdedo data for each ydati
+adatrb(ngspmx,50,nxptmx) _real    /1./   +maybeinput #outer albdedo data for each ydati
+recycw(ngspmx)   real     /ngspmx*1e-10/ +input #recycling coef. at side walls
+recypf_use(0:nx+1,ngspmx,nxptmx) _real   +maybeinput #priv flux recycling coef; user input
+recywall_use(0:nx+1,ngspmx)      _real   +maybeinput #outer wall recycling coef; user input
+recycwit(0:nx+1,ngspmx,nxptmx)   _real   +maybeinput  #tot recyc coeff on PF wall
+recycwot(0:nx+1,ngspmx)         _real    +maybeinput #tot recyc coeff on outer wall
+isrefluxclip     integer       /1/       +input #=1 prohib outward gas for inward ion
+gamsec           real       /0./         +input #secondary elec emiss coeff on plates
+sputtr           real       /0./         +input #sputtering coef. at plates
+sputtlb(0:ny+1,ngspmx,nxptmx)    _real   +input #set sputt coef. inner plate (iy,igsp)
+sputtrb(0:ny+1,ngspmx,nxptmx)    _real   +input #set sputt coef. outer plate (iy,igsp)
+sputflxlb(0:ny+1,ngspmx,nxptmx)  _real   +maybeinput #calc sput flux inner plate (iy,igsp)
+sputflxrb(0:ny+1,ngspmx,nxptmx)  _real   +maybeinput #calc sput flux outer plate (iy,igsp)
+sputflxw(0:nx+1,ngspmx)          _real   +maybeinput #calc sput flux outer wall (ix,igsp)
+sputflxpf(0:nx+1,ngspmx)         _real   +maybeinput #calc sput flux PF wall (ix,igsp)
+ngplatlb(ngspmx,nxptmx)          _real   +input #ng on inner plate if sputti < -9.9
+ngplatrb(ngspmx,nxptmx)          _real   +input #ng on outer plate if sputto < -9.9
+ipsputt_s		integer /1/      +input #start dens-index phys sputt species
+ipsputt_e		integer /1/      +input #end dens-index of phys sputt species
+npltsor     integer    /1/               +input #number sources on plates; must be <= 10
+igaslb(10,nxptmx) _real [Amp] /0./     +input #Gas cur from left-hand plate(s) (ix=0)
+igasrb(10,nxptmx) _real [Amp] /0./     +input #Gas cur from right-hand plate(s) (ix=nx)
+igspsorlb(10,nxptmx) _integer /1/      +input #gas species index, left-hand plate sources
+igspsorrb(10,nxptmx) _integer /1/      +input #gas species index, right-hand plate sources
+ygaslb(10,nxptmx)  _real [m]  /0./     +input #loc of left-plate sources wrt strike pt
+ygasrb(10,nxptmx)  _real [m]  /0./     +input #loc of right-plate sources wrt strike pt
+wgaslb(10,nxptmx)  _real [m] /100./    +input #total cos width of left-plate gas sources
+wgasrb(10,nxptmx)  _real [m] /100./    +input #total cos  width of right-plate gas sources
+fvaplb(ngspmx,nxptmx) _real     /0./  +input #scale factor left-plate evap vapor source
+avaplb(ngspmx,nxptmx) _real [k**.5/(m**2s)] /1./ +input #lin coeff left-plate evapor sor
+bvaplb(ngspmx,nxptmx) _real [K] /1./  +input #expon. coeff. left-plate evap vapor source
+fvaprb(ngspmx,nxptmx) _real     /0./  +input #scale factor right-plate evap vapor source
+avaprb(ngspmx,nxptmx) _real [k**.5/(m**2s)] /1./ +input #lin coeff right-plate evapor sor
+bvaprb(ngspmx,nxptmx) _real [K] /1./  +input #expon coeff. right-plate evap vapor source
+tvaplb(0:ny+1,nxptmx)   _real [K]     +input #left-plate temp for evap; input after alloc
+tvaprb(0:ny+1,nxptmx)   _real [K]     +input #right-plate temp for evap; input after alloc
+isextpltmod            integer  /0/   +input #=1 use ext gas plate fluxes fngxextlb,rb
                                       # and feixextlb,rb
-isextwallmod           integer  /0/   #=1 use ext gas wall fluxes fngyexti,o
+isextwallmod           integer  /0/   +input #=1 use ext gas wall fluxes fngyexti,o
                                       # and feiyexti,o
-isoutwall              integer  /0/   #=1 call outwallflux to export wall fluxes
-fngxextlb(0:ny+1,ngspmx,nxptmx) _real [1/s]#inner plt external particle flux*A
-fngxextrb(0:ny+1,ngspmx,nxptmx) _real [1/s]#outer plt external particle flux*A
-fngyexti(0:nx+1,ngspmx)         _real [1/s]#inner wall external particle flux*A
-fngyexto(0:nx+1,ngspmx)         _real [1/s]#outer wall external particle flux*A
-feixextlb(0:ny+1,nxptmx)        _real [J/s]#inner plt external energy flux*A
-feixextrb(0:ny+1,nxptmx)        _real [J/s]#outer plt external energy flux*A
-feiyexti(0:nx+1)                _real [J/s]#inner wall external energy flux*A
-feiyexto(0:nx+1)                _real [J/s]#outer wall external energy flux*A
+isoutwall              integer  /0/   +input #=1 call outwallflux to export wall fluxes
+fngxextlb(0:ny+1,ngspmx,nxptmx) _real [1/s]+maybeinput #inner plt external particle flux*A
+fngxextrb(0:ny+1,ngspmx,nxptmx) _real [1/s]+maybeinput #outer plt external particle flux*A
+fngyexti(0:nx+1,ngspmx)         _real [1/s]+maybeinput #inner wall external particle flux*A
+fngyexto(0:nx+1,ngspmx)         _real [1/s]+maybeinput #outer wall external particle flux*A
+feixextlb(0:ny+1,nxptmx)        _real [J/s]+maybeinput #inner plt external energy flux*A
+feixextrb(0:ny+1,nxptmx)        _real [J/s]+maybeinput #outer plt external energy flux*A
+feiyexti(0:nx+1)                _real [J/s]+maybeinput #inner wall external energy flux*A
+feiyexto(0:nx+1)                _real [J/s]+maybeinput #outer wall external energy flux*A
 
 ***** Fixsrc:
 #Variables for including a fix-source at (xxsrc,yysrc) with int.=a*
@@ -1171,154 +1202,155 @@ rt8opi          real            /1.595769121606e0/      #sqrt(8/pi)
 
 ***** Comtra restart:
 #Variables that contain the transport parameters.
-parvis(1:nispmx)  real          /nispmx*1./     #factor times parallel visc.
-travis(1:nispmx)  real [m**2/s] /nispmx*1./     #value of perp. visc.
-difni(1:nispmx)   real [m**2/s] /nispmx*0.5/    #value of density radial diff. coef.
-dif4order(1:nispmx) real [m**4/s] /nispmx*0./   #4th ord ion density radial diff. coef.
-difgy4order(1:ngspmx) real [m**4/s] /ngspmx*0./ #4th ord gas density radial diff. coef.
-difgx4order(1:ngspmx) real [m**4/s] /ngspmx*0./ #4th ord gas density poloid diff. coef.
-difax(1:nispmx)   real [m*2/s] /nispmx*0./      #poloid. diff coeff.,scaled with dn/dx
-difnit(1:nispmx)  real [none]   /nispmx*0./     #turb. radial diff. multiplier
-cdifnit           real [none]   /1./            #=1 for all turb., =0 all fixed, D coef
-difpr(1:nispmx)   real [m**2/s] /nispmx*0./     #value of pressure radial diff. coef.
-difni2(1:nispmx)  real [m**2/s] /nispmx*0./     #value of density e_ll x e_r diff. coef.
-difpr2(1:nispmx)  real [m**2/s] /nispmx*0./     #value of pressure e_ll x e_r diff. coef
-difutm(1:nispmx)  real [m**2/s] /nispmx*1./     #value of toroidal mom. diff. coef
-difniv(0:ny+1,1:nisp)  _real [m**2/s]   /0./	#dens diff. if isbohmcalc=3, varys w/B
-difprv(0:ny+1,1:nisp)  _real [m**2/s]   /0./	#press diff if isbohmcalc=3, varys w/B
-difniv2(0:ny+1,1:nisp) _real [m**2/s]   /0./	#dens2 diff. if isbohmcalc=3, varys w/B
-travisv(0:ny+1,1:nisp) _real [m**2/s]   /0./	#viscosity. if isbohmcalc=3, varys w/B
-kyev(0:ny+1)	_real [m**2/s]   /0./	#elec eng chi if isbohmcalc=3, vary(0:ny+1)s w/B
-kyiv(0:ny+1)	_real [m**2/s]   /0./	#ion eng chi if isbohmcalc=3, varys w/B
-difutmv(0:ny+1,1:nisp)	_real [m**2/s]   /0./	#dens diff. if isbohmcalc=3, varys w/B
-vconyv(0:ny+1,1:nisp) _real [m/s] /0./   #convec radial vel if isbohmcalc=3
-inbtdif		real		 /2/	#if isbohmcalc=3, D,chi ~1/Bt**inbtdif
-inbpdif		integer		 /1/	#if isbohmcalc=3, D,chi ~1/Bp**inbpdif
-ixbpmin         integer          /0/    #isbohmcalc=3, min bpol(ixpt2-ixbpmin,
-isbohmcalc      integer          /1/	#if=1, calc Bohm diff if facb... > 0
+parvis(1:nispmx)  real          /nispmx*1./     +input #factor times parallel visc.
+travis(1:nispmx)  real [m**2/s] /nispmx*1./     +input #value of perp. visc.
+difni(1:nispmx)   real [m**2/s] /nispmx*0.5/    +input #value of density radial diff. coef.
+dif4order(1:nispmx) real [m**4/s] /nispmx*0./   +input #4th ord ion density radial diff. coef.
+difgy4order(1:ngspmx) real [m**4/s] /ngspmx*0./ +input #4th ord gas density radial diff. coef.
+difgx4order(1:ngspmx) real [m**4/s] /ngspmx*0./ +input #4th ord gas density poloid diff. coef.
+difax(1:nispmx)   real [m*2/s] /nispmx*0./      +input #poloid. diff coeff.,scaled with dn/dx
+difnit(1:nispmx)  real [none]   /nispmx*0./     +input #turb. radial diff. multiplier
+cdifnit           real [none]   /1./            +input #=1 for all turb., =0 all fixed, D coef
+difpr(1:nispmx)   real [m**2/s] /nispmx*0./     +input #value of pressure radial diff. coef.
+difni2(1:nispmx)  real [m**2/s] /nispmx*0./     +input #value of density e_ll x e_r diff. coef.
+difpr2(1:nispmx)  real [m**2/s] /nispmx*0./     +input #value of pressure e_ll x e_r diff. coef
+difutm(1:nispmx)  real [m**2/s] /nispmx*1./     +input #value of toroidal mom. diff. coef
+difniv(0:ny+1,1:nisp)  _real [m**2/s]   /0./	+input #dens diff. if isbohmcalc=3, varys w/B
+difprv(0:ny+1,1:nisp)  _real [m**2/s]   /0./	+input #press diff if isbohmcalc=3, varys w/B
+difniv2(0:ny+1,1:nisp) _real [m**2/s]   /0./	+input #dens2 diff. if isbohmcalc=3, varys w/B
+travisv(0:ny+1,1:nisp) _real [m**2/s]   /0./	+input #viscosity. if isbohmcalc=3, varys w/B
+kyev(0:ny+1)	_real [m**2/s]   /0./	+input #elec eng chi if isbohmcalc=3, vary(0:ny+1)s w/B
+kyiv(0:ny+1)	_real [m**2/s]   /0./	+input #ion eng chi if isbohmcalc=3, varys w/B
+difutmv(0:ny+1,1:nisp)	_real [m**2/s]   /0./	+input #dens diff. if isbohmcalc=3, varys w/B
+vconyv(0:ny+1,1:nisp) _real [m/s] /0./   +input #convec radial vel if isbohmcalc=3
+inbtdif		real		 /2/	+input #if isbohmcalc=3, D,chi ~1/Bt**inbtdif
+inbpdif		integer		 /1/	+input #if isbohmcalc=3, D,chi ~1/Bp**inbpdif
+ixbpmin         integer          /0/    +input #isbohmcalc=3, min bpol(ixpt2-ixbpmin,
+isbohmcalc      integer          /1/	+input 
+                    #if=1, calc Bohm diff if facb... > 0
 					#if=2, harmonic ave of Bohm, difni, etc.
 					#if=3, D=difniv*(B0/B)**inbdif, etc
-facbni        real [ ]      /0./	#factor for Bohm density y-diff. coeff.
-facbup        real [ ]      /0./	#factor for Bohm parll v y-diff. coeff.
-facbni2       real [ ]      /0./	#factor for Bohm density 2-diff. coeff.
-facbee        real [ ]      /0./	#factor for Bohm Te diff. coeff.
-facbei	      real [ ]      /0./	#factor for Bohm Ti diff. coeff.
-vcony(1:nispmx) real [m/s] /nispmx*0./  #value of constant radial velocity
-difcng	      real [m**2/s] /50./       #constant gas diff. coeff if isgasdc=1
-isgasdc       integer       /0/         #switch to turn on constant gas dif coef
-flalfe        real          /0.21/      #|| heat flux limit factor for elec.
-flalfi        real          /0.21/    #|| heat flux limit factor for ions
-lxtemax       real [m]      /1.e10/	#max pol. scale len of elec heat-flux lim
-lxtimax       real [m]      /1.e10/	#max pol. scale len of ion heat-flux lim
-lxtgmax       real [m]      /1.e10/	#max pol. scale len of gas heat-flux lim
-flalftf	      real          /1.e20/     #elec. thermal force flux-lim factor
-flgam         real          /1./        #exponent for ion flux-limit expression
-flgamv        real          /2./        #exponent for vel flux-limit expression
-flgamg        real          /2./        #exponent for gas dens flux-limit
-flgamvg       real          /2./        #exponent for gas visc flux-limit
-flgamtg       real          /1./        #exponent for gas temp flux-limit
-fricflf       real          /1./        #flux-limiting factor for inputs to
+facbni        real [ ]      /0./	+input #factor for Bohm density y-diff. coeff.
+facbup        real [ ]      /0./	+input #factor for Bohm parll v y-diff. coeff.
+facbni2       real [ ]      /0./	+input #factor for Bohm density 2-diff. coeff.
+facbee        real [ ]      /0./	+input #factor for Bohm Te diff. coeff.
+facbei	      real [ ]      /0./	+input #factor for Bohm Ti diff. coeff.
+vcony(1:nispmx) real [m/s] /nispmx*0./  +input #value of constant radial velocity
+difcng	      real [m**2/s] /50./       +input #constant gas diff. coeff if isgasdc=1
+isgasdc       integer       /0/         +input #switch to turn on constant gas dif coef
+flalfe        real          /0.21/      +input #|| heat flux limit factor for elec.
+flalfi        real          /0.21/    +input #|| heat flux limit factor for ions
+lxtemax       real [m]      /1.e10/	+input #max pol. scale len of elec heat-flux lim
+lxtimax       real [m]      /1.e10/	+input #max pol. scale len of ion heat-flux lim
+lxtgmax       real [m]      /1.e10/	+input #max pol. scale len of gas heat-flux lim
+flalftf	      real          /1.e20/     +input #elec. thermal force flux-lim factor
+flgam         real          /1./        +input #exponent for ion flux-limit expression
+flgamv        real          /2./        +input #exponent for vel flux-limit expression
+flgamg        real          /2./        +input #exponent for gas dens flux-limit
+flgamvg       real          /2./        +input #exponent for gas visc flux-limit
+flgamtg       real          /1./        +input #exponent for gas temp flux-limit
+fricflf       real          /1./        +input #flux-limiting factor for inputs to
                                         #multispecies friction (and upi) calc
-isflxlde      integer       /0/         #=1,elec flux limit diff;=0, conv/diff
-isflxldi      integer       /2/         #=1,ion flux limit diff;=0, conv/diff
+isflxlde      integer       /0/         +input #=1,elec flux limit diff;=0, conv/diff
+isflxldi      integer       /2/         +input #=1,ion flux limit diff;=0, conv/diff
                                         #=2, diff on individ hxcij
-kxe           real          /1./        #pol Braginsk elec heat conduc factor;
+kxe           real          /1./        +input #pol Braginsk elec heat conduc factor;
                                         #prev 1.35->Balescu explain by M.Zhao 
-alfkxi        real          /0./        #reduces ion thermal conduc, K_||, if
+alfkxi        real          /0./        +input #reduces ion thermal conduc, K_||, if
                                         #|ti(ix+1)-ti(ix)|<alfkxi*ti(ix)
-alfkxe        real          /0./        #reduces elec thermal conduc, K_||, if
+alfkxe        real          /0./        +input #reduces elec thermal conduc, K_||, if
                                         #|te(ix+1)-te(ix)|<alfkxe*te(ix)
-rkxecore      real          /1./        #pol elec heat diff. reduc fac in core
-inkxc         integer       /2/         #expon on yyf/yyf(0) fac for core kxe
-kye           real [m**2/s] /0.7/       #radial electron heat diffusivity
-kye4order     real [m**2/s] /0./        #4th order Te radial diff. coef.
-kyet          real [none]   /0./        #turb. radial elec. heat diff. multiplier
-ckyet         real [none]   /1./        #=1 for all turb., =0 all fixed, chi_e
-kxi           real          /1./        #poloidal ion heat diff. multi. fac
-kxicore       real          /1./        #poloidal ion heat diff. factor in core
-kxn           real          /0./        #poloidal cx-neutral heat diff. factor
-kyi           real [m**2/s] /.2/        #radial ion heat diffusivity
-kyi4order     real [m**2/s] /0./        #4th order Ti radial diff. coef.
-kyit          real [none]   /0./        #turb. radial ion heat diff. multiplier
-ckyit         real [none]   /1./        #=1 for all turb., =0 all fixed, chi_i
-kyn           real          /0./        #radial cx-neutral heat diff. factor
-feqp          real          /1./        #(Te-Ti) equipartition multiplier
-alfeqp        real          /0./        #reduces equipart. term if te~ti
-flalfgx(10)   real          /10*1./     #poloidal gas diff. flux limit
-flalfgy(10)   real          /10*1./     #radial gas diff. flux limit
-flalfgxy(10)  real          /10*1./     #nonorthog pol-face gas flux limit
-flalfgnx      real          /1.e20/	#flux-limit on total fngx;for safety
-flalfgny      real          /1.e20/	#flux-limit on total fngy;for safety
-gcfacgx	      real	    /1./	#mult tot conv gas x-flux at ix=0 & nx
-gcfacgy	      real	    /1./	#mult tot conv gas y-flux at iy=0 & ny
-gcfacgtx      real	    /0./	#mult grad Ti conv gas x-flux ix=0 & nx
-gcfacgty      real	    /0./	#mult grad Ti conv gas y-flux iy=0 & ny
-isdifxg_aug   integer       /0/         #=1 enhances D_xgas with flx-lim factor
-isdifyg_aug   integer       /0/         #=1 enhances D_ygas with flx-lim factor
-flalfv        real          /0.5/    #parallel velocity flux limit factor
-isupdrag      integer       /0/         #=1 adds nonunif B-field drag on v_||
-con_leng      real          /1e20/ [m]  #connect length used for coll trans fac
-frac_pt       real          /0.3/       #invers aspect ratio for colliless drag
-flalftgx      real          /1./        #poloidal atom temp. diff. flux limit
-flalftgy      real          /1./        #radial atom temp. diff. flux limit
-flalftmx      real          /1./        #poloidal mol temp. diff. flux limit
-flalftmy      real          /1./        #radial mol temp. diff. flux limit
-flalfvgx      real          /1./        #poloidal gas parall viscosity flux lim
-flalfvgy      real          /1./        #radial gas parall viscosity flux limit
-flalfvgxy     real          /1./        #FL for neutral fmixy
-flalftxy      real          /1.e20/	#FL for feixy (addition to hcy FL)
-flalftgxy(ngspmx) real   /ngspmx*1./    #FL for fegxy
-rnn2cx	      real          /0.2/       #ratio of neut-neut coll. to cx coll.
-rscat2cx      real          /1./        #fraction of cx counted as visx scatt
-sigcx         real   [m**2] /1.e-18/    #cx cross-sect if icnucx=2
-sigcxms(nisp,ngsp)   _real [m**2] /1e-19/ #cx x-sect for (ifld,igsp) coll
-rcxighg(ngspmx) real      /ngspmx*0./   #ratio of charge-exchange rate for
-                                        #ng_imp+ni_hydrn -> ng_hydrn+ni_Z=1_imp
-kelhihg         real [m**3/s] /5e-16/   #elastic coll. coeff:hyd_ion+hyd_atom
-kelhghg         real [m**3/s] /5e-16/   #elastic coll. coeff:hyd_atm+hyd_atom
-kelhmhg         real [m**3/s] /5e-16/   #elastic coll. coeff:hyd_mol+hyd_atom
-kelhmhm         real [m**3/s] /5e-16/   #elastic coll. coeff:hyd_mol+hyd_mol
-kelighi(ngspmx) real [m**3/s]/0.,5*5e-16/#elastic coll. coeff:imp_gas+hyd_ion
-kelighg(ngspmx) real [m**3/s]/0.,5*5e-16/#elastic coll. coeff:imp_gas+hyd_gas
-keligii(ngspmx) real [m**3/s]/0.,5*5e-16/#elastic coll. coeff:imp_gas+imp_ion
-keligig(ngspmx) real [m**3/s]/6*5e-16/  #elastic coll. coeff:imp_gas+imp_gas
-cfmassfac       real         /1./       #scales elas scat factor 16mi/(3mg+mi)
-sigvi_floor   real [m**3/s]  /0./       #minimum of ioniz. rates allowed(1e-18)
-fupe_cur      real []        /1./       #=1 fixes cur err to upe for isimpon=6
-diffusivity(0:nx+1,0:ny+1)  _real -restart
+rkxecore      real          /1./        +input #pol elec heat diff. reduc fac in core
+inkxc         integer       /2/         +input #expon on yyf/yyf(0) fac for core kxe
+kye           real [m**2/s] /0.7/       +input #radial electron heat diffusivity
+kye4order     real [m**2/s] /0./        +input #4th order Te radial diff. coef.
+kyet          real [none]   /0./        +input #turb. radial elec. heat diff. multiplier
+ckyet         real [none]   /1./        +input #=1 for all turb., =0 all fixed, chi_e
+kxi           real          /1./        +input #poloidal ion heat diff. multi. fac
+kxicore       real          /1./        +input #poloidal ion heat diff. factor in core
+kxn           real          /0./        +input #poloidal cx-neutral heat diff. factor
+kyi           real [m**2/s] /.2/        +input #radial ion heat diffusivity
+kyi4order     real [m**2/s] /0./        +input #4th order Ti radial diff. coef.
+kyit          real [none]   /0./        +input #turb. radial ion heat diff. multiplier
+ckyit         real [none]   /1./        +input #=1 for all turb., =0 all fixed, chi_i
+kyn           real          /0./        +input #radial cx-neutral heat diff. factor
+feqp          real          /1./        +input #(Te-Ti) equipartition multiplier
+alfeqp        real          /0./        +input #reduces equipart. term if te~ti
+flalfgx(10)   real          /10*1./     +input #poloidal gas diff. flux limit
+flalfgy(10)   real          /10*1./     +input #radial gas diff. flux limit
+flalfgxy(10)  real          /10*1./     +input #nonorthog pol-face gas flux limit
+flalfgnx      real          /1.e20/	+input #flux-limit on total fngx;for safety
+flalfgny      real          /1.e20/	+input #flux-limit on total fngy;for safety
+gcfacgx	      real	    /1./	+input #mult tot conv gas x-flux at ix=0 & nx
+gcfacgy	      real	    /1./	+input #mult tot conv gas y-flux at iy=0 & ny
+gcfacgtx      real	    /0./	+input #mult grad Ti conv gas x-flux ix=0 & nx
+gcfacgty      real	    /0./	+input #mult grad Ti conv gas y-flux iy=0 & ny
+isdifxg_aug   integer       /0/         +input #=1 enhances D_xgas with flx-lim factor
+isdifyg_aug   integer       /0/         +input #=1 enhances D_ygas with flx-lim factor
+flalfv        real          /0.5/    +input #parallel velocity flux limit factor
+isupdrag      integer       /0/         +input #=1 adds nonunif B-field drag on v_||
+con_leng      real          /1e20/ [m]  +input #connect length used for coll trans fac
+frac_pt       real          /0.3/       +input #invers aspect ratio for colliless drag
+flalftgx      real          /1./        +input #poloidal atom temp. diff. flux limit
+flalftgy      real          /1./        +input #radial atom temp. diff. flux limit
+flalftmx      real          /1./        +input +input #poloidal mol temp. diff. flux limit
+flalftmy      real          /1./        +input #radial mol temp. diff. flux limit
+flalfvgx      real          /1./        +input #poloidal gas parall viscosity flux lim
+flalfvgy      real          /1./        +input #radial gas parall viscosity flux limit
+flalfvgxy     real          /1./        +input #FL for neutral fmixy
+flalftxy      real          /1.e20/	+input #FL for feixy (addition to hcy FL)
+flalftgxy(ngspmx) real   /ngspmx*1./    +input #FL for fegxy
+rnn2cx	      real          /0.2/       +input #ratio of neut-neut coll. to cx coll.
+rscat2cx      real          /1./        +input #fraction of cx counted as visx scatt
+sigcx         real   [m**2] /1.e-18/    +input #cx cross-sect if icnucx=2
+sigcxms(nisp,ngsp)   _real [m**2] /1e-19/ +input #cx x-sect for (ifld,igsp) coll
+rcxighg(ngspmx) real      /ngspmx*0./   +input #ratio of charge-exchange rate for
+                                        +input #ng_imp+ni_hydrn -> ng_hydrn+ni_Z=1_imp
+kelhihg         real [m**3/s] /5e-16/   +input #elastic coll. coeff:hyd_ion+hyd_atom
+kelhghg         real [m**3/s] /5e-16/   +input #elastic coll. coeff:hyd_atm+hyd_atom
+kelhmhg         real [m**3/s] /5e-16/   +input #elastic coll. coeff:hyd_mol+hyd_atom
+kelhmhm         real [m**3/s] /5e-16/   +input #elastic coll. coeff:hyd_mol+hyd_mol
+kelighi(ngspmx) real [m**3/s]/0.,5*5e-16/+input #elastic coll. coeff:imp_gas+hyd_ion
+kelighg(ngspmx) real [m**3/s]/0.,5*5e-16/+input #elastic coll. coeff:imp_gas+hyd_gas
+keligii(ngspmx) real [m**3/s]/0.,5*5e-16/+input #elastic coll. coeff:imp_gas+imp_ion
+keligig(ngspmx) real [m**3/s]/6*5e-16/  +input #elastic coll. coeff:imp_gas+imp_gas
+cfmassfac       real         /1./       +input #scales elas scat factor 16mi/(3mg+mi)
+sigvi_floor   real [m**3/s]  /0./       +input #minimum of ioniz. rates allowed(1e-18)
+fupe_cur      real []        /1./       +input #=1 fixes cur err to upe for isimpon=6
+diffusivity(0:nx+1,0:ny+1)  _real 
    # anomalous (turbulent) diffusivity (calculated during rhs eval)
 diffusivwrk(0:nx+1,0:ny+1)  _real -restart
    # anomalous (turbulent) diffusivity (mixed w/difni using cdifnit)
 diffusivloc(0:nx+1,0:ny+1)  _real -restart
    # anomalous (turbulent) diffusivity (local values for isturbcons=2)
-cfnus_e         real      /1.e20/ # factor mult nu_star_e for elec coll_fe
-cfnus_i         real      /1.e20/ # factor mult nu_star_i for ion coll_fi
-coll_fe(0:nx+1,0:ny+1) _real      # nu_star_e/(1+nu_star_e) for elec CF drifts
-coll_fi(0:nx+1,0:ny+1) _real      # nu_star_i/(1+nu_star_i) for ion CF drifts
-tibsep	 	[eV] real /100./  # Ion temp on sep for banana width in lconi
-tebsep	 	[eV] real /100./  # Elec temp on sep for banana width in lcone
-cfelecbwd	     real /10./	  # Factor for elec banana width in lcone; makes
+cfnus_e         real      /1.e20/ +input # factor mult nu_star_e for elec coll_fe
+cfnus_i         real      /1.e20/ +input # factor mult nu_star_i for ion coll_fi
+coll_fe(0:nx+1,0:ny+1) _real      +input # nu_star_e/(1+nu_star_e) for elec CF drifts
+coll_fi(0:nx+1,0:ny+1) _real      +input # nu_star_i/(1+nu_star_i) for ion CF drifts
+tibsep	 	[eV] real /100./  +input # Ion temp on sep for banana width in lconi
+tebsep	 	[eV] real /100./  +input # Elec temp on sep for banana width in lcone
+cfelecbwd	     real /10./	  +input # Factor for elec banana width in lcone; makes
 				  # elec banana width not to small for mesh
-fluxfacy        real  /1./        # multiples y-fluxes & v(dP/dy) for 1D sims
-isdifbetap      integer /0/       #=1 turns on betap-dependent & difniv diffusion
-iexpbp          real   /1./       #exponent for diff ~ betap**iexpbp
-dfacbp          real [m**2/s] /0./#diff. coeff dens *betap**iexpbp;dif_use,dif_use
-trfacbp         real [m**2/s] /0./#diff. coeff up *betap**iexpbp;tray_use,trax_use
-kefacbp         real [m**2/s] /0./#diff. coeff Te *betap**iexpbp;kye_use,kxe_use
-kifacbp         real [m**2/s] /0./#diff. coeff Ti *betap**iexpbp;kyi_use,kxi_use
-flalfea(0:nx+1)      _real /0./#calc:elec thermal flux-limit array (see flalfe)
-flalfia(0:nx+1)      _real /0./#calc:ion thermal flux-limit array (see flalfi)
-flalfva(0:nx+1)      _real /0./#calc:ion visc flux-limit array (see flalfv)
-flalfgxa(0:nx+1,10)  _real /0./#calc:neut pol flux-limit array (see flalfgx)
-flalfgxya(0:nx+1,10) _real /0./#calc:neut xy flux-limit array (see flalfgxy)
-flalfgya(0:ny+1,10)  _real /0./#calc:neut rad flux-limit array (see flalfgy)
-flalfvgxa(0:nx+1)  _real /0./#calc:neut part pol flux-limit array (see flalfgx)
-flalfvgxya(0:nx+1) _real /0./#calc:neut part xy flux-limit array (see flalfgxy)
-flalfvgya(0:ny+1)  _real /0./#calc:neut part rad flux-limit array (see flalfgy)
-flalftgxa(0:nx+1)  _real /0./#calc:neut part pol flux-limit array (see flalfgx)
-flalftgxya(0:nx+1) _real /0./#calc:neut part xy flux-limit array (see flalfgxy)
-flalftgya(0:ny+1)  _real /0./#calc:neut part rad flux-limit array (see flalfgy)
-cfmolcool       real     /0./ #scale factor for molec cooling if ishymol=1
+fluxfacy        real  /1./        +input # multiples y-fluxes & v(dP/dy) for 1D sims
+isdifbetap      integer /0/       +input #=1 turns on betap-dependent & difniv diffusion
+iexpbp          real   /1./       +input #exponent for diff ~ betap**iexpbp
+dfacbp          real [m**2/s] /0./+input #diff. coeff dens *betap**iexpbp;dif_use,dif_use
+trfacbp         real [m**2/s] /0./+input #diff. coeff up *betap**iexpbp;tray_use,trax_use
+kefacbp         real [m**2/s] /0./+input #diff. coeff Te *betap**iexpbp;kye_use,kxe_use
+kifacbp         real [m**2/s] /0./+input #diff. coeff Ti *betap**iexpbp;kyi_use,kxi_use
+flalfea(0:nx+1)      _real /0./+input #calc:elec thermal flux-limit array (see flalfe)
+flalfia(0:nx+1)      _real /0./+input #calc:ion thermal flux-limit array (see flalfi)
+flalfva(0:nx+1)      _real /0./+input #calc:ion visc flux-limit array (see flalfv)
+flalfgxa(0:nx+1,10)  _real /0./+input #calc:neut pol flux-limit array (see flalfgx)
+flalfgxya(0:nx+1,10) _real /0./+input #calc:neut xy flux-limit array (see flalfgxy)
+flalfgya(0:ny+1,10)  _real /0./+input #calc:neut rad flux-limit array (see flalfgy)
+flalfvgxa(0:nx+1)  _real /0./+input #calc:neut part pol flux-limit array (see flalfgx)
+flalfvgxya(0:nx+1) _real /0./+input #calc:neut part xy flux-limit array (see flalfgxy)
+flalfvgya(0:ny+1)  _real /0./+input #calc:neut part rad flux-limit array (see flalfgy)
+flalftgxa(0:nx+1)  _real /0./+input #calc:neut part pol flux-limit array (see flalfgx)
+flalftgxya(0:nx+1) _real /0./+input #calc:neut part xy flux-limit array (see flalfgxy)
+flalftgya(0:ny+1)  _real /0./+input #calc:neut part rad flux-limit array (see flalfgy)
+cfmolcool       real     /0./+input  #scale factor for molec cooling if ishymol=1
 
 
 ***** Interprettrans:
@@ -1373,28 +1405,28 @@ floyd(0:nx+1,0:ny+1)  _real [1/s] /0./ # equiv radial ion particle current
 							
 ***** Turbulence:
 # Variables used in calculating anomalous diffusivities
-kappabar      real [1/m]  /0.003/ # field-line avg'd curvature
-lambdan       real [none]   /4./  # dens(divertor) / dens(midplane)
-lambdat       real [none]   /4./  # temp(midplane) / temp(divertor)
-gammasi       real [none]   /0./  # secondary emis. coef. from ion bombard.
-lambdap       real [none]   /3.5/ # e (dPhi0 / dr0) / (dTed / dr0)
-suppress_lmode   integer    /0/   # =1 to suppress L-mode turbulence in SOL
-maxmag_lmode  real          /2./  # max magn. of step in bracketing kymax
-nky           integer       /30/  # number of ky values in search for kymax
-kybeg         real [none]  /0.05/ # lower limit of acceptable kymax
-kyend         real [none]   /3./  # upper limit of acceptable kymax
-kya           real [none]   /1.0/ # one initial point in search for kymax
-kyb           real [none]   /1.1/ # other initial point in search for kymax
-iprint_lmode  integer  /0/  # =1 for diagnostic output, =2 for more output
-tol_lmode     real [none] /1.e-6/ # abs & rel tolerance in search for kymax
-isturbnloc    integer  /1/  # =1 to turn on nonlocal dependence of D,chi
-isturbcons    integer  /1/  # =1 to make turbulent D,chi const within SOL
+kappabar      real [1/m]  /0.003/ +maybeinput # field-line avg'd curvature
+lambdan       real [none]   /4./  +maybeinput # dens(divertor) / dens(midplane)
+lambdat       real [none]   /4./  +maybeinput # temp(midplane) / temp(divertor)
+gammasi       real [none]   /0./  +maybeinput # secondary emis. coef. from ion bombard.
+lambdap       real [none]   /3.5/ +maybeinput # e (dPhi0 / dr0) / (dTed / dr0)
+suppress_lmode   integer    /0/   +maybeinput # =1 to suppress L-mode turbulence in SOL
+maxmag_lmode  real          /2./  +maybeinput # max magn. of step in bracketing kymax
+nky           integer       /30/  +maybeinput # number of ky values in search for kymax
+kybeg         real [none]  /0.05/ +maybeinput # lower limit of acceptable kymax
+kyend         real [none]   /3./  +maybeinput # upper limit of acceptable kymax
+kya           real [none]   /1.0/ +maybeinput # one initial point in search for kymax
+kyb           real [none]   /1.1/ +maybeinput # other initial point in search for kymax
+iprint_lmode  integer  /0/  +maybeinput # =1 for diagnostic output, =2 for more output
+tol_lmode     real [none] /1.e-6/ +maybeinput # abs & rel tolerance in search for kymax
+isturbnloc    integer  /1/  +maybeinput # =1 to turn on nonlocal dependence of D,chi
+isturbcons    integer  /1/  +maybeinput # =1 to make turbulent D,chi const within SOL
                             # =2 to apply radial digital filter to D,chi
-diffusrange   real [m]  /0.01/  # radial range of digital filter
-diffuslimit   integer       # no. of surfaces in half-range of digital filter
-diffuswgts(-9:9)  real [none]  # weights for radial digital filter
-islmodebeta   integer  /1/  # =1 to turn on finite-beta correction
-gradvconst    real [none] /0.005/ # factor involving rad. grad. of v(parallel)
+diffusrange   real [m]  /0.01/  +maybeinput # radial range of digital filter
+diffuslimit   integer       +maybeinput # no. of surfaces in half-range of digital filter
+diffuswgts(-9:9)  real [none]  +maybeinput # weights for radial digital filter
+islmodebeta   integer  /1/  +maybeinput # =1 to turn on finite-beta correction
+gradvconst    real [none] /0.005/ +maybeinput # factor involving rad. grad. of v(parallel)
 
 ***** Turbulence_comm:
 # Communication of variables to minimization routine for turbulent growth rate
@@ -1663,59 +1695,59 @@ spfwallr(0:nx+1,nxpt)   _real [W/m**2]#radiation pwr flux to PF wall
 
 ***** Volsrc:
 #Parameters for volume particle, mom. & power sources for electrons and ions
-pwrsore(0:nx+1,0:ny+1) _real [W]       #power src into electrons in cell ix,iy
-pwrsori(0:nx+1,0:ny+1) _real [W]       #power src into ions in cell ix,iy
-volpsor(0:nx+1,0:ny+1,1:nisp) _real [1/s]#current src into ions in cell ix,iy
-volmsor(0:nx+1,0:ny+1,1:nisp) _real [kg m/s**2] #up mom src in cell ix,iy
-voljcsor(0:nx+1,0:ny+1) _real [A]      #uniform core-region curr sor. in ix,iy
-volpsorg(0:nx+1,0:ny+1,1:ngsp) _real [1/s]#curr source for gas in cell ix,iy
-pondpot(0:nx+1,0:ny+1)  _real [V] /0./ #elec ponderomotive potential
-psgov_use(0:nx+1,0:ny+1,1:ngsp) _real [1/m**3 s]#user-specified gas source
-jcvsor                  real [A]  /0./ #total core-region current for voljcsor
-ix_sjcsor	        integer   /0/  #if nonzero, beginning ix for voljcsor
-ix_ejcsor	        integer   /0/  #if nonzero, ending ix for voljcsor
-iy_sjcsor	        integer   /0/  #if nonzero, beginning iy for voljcsor
-iy_ejcsor	        integer   /0/  #if nonzero, ending iy for voljcsor
-pvole                   real [W]  /0./ #total power into electrons
-pvoli                   real [W]  /0./ #total power into ions
-z0pe                    real [m]  /0./ #axial or x loc. of elec. power profile
-z0pi                    real [m]  /0./ #axial or x loc. of ion power profile
-r0pe                    real [m]  /0./ #radial or y loc. of elec. power profile
-r0pi                    real [m]  /0./ #radial or y loc. of ion power profile
-zwpe                    real [m] /3./  #axial or x Gauss. 1/2 width of e-power
-zwpi                    real [m] /3./  #axial or y Gaussian 1/2 width ion power
-rwpe                    real [m] /.05/ #rad. or x Gaussian 1/2 width e-power
-rwpi                    real [m] /.05/ #rad. or y Gaussian 1/2 width ion power
-ivolcur(1:nisp)        _real [A]  /0./ #total volume current
-mvolcur(1:nisp)        _real [kgA m/s] /0./ #total volume parallel mom. curr.
-z0ni                    real [m]  /0./ #axial or x loc. of ion particle profile
-r0ni                    real [m]  /0./ #rad. or y loc. of ion particle profile
-zwni                    real [m] /3./  #axial or y Gaussian 1/2 width ion prtcl
-rwni                    real [m] /.05/ #rad. or y Gaussian 1/2 width ion prtcl
-z0up                    real [m]  /0./ #axial or x loc. of ion mom. profile
-r0up                    real [m]  /0./ #rad. or y loc. of ion mom. profile
-zwup                    real [m] /3./  #axial or y Gaussian 1/2 width ion mom.
-rwup                    real [m] /.05/ #rad. or y Gaussian 1/2 width ion mom.
-ponderompot             real [V] /0./  #peak elec ponderomotive potential
-z0pondp                 real [m]  /0./ #axial or x loc. of ion mom. profile
-r0pondp                 real [m]  /0./ #rad. or y loc. of ion mom. profile
-zwpondp                 real [m] /3./  #axial or y Gaussian 1/2 width ion mom.
-rwpondp                 real [m] /.05/ #rad. or y Gaussian 1/2 width ion mom.
-thetarot		real [rad]/0./ #rotation angle for R,Z with effec. R,Z
+pwrsore(0:nx+1,0:ny+1) _real [W]       +maybeinput #power src into electrons in cell ix,iy
+pwrsori(0:nx+1,0:ny+1) _real [W]       +maybeinput #power src into ions in cell ix,iy
+volpsor(0:nx+1,0:ny+1,1:nisp) _real [1/s]+maybeinput #current src into ions in cell ix,iy
+volmsor(0:nx+1,0:ny+1,1:nisp) _real [kg m/s**2] +maybeinput #up mom src in cell ix,iy
+voljcsor(0:nx+1,0:ny+1) _real [A]      +maybeinput #uniform core-region curr sor. in ix,iy
+volpsorg(0:nx+1,0:ny+1,1:ngsp) _real [1/s]+maybeinput #curr source for gas in cell ix,iy
+pondpot(0:nx+1,0:ny+1)  _real [V] /0./ +maybeinput #elec ponderomotive potential
+psgov_use(0:nx+1,0:ny+1,1:ngsp) _real [1/m**3 s]+maybeinput #user-specified gas source
+jcvsor                  real [A]  /0./ +maybeinput #total core-region current for voljcsor
+ix_sjcsor	        integer   /0/  +maybeinput #if nonzero, beginning ix for voljcsor
+ix_ejcsor	        integer   /0/  +maybeinput #if nonzero, ending ix for voljcsor
+iy_sjcsor	        integer   /0/  +maybeinput #if nonzero, beginning iy for voljcsor
+iy_ejcsor	        integer   /0/  +maybeinput #if nonzero, ending iy for voljcsor
+pvole                   real [W]  /0./ +maybeinput #total power into electrons
+pvoli                   real [W]  /0./ +maybeinput #total power into ions
+z0pe                    real [m]  /0./ +maybeinput #axial or x loc. of elec. power profile
+z0pi                    real [m]  /0./ +maybeinput #axial or x loc. of ion power profile
+r0pe                    real [m]  /0./ +maybeinput #radial or y loc. of elec. power profile
+r0pi                    real [m]  /0./ +maybeinput #radial or y loc. of ion power profile
+zwpe                    real [m] /3./  +maybeinput #axial or x Gauss. 1/2 width of e-power
+zwpi                    real [m] /3./  +maybeinput #axial or y Gaussian 1/2 width ion power
+rwpe                    real [m] /.05/ +maybeinput #rad. or x Gaussian 1/2 width e-power
+rwpi                    real [m] /.05/ +maybeinput #rad. or y Gaussian 1/2 width ion power
+ivolcur(1:nisp)        _real [A]  /0./ +maybeinput #total volume current
+mvolcur(1:nisp)        _real [kgA m/s] /0./ +maybeinput #total volume parallel mom. curr.
+z0ni                    real [m]  /0./ +maybeinput #axial or x loc. of ion particle profile
+r0ni                    real [m]  /0./ +maybeinput #rad. or y loc. of ion particle profile
+zwni                    real [m] /3./  +maybeinput #axial or y Gaussian 1/2 width ion prtcl
+rwni                    real [m] /.05/ +maybeinput #rad. or y Gaussian 1/2 width ion prtcl
+z0up                    real [m]  /0./ +maybeinput #axial or x loc. of ion mom. profile
+r0up                    real [m]  /0./ +maybeinput #rad. or y loc. of ion mom. profile
+zwup                    real [m] /3./  +maybeinput #axial or y Gaussian 1/2 width ion mom.
+rwup                    real [m] /.05/ +maybeinput #rad. or y Gaussian 1/2 width ion mom.
+ponderompot             real [V] /0./  +maybeinput #peak elec ponderomotive potential
+z0pondp                 real [m]  /0./ +maybeinput #axial or x loc. of ion mom. profile
+r0pondp                 real [m]  /0./ +maybeinput #rad. or y loc. of ion mom. profile
+zwpondp                 real [m] /3./  +maybeinput #axial or y Gaussian 1/2 width ion mom.
+rwpondp                 real [m] /.05/ +maybeinput #rad. or y Gaussian 1/2 width ion mom.
+thetarot		real [rad]/0./ +maybeinput #rotation angle for R,Z with effec. R,Z
 		                       # R_e= R0+(R-R0)cos(th)+(Z-Z0)sin(th),
 		                       # Z_e= Z0-(R-R0)sin(th)+(Z-Z0)cos(th),
-rcutmin			real [m] /0./  #source zero if R<rcutmin
-zcutmin			real [m] /0./  #source zero if Z<zcutmin
+rcutmin			real [m] /0./  +maybeinput #source zero if R<rcutmin
+zcutmin			real [m] /0./ +maybeinput  #source zero if Z<zcutmin
 effvng(1:ngsp)	       _real [m] /0./  # normalizing factor of gas source; calc
-ivolcurg(1:ngsp)       _real [A] /0./  #tot. volumn gas source strength
-z0ng(1:ngsp)	       _real [m] /0./  #axial or x loc. of gas particle profile
-r0ng(1:ngsp)           _real [m] /0./  #rad. or y loc. of gas particle profile
-zwng(1:ngsp)           _real [m] /3./  #axial or y Gaussian 1/2 width gas prtcl
-rwng(1:ngsp)           _real [m] /.05/ #rad. or y Gaussian 1/2 width gas prtcl
+ivolcurg(1:ngsp)       _real [A] /0./  +maybeinput #tot. volumn gas source strength
+z0ng(1:ngsp)	       _real [m] /0./  +maybeinput #axial or x loc. of gas particle profile
+r0ng(1:ngsp)           _real [m] /0./  +maybeinput #rad. or y loc. of gas particle profile
+zwng(1:ngsp)           _real [m] /3./  +maybeinput #axial or y Gaussian 1/2 width gas prtcl
+rwng(1:ngsp)           _real [m] /.05/ +maybeinput #rad. or y Gaussian 1/2 width gas prtcl
 
 ***** Bfield:
 #Variables for the B-field and grad_B drift geo/B-field factors
-b0                     real /1./ +restart
+b0                     real /1./ +input
                                  #scale factor for magnetic field
 b02d(0:nx+1,0:ny+1)   _real      #net B-field scale fac. =b0+b0_use present iter.
 b0old(0:nx+1,0:ny+1)  _real      #net B-field scale factor at last iter.
@@ -1730,7 +1762,7 @@ gradby(0:nx+1,0:ny+1)  _real [1/mT] #grad_B drift (p_perp) drift factor, y-face
 gradb2(0:nx+1,0:ny+1)  _real [1/mT] #grad_B drift (p_perp) drift factor, x-face
 dbm2dx(0:nx+1,0:ny+1) _real [1/T**2m] #pol deriv of 1/B**2 on x-face
 dbm2dy(0:nx+1,0:ny+1) _real [1/T**2m] #rad deriv of 1/B**2 on y-face
-isrozhfac            integer  /0/   #=0 sets bfacx,yrozh=1; =1 computes ave
+isrozhfac            integer  /0/   +maybeinput #=0 sets bfacx,yrozh=1; =1 computes ave
 bfacxrozh(0:nx+1,0:ny+1) _real [ ]  #[1-B**2/B**2_ave], x-face; Rozhansky
 bfacyrozh(0:nx+1,0:ny+1) _real [ ]  #[1-B**2/B**2_ave], y-face; Rozhansky
 
@@ -1748,7 +1780,7 @@ vy0(0:nx+1,0:ny+1,1:nisp)  _real [m/s]   #old radial velocity
 ***** Comflo:
 #Variables in common -- flows
 fqp(0:nx+1,0:ny+1)         _real [Amp]  #pol proj of par cur, east face
-cfparcur                    real /0./   #scale fac fqp=cfparcur*parcurrent if	
+cfparcur                    real /0./   +input #scale fac fqp=cfparcur*parcurrent if	
                                         #isimpon=5 (fmombal from Hirshman)
 fq2(0:nx+1,0:ny+1)         _real [Amp]  #pol proj of 2 cur, east face
 fqx(0:nx+1,0:ny+1)         _real [Amp]  #net poloidal current, east face
@@ -1800,8 +1832,8 @@ feiy(0:nx+1,0:ny+1)        _real [J/s]  #radial ion thermal current, north face
 fegx(0:nx+1,0:ny+1,ngsp)   _real [J/s]  #poloidal neut thermal curr, east face ### IJ 2016/09/2
 fegy(0:nx+1,0:ny+1,ngsp)   _real [J/s]  #radial neut thermal curr, north face  ### IJ 2016/09/22
 fegxy(0:nx+1,0:ny+1,ngsp)  _real [J/s]  #pol. nonog neut thermal curr, north face 
-isfegxyqflave            integer  /0/   #=0fegxy T*vt,ng ave;=1, use harm aves
-cfegxy                      real  /1./  #coeff multiple fegxy
+isfegxyqflave            integer  /0/   +input #=0fegxy T*vt,ng ave;=1, use harm aves
+cfegxy                      real  /1./  +input #coeff multiple fegxy
 qipar(0:nx+1,0:ny+1,nisp)  _real [J/m**2s] #parallel conductive ion heat flux
 qgpar(0:nx+1,0:ny+1,ngsp)  _real [J/m**2s] #parallel conductive gas heat flux
 fniycbo(0:nx+1,1:nisp)     _real [1/s]  #fniy cor. iy=0 bdry for grad_B, grad_P
@@ -1860,48 +1892,48 @@ njen(ngrid)        _integer        #cum. Jacobian evals. for Newton iter.
 
 ***** Poten:
 #Variables required for the calculation of the potential.
-newbcl(nxptmx)     integer /nxptmx*0/ +restart #switch on new sheath model
-newbcr(nxptmx)     integer /nxptmx*0/ +restart #switch on new sheath model
-iskaplex           integer /0/  #=1 if kappal is set externally (from parser)
-iskaprex           integer /0/  #=1 if kappar is set externally (from parser)
-bcee               real  /4./ +restart
+newbcl(nxptmx)     integer /nxptmx*0/ +input #switch on new sheath model
+newbcr(nxptmx)     integer /nxptmx*0/ +input #switch on new sheath model
+iskaplex           integer /0/  +input #=1 if kappal is set externally (from parser)
+iskaprex           integer /0/  +input #=1 if kappar is set externally (from parser)
+bcee               real  /4./ +input
                                 #electron sheath energy trans. factor(newbc=0)
-bcei               real  /2.5/ +restart
+bcei               real  /2.5/ +input
                                 #ion sheath energy trans. factor(newbc=0)
-bceew              real  /4./   #elec wall energy trans factor
-bceiw              real  /2.5/  #ion wall energy trans factor
-bcen               real  /0./   #neut energy trans. factor on plates 
+bceew              real  /4./   +input #elec wall energy trans factor
+bceiw              real  /2.5/  +input #ion wall energy trans factor
+bcen               real  /0./   +input #neut energy trans. factor on plates 
                                 #For combined neutral+ion energy equation
-bcenw              real  /0./   #neut eng trans fac on walls
-isfdiax            real  /0./   #switch to turn on diamagnetic drift for sheath
+bcenw              real  /0./   +input #neut eng trans fac on walls
+isfdiax            real  /0./   +input #switch to turn on diamagnetic drift for sheath
 				#potential calculation
-cthe               real  /0.71/ #electron thermal force coeff.
-cthi               real  /4.05/ #?ion thermal force coeff.?; enters if zeff.ne.1
-sigma1             real [1/(eV**1.5_Ohm_m)] /1490./#parallel conductivity coeff.
+cthe               real  /0.71/ +input #electron thermal force coeff.
+cthi               real  /4.05/ +input #?ion thermal force coeff.?; enters if zeff.ne.1
+sigma1             real [1/(eV**1.5_Ohm_m)] /1490./+input #parallel conductivity coeff.
                         #sigma1=1/(5.19e-5*Z*ln_lambda) & Z=1, ln_lambda=12.9
-cfsigm		   real   /1./  #scale factor for parallel cond. sigma1
-rsigpl             real  /0./   #ad hoc radial electrical conductivity - global
-rsigplcore         real  /0./   #ad hoc radial electrical conduct - core only
+cfsigm		   real   /1./  +input #scale factor for parallel cond. sigma1
+rsigpl             real  /0./   +input #ad hoc radial electrical conductivity - global
+rsigplcore         real  /0./   +input #ad hoc radial electrical conduct - core only
                                 #ratio of perp to parallel conductivity
-bcel(0:ny+1,nxpt)      _real  [ ]   #electron sheath energy transmission factor
+bcel(0:ny+1,nxpt)      _real  [ ]   +maybeinput #electron sheath energy transmission factor
                                     #on the left boundary
-bcer(0:ny+1,nxpt)      _real  [ ]   #electron sheath energy transmission factor
+bcer(0:ny+1,nxpt)      _real  [ ]   +maybeinput #electron sheath energy transmission factor
                                     #on the right boundary
-bcil(0:ny+1,nxpt)      _real  [ ]   #ion sheath energy transmission factor
+bcil(0:ny+1,nxpt)      _real  [ ]   +maybeinput #ion sheath energy transmission factor
                                     #on the left boundary
-bcir(0:ny+1,nxpt)      _real  [ ]   #ion sheath energy transmission factor
+bcir(0:ny+1,nxpt)      _real  [ ]   +maybeinput #ion sheath energy transmission factor
                                     #on the right boundary
-kappal(0:ny+1,nxpt)  _real  [ ]	#sheath pot'l drop on left  boundary, phi/Te
-kappar(0:ny+1,nxpt)  _real  [ ]	#sheath pot'l drop on right boundary, phi/Te
-bctype(0:ny+1)    _integer #/0,ny*0,0/
-phi0r(0:ny+1,nxpt)	_real [V] /0./ #plate pot'l at right poloidal boundary
-phi0l(0:ny+1,nxpt)	_real [V] /0./ #plate pot'l at left  poloidal boundary
-capx(1:ny)        _real    #/ny*0.0/
-dphi_iy1(0:nx+1)  _real [V] #/(nx+2)*0./  #incremental phi at iy=1 to have
+kappal(0:ny+1,nxpt)  _real  [ ]	+maybeinput #sheath pot'l drop on left  boundary, phi/Te
+kappar(0:ny+1,nxpt)  _real  [ ]	+maybeinput #sheath pot'l drop on right boundary, phi/Te
+bctype(0:ny+1)    _integer #/0,ny*0,0/+maybeinput 
+phi0r(0:ny+1,nxpt)	_real [V] /0./ +maybeinput #plate pot'l at right poloidal boundary
+phi0l(0:ny+1,nxpt)	_real [V] /0./ +maybeinput #plate pot'l at left  poloidal boundary
+capx(1:ny)        _real    #/ny*0.0/+maybeinput 
+dphi_iy1(0:nx+1)  _real [V] #/(nx+2)*0./  +maybeinput #incremental phi at iy=1 to have
                                           #Te=constant for second phi BC
-kincorlb(0:ny+1,nxpt)   _real [ ]   # kinetic corr. factor for elec part. loss, left b
-kincorrb(0:ny+1,nxpt)   _real [ ]   # kinetic corr. factor for elec part. loss, right b
-cfkincor            real     [ ] /0.5/ # factor for kincorlb,rb denom. factor
+kincorlb(0:ny+1,nxpt)   _real [ ]   +maybeinput # kinetic corr. factor for elec part. loss, left b
+kincorrb(0:ny+1,nxpt)   _real [ ]   +maybeinput # kinetic corr. factor for elec part. loss, right b
+cfkincor            real     [ ] /0.5/ +input # factor for kincorlb,rb denom. factor
 #Variables for the grid-sequencing.
 #yet to be defined?
 
@@ -1910,7 +1942,7 @@ cfkincor            real     [ ] /0.5/ # factor for kincorlb,rb denom. factor
 ex(0:nx+1,0:ny+1)           _real  [V/m]  #poloidal electric field
 ey(0:nx+1,0:ny+1)           _real  [V/m]  #radial electric field
 eymask1d(0:nx+1,0:ny+1)     _real  [V/m]  #set ey=0 in core+sep if isphicore0=1
-einduc			     real  [V/m]  #inductive tor. E-field - input
+einduc			     real  [V/m]  +input #inductive tor. E-field - input
 gpix(0:nx+1,0:ny+1,1:nisp)  _real  [Pa/m] #X-gradient of ion pressure
 gpiy(0:nx+1,0:ny+1,1:nisp)  _real  [Pa/m] #Y-gradient of ion pressure
 gpex(0:nx+1,0:ny+1)         _real  [Pa/m] #X-gradient of el. pressure
@@ -1925,16 +1957,16 @@ gpondpotx(0:nx+1,0:ny+1)    _real  [V/m]  #X-gradient of elec pondom pot
 
 ***** Cfric:
 #Coulomb friction terms for parallel transport
-frice(0:nx+1,0:ny+1)      _real [J/m**4]  #Electron parallel Coulomb friction
-frici(0:nx+1,0:ny+1,nisp) _real [J/m**4]  #Ion parallel Coulomb friction
-fricnrl(0:nx+1,0:ny+1,nusp) _real [J/m**4] #NRL ion par fric ni*mi*nu*(up1-up2)
-cfgti             /1./     real           #scale factor for ion thermal force
-cfgte             /1./     real           #scale factor for elec. thermal force
-cftaud            /1./     real           #scale factor for ion-ion drag time
-isalfecalc(1:nisp) /1/    _integer        #=1 for internal calc of alfe
-isbetaicalc(1:nisp)/1/    _integer        #=1 for internal calc of betai
-alfe(1:nisp)       /1./   _real         #grad_Te thm force coeff isalfecalc=0
-betai(1:nisp)      /1./   _real         #grad_Ti thm force coeff isbetaicalc=0
+frice(0:nx+1,0:ny+1)      _real [J/m**4]  +maybeinput #Electron parallel Coulomb friction
+frici(0:nx+1,0:ny+1,nisp) _real [J/m**4]  +maybeinput #Ion parallel Coulomb friction
+fricnrl(0:nx+1,0:ny+1,nusp) _real [J/m**4] +maybeinput #NRL ion par fric ni*mi*nu*(up1-up2)
+cfgti             /1./     real           +input #scale factor for ion thermal force
+cfgte             /1./     real           +input #scale factor for elec. thermal force
+cftaud            /1./     real           +input #scale factor for ion-ion drag time
+isalfecalc(1:nisp) /1/    _integer        +input #=1 for internal calc of alfe
+isbetaicalc(1:nisp)/1/    _integer        +input #=1 for internal calc of betai
+alfe(1:nisp)       /1./   _real         +input #grad_Te thm force coeff isalfecalc=0
+betai(1:nisp)      /1./   _real         +input #grad_Ti thm force coeff isbetaicalc=0
 
 ***** Grid:
 ngrid          /1/	 integer +regrid
@@ -1994,38 +2026,38 @@ hcxineo(0:nx+1,0:ny+1)      _real [1/m s] #neocl. pol. ion+neut therm. conduct.
 hcyi(0:nx+1,0:ny+1)         _real [1/m s] #summed rad. ion+neut therm. conduct.
 hcxn(0:nx+1,0:ny+1)         _real [1/m s] #poloidal neutral therm. conduct.
 hcyn(0:nx+1,0:ny+1)         _real [1/m s] #radial neutral therm. conduct.
-kxbohm(0:nx+1,0:ny+1)	    _real [m**2/s]#spatially depend. diff. on x-face
+kxbohm(0:nx+1,0:ny+1)	    _real [m**2/s] +input #spatially depend. diff. on x-face
 					  #set by user; Bohm if isbohmcalc=1
-kybohm(0:nx+1,0:ny+1)	    _real [m**2/s]#spatially depend. diff. on y-face
+kybohm(0:nx+1,0:ny+1)	    _real [m**2/s] +input #spatially depend. diff. on y-face
 					  #set by user; Bohm if isbohmcalc=1
-vybohm(0:nx+1,0:ny+1)       _real [m/s]   #spatially depend. convect. y-vel
+vybohm(0:nx+1,0:ny+1)       _real [m/s]   +input #spatially depend. convect. y-vel
 					  #set user if isbohmcalc=0; else =0
-dif_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]#spatially depend. diff; if
+dif_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s] +input #spatially depend. diff; if
 					  #isbohmcalc=1, user input if all
 					  #facbni+facbup+facbee+facbei =0,
 					  # or kybohm if facbni, etc. > 0;
 					  # if isbohmcalc=2, then
 					  # D = difni*kybohm/(difni+kybohm)
-difp_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]#for gen pr diff; see dif_use comment
-dif2_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]#for dif2; see dif_use comment
-tray_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]#for travis; see dif_use comment
-trax_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]#pol. analog to tra_use
-kye_use(0:nx+1,0:ny+1)        _real [m**2/s]#for kye; see dif_use comment
-kyi_use(0:nx+1,0:ny+1)        _real [m**2/s]#for kyi; see dif_use comment
-kxe_use(0:nx+1,0:ny+1)        _real [m**2/s]#user elec pol. heat cond
-kxi_use(0:nx+1,0:ny+1)        _real [m**2/s]#user ion pol. heat cond.
-kxg_use(0:nx+1,0:ny+1,1:ngsp) _real [m**2/s]#user gas pol. heat cond.
-kyg_use(0:nx+1,0:ny+1,1:ngsp) _real [m**2/s]#user gas rad. heat cond.
-dutm_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]#for difutm; see dif_use comment
-vy_use(0:nx+1,0:ny+1,1:nisp) _real [m/s]  #user-set rad vel;for isbohmcalc=0
-vyup_use(0:nx+1,0:ny+1)     _real  [m/s]  #user-set conv vel of ion || vel, up
-vyte_use(0:nx+1,0:ny+1)     _real  [m/s]  #user-set rad elec eng vel
-vyti_use(0:nx+1,0:ny+1)     _real  [m/s]  #user-set rad ion eng vel
-pondomfpare_use(0:nx+1,0:ny+1) _real [N/m**3] #user-in elec parallel pondero force
-pondomfpari_use(0:nx+1,0:ny+1,1:nisp) _real [N/m**3] #user-in parallel ion ponder. force
-fniyos_use(0:nx+1,0:ny+1,1:nisp) _real [1/s m**2] #user-set particle flux
-feeyosn_use(0:nx+1,0:ny+1)  _real  [J/s m**2]    #user-set Te energy flux
-feiyosn_use(0:nx+1,0:ny+1)  _real  [J/s m**2]    #user-set Ti energy flux
+difp_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]   +input #for gen pr diff; see dif_use comment
+dif2_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]   +input #for dif2; see dif_use comment
+tray_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]   +input #for travis; see dif_use comment
+trax_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]   +input #pol. analog to tra_use
+kye_use(0:nx+1,0:ny+1)        _real [m**2/s]    +input #for kye; see dif_use comment
+kyi_use(0:nx+1,0:ny+1)        _real [m**2/s]    +input #for kyi; see dif_use comment
+kxe_use(0:nx+1,0:ny+1)        _real [m**2/s]    +input #user elec pol. heat cond
+kxi_use(0:nx+1,0:ny+1)        _real [m**2/s]    +input #user ion pol. heat cond.
+kxg_use(0:nx+1,0:ny+1,1:ngsp) _real [m**2/s]    +input #user gas pol. heat cond.
+kyg_use(0:nx+1,0:ny+1,1:ngsp) _real [m**2/s]    +input #user gas rad. heat cond.
+dutm_use(0:nx+1,0:ny+1,1:nisp) _real [m**2/s]   +input #for difutm; see dif_use comment
+vy_use(0:nx+1,0:ny+1,1:nisp) _real [m/s]  +input #user-set rad vel;for isbohmcalc=0
+vyup_use(0:nx+1,0:ny+1)     _real  [m/s]  +input #user-set conv vel of ion || vel, up
+vyte_use(0:nx+1,0:ny+1)     _real  [m/s]  +input #user-set rad elec eng vel
+vyti_use(0:nx+1,0:ny+1)     _real  [m/s]  +input #user-set rad ion eng vel
+pondomfpare_use(0:nx+1,0:ny+1) _real [N/m**3] +input #user-in elec parallel pondero force
+pondomfpari_use(0:nx+1,0:ny+1,1:nisp) _real [N/m**3] +input #user-in parallel ion ponder. force
+fniyos_use(0:nx+1,0:ny+1,1:nisp) _real [1/s m**2] +input #user-set particle flux
+feeyosn_use(0:nx+1,0:ny+1)  _real  [J/s m**2]    +input #user-set Te energy flux
+feiyosn_use(0:nx+1,0:ny+1)  _real  [J/s m**2]    +input #user-set Ti energy flux
 vy_cft(0:nx+1,0:ny+1,1:nisp) _real [m/s]  #calc vy from fniyos_use (fix flux)
 vyte_cft(0:nx+1,0:ny+1)     _real  [m/s]  #calc vyte from feeyos_use (fix flux)
 vyti_cft(0:nx+1,0:ny+1)     _real  [m/s]  #calc vyte from feiyos_use (fix flux)
@@ -2035,31 +2067,31 @@ nucxi(0:nx+1,0:ny+1,nisp)   _real  [1/s]  #charge-exchg rate for ion (sigv*ng)
 nueli(0:nx+1,0:ny+1,nisp)   _real  [1/s]  #elast scatt rate for ion (sigv*ng)
 nuelg(0:nx+1,0:ny+1,ngsp)   _real  [1/s]  #elast scatt rate for gas (sigv*nimp)
 nuix(0:nx+1,0:ny+1,ngsp)    _real  [1/s]  #fnuizx*nuiz+fnucxx*nucx
-fnuizx                       real    /0./ #fraction of nuiz in nuix (see nuix)
-fnucxx                       real    /1./ #fraction of nucx in nuix (see nuix)
+fnuizx                       real    /0./ +input #fraction of nuiz in nuix (see nuix)
+fnucxx                       real    /1./ +input #fraction of nucx in nuix (see nuix)
 nurc(0:nx+1,0:ny+1,ngsp)    _real  [1/s]  #recombination rate
 nuvl(0:nx+1,0:ny+1,nisp)    _real  [1/s]  #vol loss rate, ~cs/l_parloss for 1-D
-cfvlh			     real         #scal fac for hyd rate in nuvl
-cfvli(nisp)		    _real #/nisp*0./#scal fac for individ ion rate nuvl
-l_parloss		     real [m] /1.e20/ #parall length for nuvl loss rate
+cfvlh			     real         +input #scal fac for hyd rate in nuvl
+cfvli(nisp)		    _real #/nisp*0./+input #scal fac for individ ion rate nuvl
+l_parloss		     real [m] /1.e20/ +input #parall length for nuvl loss rate
 eqp(0:nx+1,0:ny+1)          _real [1/m**3]#Te,i equipart. fact; needs *(Te-Ti)*vol
 eqpg(0:nx+1,0:ny+1,ngsp)    _real [1/m**3]#Tg,i equipart. fact; needs *(Tg-Ti)*vol
 engcoolm(0:nx+1,0:ny+1)     _real [J/s]   #cool rate ion/atoms by mols if ishymol=1
 eeli(0:nx+1,0:ny+1)         _real  [J]    #electron energy loss per ionization
 pradhyd(0:nx+1,0:ny+1)      _real [W/m**3] /0./#power radiated by hydrogen
-tdiflim                      real [s] /0./ #lim on hcxe/ne; reduces hcxe if >0
-lmfplim			     real [m] /1.e20/#hcxe,i -> hcxe,i/(1+lmfp/lmfelim)
-eta1(0:nx+1,0:ny+1)	    _real [J-s/m**3] #Braginskii ion visc coeff eta_1
-cfeta1                       real   /0./  # scale factor for eta1
-rtaue(0:nx+1,0:ny+1)        _real [s/kg]  #Brag. R coeff (t_e/me)/(w_ce*t_e)**2
-cfrtaue			     real   /0./  # scale factor for cfrtaue
+tdiflim                      real [s] /0./ +input #lim on hcxe/ne; reduces hcxe if >0
+lmfplim			     real [m] /1.e20/+input #hcxe,i -> hcxe,i/(1+lmfp/lmfelim)
+eta1(0:nx+1,0:ny+1)	    _real [J-s/m**3] +maybeinput #Braginskii ion visc coeff eta_1
+cfeta1                       real   /0./  +input # scale factor for eta1
+rtaue(0:nx+1,0:ny+1)        _real [s/kg]  +maybeinput #Brag. R coeff (t_e/me)/(w_ce*t_e)**2
+cfrtaue			     real   /0./  +input # scale factor for cfrtaue
 dclass_e(0:nx+1,0:ny+1)     _real [m**2/s]#classical elec perp heat conduc.
 dclass_i(0:nx+1,0:ny+1)     _real [m**2/s]#classical ion perp heat conduc.
-cfcl_e	                     real  /0./   #scale fac for dclass_e
-cfcl_i	                     real  /0./   #scale fac for dclass_i
-omgci_taui		     real  /10./  #ion gy_freq*coll_rate for cl_model
-omgce_taue		     real  /10./  #elec gy_freq*coll_rate for cl_model
-nuneo			     real  /0./   #neoclass pol. damping rate; for fqyn
+cfcl_e	                     real  /0./   +input #scale fac for dclass_e
+cfcl_i	                     real  /0./   +input #scale fac for dclass_i
+omgci_taui		     real  /10./  +input #ion gy_freq*coll_rate for cl_model
+omgce_taue		     real  /10./  +input #elec gy_freq*coll_rate for cl_model
+nuneo			     real  /0./   +input #neoclass pol. damping rate; for fqyn
 visxneo(0:nx+1,0:ny+1,1:nisp) _real [kg/m s] #Braginskii eta_0 neo-modified
 visvol_v(0:nx+1,0:ny+1,1:nisp) _real #vel-based viscosity in (n*m*up)^dot eqn
 visvol_q(0:nx+1,0:ny+1,1:nisp) _real #heat-flux-based viscosity (n*m*up)^dot eqn
@@ -2150,45 +2182,45 @@ ismcnvar	integer		/0/
 # ismcnvar=1  --> MCN plasma source terms scale with plate currents
 
 #Special case of neutral atoms emitted with finite energy from walls
-eedisspl 	real /0/ [eV] #energy loss for prompt dissociation at left plate
-eedisspr 	real /0/ [eV] #energy loss for prompt dissociation at right plate
-eidisspl 	real /0/ [eV] #energy gain for prompt dissociation at left plate
-eidisspr 	real /0/ [eV] #energy gain for prompt dissociation at right plate
-cmntgpl 	real /0/ #coeff. for neutral energy at left plate:  cmntipl*ti
-cmntgpr 	real /0/ #coeff. for neutral energy at right plate: cmntipr*ti
-edisswo		real /0/ [eV] #energy for prompt dissociation loss at outer wall
-edisswi		real /0/ [eV] #energy for prompt dissociation loss at private flux wall
-cmntgwo 	real /0/ #coeff. for neutral energy at outer plate:  cmntiwo*ti
-cmntgwi 	real /0/ #coeff. for neutral energy at private flux plate: cmntiwi*ti
-
-#cfneut    		real /1./    #Coef to turn on all fluid neutrals contrib's to resid's
-cfneutsor_ni	real /1/	#coeff. for fluid neutral particle source in resco
-cfneutsor_mi	real /1/	#coeff. for fluid neutral momentum source in resmo
-cfneutsor_ei	real /1/	#coeff. for fluid neutral energy source in resei
-cfneutsor_ee	real /1/	#coeff. for fluid neutral energy source in resee
-
-#cmneut    		real /0./    #Coef to turn on all Monte Carlo neutral sources
-cmneutsor_ni	real /1/	#coeff. for MC neutral particle source in resco
-cmneutsor_mi	real /1/	#coeff. for MC neutral momentum source in resmo
-cmneutsor_ei	real /1/	#coeff. for MC neutral energy source in resei
-cmneutsor_ee	real /1/	#coeff. for MC neutral energy source in resee
-
-cfneutdiv		real /1/	#coeff. to turn on divergence of all fluid neutral fluxes
-cfneutdiv_fng	real /1/	#coeff. for div. fluid neutral particle flux in resng
-cfneutdiv_fmg	real /1/	#coeff. for div. fluid neutral momentum flux in resmo
-cfneutdiv_feg	real /1/	#coeff. for div. fluid neutral energy flux in resei
-
-cmneutdiv		real /0/	#coeff. to turn on divergence of all MC neutral fluxes
-cmneutdiv_fng	real /1/	#coeff. for div. fluid neutral particle flux in resng
-cmneutdiv_fmg	real /1/	#coeff. for div. fluid neutral momentum flux in resmo
-cmneutdiv_feg	real /1/	#coeff. for div. fluid neutral energy flux in resei
-
-
-mcalpha_ng  real /2/  #coeff. for blending kinetic and fluid ng
-mcalpha_pg  real /2/  #coeff. for blending kinetic and fluid pg
-mcalpha_fng real /2/  #coeff. for blending kinetic and fluid fng
-mcalpha_fmg real /2/  #coeff. for blending kinetic and fluid fmg
-mcalpha_feg real /2/  #coeff. for blending kinetic and fluid feg
+eedisspl 	real /0/ [eV] +mcinput #energy loss for prompt dissociation at left plate
+eedisspr 	real /0/ [eV] +mcinput #energy loss for prompt dissociation at right plate
+eidisspl 	real /0/ [eV] +mcinput #energy gain for prompt dissociation at left plate
+eidisspr 	real /0/ [eV] +mcinput #energy gain for prompt dissociation at right plate
+cmntgpl 	real /0/ +mcinput #coeff. for neutral energy at left plate:  cmntipl*ti
+cmntgpr 	real /0/ +mcinput #coeff. for neutral energy at right plate: cmntipr*ti
+edisswo		real /0/ [eV] +mcinput #energy for prompt dissociation loss at outer wall
+edisswi		real /0/ [eV] +mcinput #energy for prompt dissociation loss at private flux wall
+cmntgwo 	real /0/ +mcinput #coeff. for neutral energy at outer plate:  cmntiwo*ti
+cmntgwi 	real /0/ +mcinput #coeff. for neutral energy at private flux plate: cmntiwi*ti
+
+#cfneut    		real /1./   +mcinput  #Coef to turn on all fluid neutrals contrib's to resid's
+cfneutsor_ni	real /1/	+mcinput #coeff. for fluid neutral particle source in resco
+cfneutsor_mi	real /1/	+mcinput #coeff. for fluid neutral momentum source in resmo
+cfneutsor_ei	real /1/	+mcinput #coeff. for fluid neutral energy source in resei
+cfneutsor_ee	real /1/	+mcinput #coeff. for fluid neutral energy source in resee
+
+#cmneut    		real /0./    +mcinput #Coef to turn on all Monte Carlo neutral sources
+cmneutsor_ni	real /1/	+mcinput #coeff. for MC neutral particle source in resco
+cmneutsor_mi	real /1/	+mcinput #coeff. for MC neutral momentum source in resmo
+cmneutsor_ei	real /1/	+mcinput #coeff. for MC neutral energy source in resei
+cmneutsor_ee	real /1/	+mcinput #coeff. for MC neutral energy source in resee
+
+cfneutdiv		real /1/	+mcinput #coeff. to turn on divergence of all fluid neutral fluxes
+cfneutdiv_fng	real /1/	+mcinput #coeff. for div. fluid neutral particle flux in resng
+cfneutdiv_fmg	real /1/	+mcinput #coeff. for div. fluid neutral momentum flux in resmo
+cfneutdiv_feg	real /1/	+mcinput #coeff. for div. fluid neutral energy flux in resei
+
+cmneutdiv		real /0/	+mcinput #coeff. to turn on divergence of all MC neutral fluxes
+cmneutdiv_fng	real /1/	+mcinput #coeff. for div. fluid neutral particle flux in resng
+cmneutdiv_fmg	real /1/	+mcinput #coeff. for div. fluid neutral momentum flux in resmo
+cmneutdiv_feg	real /1/	+mcinput #coeff. for div. fluid neutral energy flux in resei
+
+
+mcalpha_ng  real /2/  +mcinput #coeff. for blending kinetic and fluid ng
+mcalpha_pg  real /2/  +mcinput #coeff. for blending kinetic and fluid pg
+mcalpha_fng real /2/  +mcinput #coeff. for blending kinetic and fluid fng
+mcalpha_fmg real /2/  +mcinput #coeff. for blending kinetic and fluid fmg
+mcalpha_feg real /2/  +mcinput #coeff. for blending kinetic and fluid feg
 
 ### Scalars ###
 ng_mc(0:nx+1,0:ny+1,nfl)		_real	[part/m**3]
@@ -2559,7 +2591,7 @@ mpicmd     	character*64 	/"mpirun"/ 				# MPI command
 npopt       character*8     /"-np"/                 # option to specify # procs
 npext      	integer 		/2/						# number of procs for external system call
 
-runid       character*80    /" "/					# description of run
+runid_ext   character*80    /" "/					# description of run
 
 get_neutral_sources		logical		/.true./			#whether to use neutral source data
 get_neutral_moments		logical		/.false./			#whether to use neutral moment data
@@ -2839,18 +2871,19 @@ iwkd2(ndiagmx) _integer       # work array used by cdiagsrt
 
 ***** UEint:
 #Auxiliary variables for Ueinit.
-GridFileName   character*200 /"gridue"/ # name of Grid file to be read
-newgeo         integer   /1/  #flag to calculate new grid (1=yes)
-mhdgeo         integer  /-1/  #flag for grid geometry
+GridFileName   character*200 /"gridue"/ +input
+                              # name of Grid file to be read
+newgeo         integer   /1/  +input #flag to calculate new grid (1=yes)
+mhdgeo         integer  /-1/  +input #flag for grid geometry
                               #mhdgeo =  2 ==> toroidal circular limiter
                               #mhdgeo =  1 ==> toroidal MHD equilibrium
                               #mhdgeo =  0 ==> cylindrical geometry
                               #mhdgeo = -1 ==> cartesian geometry
                               #mhdgeo = -2 ==> mag mirror (FRC-annulus)
-gengrid        integer   /1/  #flag to generate grid, else read from file GridFileName
+gengrid        integer   /1/  +input #flag to generate grid, else read from file GridFileName
 isgindx        integer   /1/  #=1 for interpolating grid based on indices
 nfmax          integer   /10/
-restart        integer   /0/  #flag for restart from previous case(yes=1)
+restart        integer   /0/  +input #flag for restart from previous case(yes=1)
 initsol        integer   /0/  #flag to initially solve algebraic eqns for
                               #DASPK (yes=1)
 ttbeg          real                  #initial Te in Joules = tinit/ev (calc)
@@ -2859,28 +2892,30 @@ tscal          real      /.5/        #ratio of initial Ti & Tg to Te
 ngscal(ngspmx) real   /ngspmx*.1/    #ratio of initial gas density to ion dens
 xgscal         real      /1./        #exponential scale of initial gas (m)
 nibeg(1:nispmx) real  /nispmx*2.e19/ #initial ion density
-minu(1:nispmx)  real  /nispmx*2./    #ion mass in units of proton mass (AMU)
-ziin(1:nispmx)  real  /nispmx*1./    #ion charge read in, used to reset zi in
+minu(1:nispmx)  real  /nispmx*2./ +input
+                                     #ion mass in units of proton mass (AMU)
+ziin(1:nispmx)  real  /nispmx*1./ +input
+                                     #ion charge read in, used to reset zi in
                                      #group Compla which gets erased on gallot
-znuclin(1:nispmx) integer /nispmx*1./ #total nuclear charge of ion (i.d. isotope)
+znuclin(1:nispmx) integer /nispmx*1./ +input #total nuclear charge of ion (i.d. isotope)
 isallloc		integer   /0/        #=1 for local process. allocation with mpi
-newaph			integer  /1/ #=1 calls aphread for hyd. atomic data;=0 not
-newapi		integer /1/	     #=1, call readmc for new imp. data;=0, no						
+newaph			integer  /1/ +input #=1 calls aphread for hyd. atomic data;=0 not
+newapi		integer /1/	     +input #=1, call readmc for new imp. data;=0, no						
 pyrestart_file    character*80 /""/ #Python file that can also be used to restart
-read_diffs		integer /0/	     #=0,a flag to signal whether to read diffusivities
-dif_io		integer /0/	     #=0,a flag to signal whether to read/write dif_use
-tra_io		integer /0/	     #=0,a flag to signal whether to read/write tra_use
-dutm_io		integer /0/	     #=0,a flag to signal whether to read/write dutm_use
-kye_io		integer /0/	     #=0,a flag to signal whether to read/write kye_use
-kyi_io		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-vy_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-vyup_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-vyte_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-vyti_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-fniyos_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-feeyosn_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-feiyosn_io 		integer /0/	     #=0,a flag to signal whether to read/write kyi_use
-isvolsorext             integer /0/   #volsor sources if =0; or user sors if =1
+read_diffs		integer /0/	     +maybeinput #=0,a flag to signal whether to read diffusivities
+dif_io		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write dif_use
+tra_io		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write tra_use
+dutm_io		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write dutm_use
+kye_io		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kye_use
+kyi_io		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+vy_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+vyup_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+vyte_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+vyti_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+fniyos_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+feeyosn_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+feiyosn_io 		integer /0/	     +maybeinput #=0,a flag to signal whether to read/write kyi_use
+isvolsorext             integer /0/   +maybeinput #volsor sources if =0; or user sors if =1
 
 ***** Interp:
 #Variables for the interpolation
@@ -2927,7 +2962,7 @@ ix2g(0:nx+1,0:ny+1)          _integer  #ix index for sec. interm. (ix,iy) pt.
 iy2g(0:nx+1,0:ny+1)          _integer  #iy index for sec. interm. (ixo,iy) pt.
 ixv2g(0:nx+1,0:ny+1)         _integer  #ixv index for sec. interm.(ixvo,iy) pt.
 iyv2g(0:nx+1,0:ny+1)         _integer  #iyv index for sec.interm.(ixvo,iy) pt.
-nis(0:nxold+1,0:nyold+1,1:nisp) _real [m^-3] +restart
+nis(0:nxold+1,0:nyold+1,1:nisp) _real [m^-3] +state
                                              #ion dens at last success. calc
 tes(0:nxold+1,0:nyold+1)        _real [J]    #elec. temp at last success. calc
 tis(0:nxold+1,0:nyold+1)        _real [J]    #ion temp at last success. calc
@@ -2935,7 +2970,7 @@ tgs(0:nxold+1,0:nyold+1,1:ngsp) _real [J]    #gas temp at last success. calc
 phis(0:nxold+1,0:nyold+1)       _real [V]    #potential at last success. calc
 ups(0:nxold+1,0:nyold+1,1:nisp) _real [m/s]  #parall. vel at last success. calc
 ngs(0:nxold+1,0:nyold+1,1:ngsp) _real [m^-3] #gas dens at last success. calc.
-afracs(0:nxold+1,0:nyold+1)     _real [ ]    #rel. imp. frac at last succ. calc
+afracs(0:nxold+1,0:nyold+1)     _real [ ]    +input #rel. imp. frac at last succ. calc
 
 ***** Global_vars:
 # Arrays for primary variables over full mesh for domain decomposition
@@ -3630,7 +3665,7 @@ plateflux					subroutine
 
 ***** Imprad:
 # variables associated with impurity radiation
-isimpon                 integer   /0/ +restart
+isimpon                 integer   /0/ +input
                                # switch for impurity model:
                                # 0 for no impurities
                                # 2 for fixed-fraction model
@@ -3643,7 +3678,7 @@ isimpon                 integer   /0/ +restart
                                #       multi-charge-state (isimpon=6) models
 nusp_imp        integer  /0/   # fixes nusp for total num. of par. mom. eqns.
 isupimpap       integer  /1/   # =1 includes imp atm phys in up eqn; =0, omits
-ismctab		integer		/1/	+restart
+ismctab		integer		/1/	+input
 # Determines which data is used for multi-charge-state rates.
 #	=1  tables originally generated by R. Campbell for D. Knoll,
 #	    data file name is specified by inelmc=....
@@ -3675,9 +3710,9 @@ ntau(0:nx+1,0:ny+1)	_real	[sec/m**3]
                                # confinement parameter for impurity (=atau*ne)
 nratio(0:nx+1,0:ny+1)	_real
                                # ratio of neutrals to electrons
-afrac(0:nx+1,0:ny+1)	_real	/.00/ +restart
+afrac(0:nx+1,0:ny+1)	_real	/.00/ +maybeinput
                                # atomic impur conc; set internally to afracs
-atau(0:nx+1,0:ny+1)	_real	/1./	[sec] +restart
+atau(0:nx+1,0:ny+1)	_real	/1./	[sec] +input
                                # lifetime of impurity
 tau1(0:nx+1,0:ny+1)	_real	# time to escape to inboard divertor plate
 tau2(0:nx+1,0:ny+1)	_real	# time to escape to outboard divertor plate
@@ -3862,7 +3897,7 @@ alfz             real     /10./
 vrfac            real     /1./      # scales convective velocity
 sp               real     /20./
 courant          real     /0.9/
-tend             real     /0.1/     # final time
+tendoned         real     /0.1/     # final time
 ndtmax           integer  /10000/   # max number of timesteps allowed
 ntim             integer  /50/      # number of output times
 ito              integer   /1/
diff --git a/bbb/ext_neutrals.m b/bbb/ext_neutrals.m
index cb92f1a8..9d477114 100755
--- a/bbb/ext_neutrals.m
+++ b/bbb/ext_neutrals.m
@@ -173,10 +173,10 @@ c     call gchange("MCN_sources",0) #wsor, sni, ... see
 
 c ... Write uedge plasma data
       if(isechocmdon) then
-        cmd="call writemcnfile("""//trim(bkufile)//""","""//trim(runid)//""")"
+        cmd="call writemcnfile("""//trim(bkufile)//""","""//trim(runid_ext)//""")"
         print *,trim(cmd)
       else
-	    call writemcnfile(bkufile,runid)	  	  	 
+	    call writemcnfile(bkufile,runid_ext)	  	  	 
       end if
 
 c ... Process plasma data into degas2 background file format 
diff --git a/bbb/odesetup.m b/bbb/odesetup.m
index 5e894b1b..71dcb65c 100755
--- a/bbb/odesetup.m
+++ b/bbb/odesetup.m
@@ -58,8 +58,6 @@ cc      Use(Rccoef)
 * --  local variables
       integer lda, lenk, ngspon, nispon, nuspon, ntgspon, ifld, isor, id
       character*60 runid
-      integer iprt_tfcx_warn
-      data iprt_tfcx_warn/1/
       #Former Aux module variables
       integer igsp
 
@@ -204,13 +202,6 @@ call xerrab("")
          endif
       enddo
 
-c ... Check attempt to use deprecated variables fchemywi and fchemywo 
-      if (fchemywi .ne. 1. .or. fchemywo .ne. 1.) then
-	call remark('**Input error: change fchemywi --> fchemygwi(igsp)
-     .               and fchemywo --> fchemygwo(igsp)')
-        call xerrab("")
-      endif
-
 c ... Check consistency of cngmom; should be zero if inertial neutrals
       if (isupgon(1).eq. 1 .and. cngmom(1).ne.0) then
          call remark('*** WARNING, likely Error: cngmom=1, isupgon=1')
@@ -264,11 +255,6 @@ call remark('*** ERROR: use cgengpl, not cgpl for neut eng loss')
 	 call remark('*** Warning: yinc=2 recommended when isphion=1')
       endif
 
-c ... Check if tfcx or tfcy set in input file
-      if ((tfcx>1.e-10 .or. tfcy>1.e-10) .and. iprt_tfcx_warn==1) then
-        call remark('*** WARNING: tfcx,y not active; see tgas instead')
-        iprt_tfcx_warn = 0
-        endif
 c ... Check if isnfmiy=1 when geometry is snowflake > SF15
       if (geometry=="snowflake45" .or. geometry=="snowflake75" .or.
      .    geometry=="snowflake105" .or. geometry=="snowflake135" .or.
@@ -7425,7 +7411,7 @@ call gchange("Convdiffeqn",0)
       delt = courant*min(delx/vrzmax, 0.5*delx**2/drzmax)
       write(*,*) 'delt = ',delt
       dtdx = delt/delx
-      delto = tend/float(ntim)
+      delto = tendoned/float(ntim)
       ito = 1
       timo(1) = 0.
 
@@ -7461,7 +7447,7 @@ cc          dens(1) = (4.*dens(2) - dens(3))/3.     # Update boundary vals
             gampzt(ix,ito) = gampz(ix)
           enddo
         endif
-        if (tim > tend) exit
+        if (tim > tendoned) exit
       enddo
       return
       end
diff --git a/com/com.v b/com/com.v
index a74a4cb1..af44091d 100755
--- a/com/com.v
+++ b/com/com.v
@@ -14,20 +14,20 @@ glbwrlog(ioun)          function
 
 ***** Dim:
 # Variables that contain widely-used dimensions
-nx	integer	/8/	# number of cells in x (poloidal) direc. (see also nxm)
-ny	integer	/4/	# number of cells in y (radial) direction
+nx	integer	/8/ +griddata	# number of cells in x (poloidal) direc. (see also nxm)
+ny	integer	/4/ +griddata	# number of cells in y (radial) direction
 nxm	integer	/8/	# total number of cells in x direc.; nxm = nx+|nxomit|
 nym     integer /4/     # total number of cells in y direc.; nym = ny+nyomitmx
 nxpt	integer /1/	# number of x-points in (R,Z) simulation domain
-nhsp	integer	/1/	# number of hydrogenic species
-nzsp(1:ngspmx-1) integer /5*0/ # number of impurity species per gas species
+nhsp	integer	/1/	+input # number of hydrogenic species
+nzsp(1:ngspmx-1) integer /5*0/ +input # number of impurity species per gas species
 nzspt   integer /1/     # total number of impurity species
 nzspmx  integer	   /10/	# maximum of nzsp(igsp) used for storage allocation
-nisp	integer	/1/	# number of ion species
-nusp	integer		# number of parallel momentum equations
-nfsp	integer		# number of cont. eqns or flux species (calc internal)
-ngsp	integer	/1/ +restart +regrid	# number of gas species
-nhgsp   integer /1/     # number of hydrogen gas species (prepare for tritium)
+nisp	integer	/1/	+input # number of ion species
+nusp	integer		+input # number of parallel momentum equations
+nfsp	integer		+input # number of cont. eqns or flux species (calc internal)
+ngsp	integer	/1/ +input +regrid	# number of gas species
+nhgsp   integer /1/     +input # number of hydrogen gas species (prepare for tritium)
 imx     integer /50/    # size in x of Zagorski arrays
 imy     integer /40/    # size in y of Zagorski arrays
 lnst	integer /43/    # size of impurity species(?) for Zagorski
@@ -60,25 +60,25 @@ bcentr  real    [Tesla]
      # reference toroidal field
 rcentr  real    [m]
      # major radius where vacuum toroidal field is bcentr
-rmagx   real    [m]
+rmagx   real    [m] +griddata
      # major radius of magnetic axis
-zmagx   real    [m]
+zmagx   real    [m] +griddata
      # vertical position of magnetic axis
-simagx  real    [volt-sec/radian]
+simagx  real    [volt-sec/radian] +griddata
      # poloidal magnetic flux at the magnetic axis
-sibdry  real    [volt-sec/radian]
+sibdry  real    [volt-sec/radian] +griddata
      # poloidal magnetic flux at primary x-point
-sibdry1  real    [volt-sec/radian]
+sibdry1  real    [volt-sec/radian] +griddata
      # poloidal magnetic flux at the lower x-point
-sibdry2  real    [volt-sec/radian]
+sibdry2  real    [volt-sec/radian] +griddata
      # poloidal magnetic flux at the upper x-point
 xdim    real    [m]
      # horizontal (radial) extent of EFIT computational grid
 zdim    real    [m]
      # vertical extent of EFIT computational grid
-zmid	real	[m]
+zmid	real	[m] +griddata
      # vertical height of midplane above bottom of EFIT mesh
-zshift	real	[m]
+zshift	real	[m] +griddata
      # vertical shift of EFIT data to put z=0 at the bottom
 workk(nxefit)   _real
      # dummy array for neqdsk output
@@ -96,9 +96,9 @@ rbdry(nbdry)    _real   [m]
      # radial coordinates of last closed flux surface from EFIT
 zbdry(nbdry)    _real   [m]
      # vertical coordinates of last closed flux surface from EFIT
-xlim(nlim)      _real   [m]
+xlim(nlim)      _real   [m] +griddata
      # radial coordinates of limiter/vessel boundary from EFIT
-ylim(nlim)      _real   [m]
+ylim(nlim)      _real   [m] +griddata
      # vertical coordinates of limiter/vessel boundary from EFIT
 bscoef(nxefit,nyefit)    _real
      # 2-d spline coefficients 
@@ -150,25 +150,25 @@ eshot   integer
      # shot number from EFIT
 etime   real    [msec]
      # time slice from EFIT
-rseps   real    [m]
+rseps   real    [m] +griddata
      # major radius of lower x-point
-zseps   real    [m]
+zseps   real    [m] +griddata
      # vertical position of lower x-point
-rseps1   real    [m]
+rseps1   real    [m] +griddata
      # major radius of lower x-point
-zseps1  real    [m]
+zseps1  real    [m] +griddata
      # vertical position of lower x-point
-rseps2   real    [m]
+rseps2   real    [m] +griddata
      # major radius of upper x-point
-zseps2  real    [m]
+zseps2  real    [m] +griddata
      # vertical position of upper x-point
-rvsin   real    [m]
+rvsin   real    [m] +griddata
      # major radius of inboard strike point
-zvsin   real    [m]
+zvsin   real    [m] +griddata
      # vertical position of inboard strike point
-rvsout  real    [m]
+rvsout  real    [m] +griddata
      # major radius of outboard strike point
-zvsout  real    [m]
+zvsout  real    [m] +griddata
      # vertical position of outboard strike point
 mco2v	integer	/3/
      # number of vertical co2 chords
@@ -203,18 +203,18 @@ aeqdskfname  character*128 /'aeqdsk'/
 
 ***** RZ_grid_info:
 # RZ grid location data and magnetic-field info at those locations
-rm(0:nxm+1,0:nym+1,0:4)     _real [m]    # radial cell position, 0 is center
-zm(0:nxm+1,0:nym+1,0:4)     _real [m]    # vertical cell position, 0 is center
-rmt(0:nxm+1,0:nym+1,0:4)    _real [m]    # temp rad cell position, 0 is center
-zmt(0:nxm+1,0:nym+1,0:4)    _real [m]    # temp vert cell position, 0 is center
+rm(0:nxm+1,0:nym+1,0:4)     _real [m]    +griddata # radial cell position, 0 is center
+zm(0:nxm+1,0:nym+1,0:4)     _real [m]    +griddata # vertical cell position, 0 is center
+rmt(0:nxm+1,0:nym+1,0:4)    _real [m]    +griddata # temp rad cell position, 0 is center
+zmt(0:nxm+1,0:nym+1,0:4)    _real [m]    +griddata # temp vert cell position, 0 is center
 rv(0:nxm+2,-1:nym+1)        _real [m]    # rad position velocity cell corner
 zv(0:nxm+2,-1:nym+1)        _real [m]    # vert position velocity cell corner
-psi(0:nxm+1,0:nym+1,0:4)    _real [Tm^2] # polodial magnetic flux
-br(0:nxm+1,0:nym+1,0:4)     _real [T]    # radial magnetic field, 0 is center
-bz(0:nxm+1,0:nym+1,0:4)     _real [T]    # vert magnetic field, 0 is center
-bpol(0:nxm+1,0:nym+1,0:4)   _real [T]    # pol. magnetic field, 0 is center
-bphi(0:nxm+1,0:nym+1,0:4)   _real [T]    # tor.l magnetic field, 0 is center
-b(0:nxm+1,0:nym+1,0:4)      _real [T]    # total magnetic field, 0 is center
+psi(0:nxm+1,0:nym+1,0:4)    _real [Tm^2] +griddata # polodial magnetic flux
+br(0:nxm+1,0:nym+1,0:4)     _real [T]    +griddata # radial magnetic field, 0 is center
+bz(0:nxm+1,0:nym+1,0:4)     _real [T]    +griddata # vert magnetic field, 0 is center
+bpol(0:nxm+1,0:nym+1,0:4)   _real [T]    +griddata # pol. magnetic field, 0 is center
+bphi(0:nxm+1,0:nym+1,0:4)   _real [T]    +griddata # tor.l magnetic field, 0 is center
+b(0:nxm+1,0:nym+1,0:4)      _real [T]    +griddata # total magnetic field, 0 is center
 bsqr(0:nxm+1,0:nym+1)       _real [T]    # B**2 at density-cell center
 b12(0:nxm+1,0:nym+1)        _real [T]    # B**0.5 at vel-cell center/dens face
 b12ctr(0:nxm+1,0:nym+1)     _real [T]    # B**0.5 at density-cell center
@@ -233,25 +233,26 @@ bg(0:nxm+1,0:nym+1,0:4)     _real [T]    # global total B field, 0 is center
 
 ***** Share:
 # Variables used by more than one package
-nycore(30)	integer	/30*0/	+regrid
+nycore(30)	integer	/30*0/	+regrid +gridgen
    # number of radial zones in the core region of the edge plasma
-nysol(30)	integer	/30*2/	+regrid
+nysol(30)	integer	/30*2/	+regrid +gridgen
    # number of radial zones in the open flux surface region of the edge plasma
-nyout(30)	integer	/30*0/	+regrid
+nyout(30)	integer	/30*0/	+regrid +gridgen
    # number of radial zones beyond second separatrix of full double-null
-nxleg(30,2)	integer	/0, 59*2/	+regrid
+nxleg(30,2)	integer	/0, 59*2/	+regrid +gridgen
    # number of cells along divertor legs:  (,1) inside, (,2) outside
-nxcore(30,2)	integer	/0, 59*4/	+regrid
+nxcore(30,2)	integer	/0, 59*4/	+regrid +gridgen
    # number of cells along core boundary:  (,1) inside, (,2) outside
-nxomit		integer /0/
+nxomit		integer /0/ +gridgen
    # number of x-cells to omit from ix=0; if <0, omit from ix=nx for fluid eqns
    # done typically for isfixlb=1,2 cases with reflection b.c. at left boundary
-nxxpt
+nxxpt +gridgen
    # number of extra poloidal cells at x-point (per quadrant)
-nyomitmx	integer /0/
+nyomitmx	integer /0/ +gridgen
    # 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)
-geometry	character*16 /"snull"/
+isgriduehdf5   integer /0/  
+geometry	character*16 /"snull"/ +input
 				# specifies magnetic configuration, e.g.,
 				# ='snull' for lower single null
 				# ='uppersn' for upper single null
@@ -267,18 +268,18 @@ geometry	character*16 /"snull"/
 nxc		integer	/4/	# center index of x-grid, normally nx/2,
                                 # OR
                                 # guard cell index for 'dnbot' symmetry b.c.
-simagxs         real            # "shared" value of simagx from flx package
-sibdrys         real            # "shared" value of sibdry from flx package
+simagxs         real            +griddata # "shared" value of simagx from flx package
+sibdrys         real            +griddata # "shared" value of sibdry from flx package
 nxpt2msh        integer /0/     # number of 1D cells above ixpt2 reset/no-cross
 nxpt2psh        integer /0/     # number of 1D cells below ixpt2 reset/no-cross
 zxpt2msh        real /0.01/ [m] # spacing iy=1 1D vertices reset above ixpt2
 rxpt2msh        real /0.0/  [m] # spacing iy=1 1D vertices reset above ixpt2
 zxpt2psh        real /0.01/ [m] # spacing iy=1 1D vertices reset below ixpt2
 rxpt2psh        real /0.0/  [m] # spacing iy=1 1D vertices reset below ixpt2
-ismpsym         integer /0/     # =1 re-constructs "guard" cells at midplane
+ismpsym         integer /0/     +gridgen # =1 re-constructs "guard" cells at midplane
                                 # of "dnbot" via up/down symmetry
-isudsym         integer /0/     #=1 up-down symmetric setup (only down part is modeled)
-islimon		integer	/0/
+isudsym         integer /0/     +input #=1 up-down symmetric setup (only down part is modeled)
+islimon		integer	/0/ +input
 	# option switch to apply b.c.'s at ix_lim and ix_lim+1
 	# =1 turns on limiter/continuity b.c.'s
 ix_lim          integer
@@ -287,8 +288,8 @@ iy_lims         integer	/9999/
 	# radial index of 1st flux surface where limiter b.c.'s apply
 theta_split	real	/1.570796326794896/
 	# (computed) poloidal angle where in/outboard regions of the mesh meet
-isnonog		integer /0/	# is 9-point (non-orthog) differencing on
-ismmon          integer /0/
+isnonog		integer /0/	+input # is 9-point (non-orthog) differencing on
+ismmon          integer /0/ +gridgen
 	# flag that controls mesh modification
 	#      = 0    strictly orthogonal mesh and divertor plates
 	#      = 1    non-orthogonal mesh, compressed distrib'n on each surface
@@ -296,24 +297,24 @@ ismmon          integer /0/
 	#      = 3    combination of options 1 and 2 using weight factor
         #             wtmesh1
 isoldgrid       integer /0/     # =1 returns to pre-1/25/96 nonorthog grid
-isgrdsym        integer /0/	# =1 makes symmetric grid for mhdgeo.ne.1,
+isgrdsym        integer /0/	+gridgen # =1 makes symmetric grid for mhdgeo.ne.1,
                                 # requires nxm,ixpt2 even
 cutlo           real  /1.e-300/ #rough range of a small number(avoids R1MACH(2))
                                 #CAUTION; this could be machine dependent
                                 #1.e-300 is generally conservative for 64-bit
                                 #words; on SUN double-p (e-330); C-90 (e-2500)
 epslon		real /1e-6/     #scale factor for relative guard-cell size
-spheromak	integer /0/	# =0 for tokamak, use vacuum toroidal field
+spheromak	integer /0/	+input # =0 for tokamak, use vacuum toroidal field
 				# =1 for spheromak, use bphi=fpoloidal(psi)/rm
-isfrc	integer	/0/	# =1 for field-reversed-configuration mesh options
-ishalfm	integer	/0/	# =1 for doing outboard half-mesh only
-isbphicon integer /0/   # =0 gives bphi=bcentrg*rcentrg/rm; =1 gives bphi=bcentrg
+isfrc	integer	/0/	+gridgen # =1 for field-reversed-configuration mesh options
+ishalfm	integer	/0/	+gridgen # =1 for doing outboard half-mesh only
+isbphicon integer /0/   +gridgen # =0 gives bphi=bcentrg*rcentrg/rm; =1 gives bphi=bcentrg
 nhdf      integer /1/   # number of hydrogenic b2frates-format data files
 hdfilename(1:12)   Filename  /12*'b2frates'/  # names of hydrogenic data files
 nzdf	  integer /1/	# number of impurity   b2frates-format data files
-mcfilename(1:12)   Filename  /12*'b2frates'/  # names of impurity   data files
-coronalimpfname  character*120 /'mist.dat'/   # name coronal impurity rate file
-istabon	integer	/7/ +restart
+mcfilename(1:12)   Filename  /12*'b2frates'/  +input # names of impurity   data files
+coronalimpfname  character*120 /'mist.dat'/   +input # name coronal impurity rate file
+istabon	integer	/7/ +input
                        #turns on look-up table for hydrogenic rate coefficients
 #	= 0  simple analytic rates and constant energy loss per ionization
 #	= 1  table look-up from ADPAK; rates.adpak
@@ -341,14 +342,14 @@ reset_core_og			integer /0/
 
 ***** Xpoint_indices:
 # target plate, x-point and separatrix indices
-ixlb(1:nxpt)	_integer	# ix index of left boundary
-ixpt1(1:nxpt)	_integer	# ix index of first x-point
-ixmdp(1:nxpt)	_integer	# ix index of midplane
-ixpt2(1:nxpt)	_integer	# ix index of second x-point
-ixrb(1:nxpt)	_integer	# ix index of right boundary
-iysptrx1(1:nxpt)	_integer	# iy index of first x-point
-iysptrx2(1:nxpt)	_integer	# iy index of second x-point
-iysptrx			integer		# iy index of last closed flux surface
+ixlb(1:nxpt)	_integer +griddata	# ix index of left boundary
+ixpt1(1:nxpt)	_integer +griddata	# ix index of first x-point
+ixmdp(1:nxpt)	_integer +griddata	# ix index of midplane
+ixpt2(1:nxpt)	_integer +griddata	# ix index of second x-point
+ixrb(1:nxpt)	_integer +griddata	# ix index of right boundary
+iysptrx1(1:nxpt)	_integer +griddata	# iy index of first x-point
+iysptrx2(1:nxpt)	_integer +griddata	# iy index of second x-point
+iysptrx			integer	 +griddata	# iy index of last closed flux surface
 
 ***** Cut_indices:
 # Indices for cut location (in x) and length (in y)
@@ -620,18 +621,18 @@ rtlqa(0:rtnt,0:rtnn,0:rtnsd-1)	_real
      # ln(rtqa) where rtqa[eV*m**3/s] is 'b2frates' data for elec energy loss
 rtlcx(0:rtnt,0:rtnn,0:rtnsd-1)	_real
      # ln(rtcx); rtcx[m**3/s] is 'b2frates' data for c-x on neutral hydrogen
-iscxfit	 real /1./	# flag for C ion c-x on neutral H
+iscxfit	 real /1./ +input	# flag for C ion c-x on neutral H
      #=0 use analytic forms in Braams' rate package
      #=1 use polynomial fit to C.F. Maggi curves (1997)
      #=2 same as =1, except Z=1 has lower rate from Pigarov
-isrtndep  integer /1/   # flag for turning on ne-dep atomic rates when
+isrtndep  integer /1/ +input   # flag for turning on ne-dep atomic rates when
      # ismctab=2 (impurities) and/or istabon=16 (hydrogen)
 mcfformat(1:12) integer /12*0/ # flag read from mcfilename rate files to distingu
      # pre-2012 format (0) from 2012 format (1) for rates;
      # assoc. with how ebindz is used.
-chgstate_format(0:rtnsd-1) _integer # flag denoting data format used for
+chgstate_format(0:rtnsd-1) _integer +input # flag denoting data format used for
      # each charge state; see mcfformat
-ispradextrap integer /0/ #=1 extrapolated neutral prad below table min
+ispradextrap integer /0/ +input #=1 extrapolated neutral prad below table min
 
 ***** Fitdata:
 # Arrays and variables for the tanh and b-spline fits to DIII-D radial profiles
diff --git a/flx/flx.v b/flx/flx.v
index a2900088..8777987c 100755
--- a/flx/flx.v
+++ b/flx/flx.v
@@ -23,25 +23,25 @@ nsearch integer /NSEARCH/
      # maximum number search regions for contouring package
 
 ***** Flxin:
-istchkon	integer	/0/
+istchkon	integer	/0/ +gridgen
      # switch for imposing limits on the polar angle about (rmagx,zmagx)
      # of (r,z) points on flux contours.
      #	=0 no limits
      #	=1 limits are defined by theta_split, thetax, dtheta_exclude,
      #             dtheta_overlap_sol and dtheta_overlap_pf
-isthmmxn	integer	/1/
+isthmmxn	integer	/1/ +gridgen
      # switch that controls expressions for thetamin and thetamax when
      # istchkon=1 for 'dnbot' configurations:
      # =0     uses same theta_split for in/outboard halves
      # =1     uses pi/twopi in place of theta_split for in/outboard halves
-dtheta_exclude(1:2)	real	[radians]	/2*1.5/
+dtheta_exclude(1:2)	real	[radians]	/2*1.5/ +gridgen
      # angular width of region where SOL flux contours are excluded
      # index 1 refers to inboard flux contours; 2 refers to outboard contours
-dtheta_overlap_sol(1:2)	real	[radians]	/2*0.5/
+dtheta_overlap_sol(1:2)	real	[radians]	/2*0.5/ +gridgen
      # angular width over which SOL flux contours can overlap
      # with flux contours in the adjacent region.
      # index 1 refers to inboard flux contours; 2 refers to outboard contours
-dtheta_overlap_pf(1:2)	real	[radians]	/2*0.25/
+dtheta_overlap_pf(1:2)	real	[radians]	/2*0.25/ +gridgen
      # angular width over which p.f. flux contours can overlap
      # with flux contours in the adjacent region.
 thetax			real	[radians]
@@ -52,13 +52,13 @@ thetamin(1:2)		real	[radians]
 thetamax(1:2)		real	[radians]
      # computed maximum poloidal angle of flux contour data
      # index 1 refers to inboard flux contours; 2 refers to outboard contours
-theta1fac	real	/1.0/
+theta1fac	real	/1.0/ +gridgen
      # multiplicative factor for theta1 boundary of inner-half pf region
-theta2fac	real	/0.0/
+theta2fac	real	/0.0/ +gridgen
      # multiplicative factor for theta2 boundary of outer-half pf region
-ymax1fac        real    /1.0/
+ymax1fac        real    /1.0/ +gridgen
      # multiplies zmagx to set upper bound on search region 1
-ymax2fac        real    /3.0/
+ymax2fac        real    /3.0/ +gridgen
      # multiplies zseps to set upper bound on search region 2
 imagx		integer
      # horizontal (R) index of the refined-EFIT cell containing the magnetic axis
@@ -72,99 +72,99 @@ icutoff1	integer
      # horizontal (R) index of the refined-EFIT cell containing xcutoff1
 jcutoff1	integer
      # vertical (Z) index of the refined-EFIT cell containing ycutoff1
-slpyt		real	/1.0/
+slpyt		real	/1.0/ +gridgen
 # scaling factor for radial mesh near double-null separatrices -
 #    - mesh size is scaled by slpyt near inner separatrix
 #    - mesh size is scaled by 1/slpyt near outer separatrix
-slp2fac		real	/1.0/
+slp2fac		real	/1.0/ +gridgen
 # scale factor for radial mesh in asymmetric double-null configurations
 # (see function rho3dn for details)
 # = 1. for uniform mesh between separatrices
 # < 1. for finer mesh at innermost separatrix
 # > 1. for coarser mesh at innermost separatrix
-slp3fac		real	/1.0/
+slp3fac		real	/1.0/ +gridgen
 # scale factor for radial mesh in asymmetric double-null configurations
 # (see function rho3dn for details)
 # = 1. for uniform mesh between separatrices
 # < 1. for finer mesh at outermost separatrix
 # > 1. for coarser mesh at outermost separatrix
-psifac		real	/1.0005/
+psifac		real	/1.0005/ +gridgen
 # multiplicative factor in normalized separatrix flux
 # to ensure that contour is just outside the x-point.
 psi0sep1	real
 # normalized flux value at lower x-point
 psi0sep2	real
 # normalized flux value at upper x-point
-psi0max_inner		real	/1.07/ +regrid
+psi0max_inner		real	/1.07/ +regrid +gridgen
 # normalized flux value at wall on inboard side of magnetic axis
-psi0max_outer		real	/1.07/ +regrid
+psi0max_outer		real	/1.07/ +regrid +gridgen
 # normalized flux value at wall on outboard side of magnetic axis
-psi0min2_upper		real	/0.98/ +regrid
+psi0min2_upper		real	/0.98/ +regrid +gridgen
 # normalized flux value at private flux boundary near upper x-point
-psi0min2_lower		real	/0.98/ +regrid
+psi0min2_lower		real	/0.98/ +regrid +gridgen
 # normalized flux value at private flux boundary near lower x-point
-psi0min1	real	/0.98/ +regrid
+psi0min1	real	/0.98/ +regrid +gridgen
      # normalized flux value at innermost core flux surface
-psi0min2	real	/0.98/ +regrid
+psi0min2	real	/0.98/ +regrid +gridgen
      # normalized flux value at innermost private flux surface
-psi0sep		real	/1.00001/ +regrid
+psi0sep		real	/1.00001/ +regrid +gridgen
      # normalized flux value at separatrix flux surface (just slightly outside)
-psi0max			real	/1.07/ +regrid
+psi0max			real	/1.07/ +regrid +gridgen
      # normalized flux value at wall on outboard side of magnetic axis
-psi0lim		real
+psi0lim		real +gridgen
      # normalized flux value where core radial mesh can be concentrated
-sfaclim		real	/1.0/
+sfaclim		real	/1.0/ +gridgen
      # multiplicative factor for slope of psi0(iy) distribution at psi0lim
      #	sfaclim = 1	-->	nearly uniform
      #	sfaclim < 1	-->	more concentrated near psi0lim
-alfcy_inner	real	/.0001/ +regrid
+alfcy_inner	real	/.0001/ +regrid +gridgen
      # exponential factor for  distribution of SOL flux contours (inboard)
      #	alfcy << 1	-->	uniform
      #	alfcy >> 1	-->	concentrated near separatrix
-alfcy		real	/.0001/ +regrid
+alfcy		real	/.0001/ +regrid +gridgen
      # exponential factor for  distribution of SOL flux contours (outboard)
      #	alfcy << 1	-->	uniform
      #	alfcy >> 1	-->	concentrated near separatrix
-xoverlap(2)	real	/5.0,4.0/
+xoverlap(2)	real	/5.0,4.0/ +gridgen +gridgen
      # overlap parameters for inboard and outboard flux contours
      # (in units of dxefit)
 rho(0:nym)	_real
      # temporary array for normalized flux values on B2/UEDGE flux surfaces
 tflx(0:nym)	_real
      # temporary array for indicies of B2/UEDGE flux surfaces
-psitop(1:jdim)	_real
+psitop(1:jdim)	_real +gridgen
      # array of un-normalized pol. mag. flux values across the midplane 
-psibot(1:jdim)	_real
+psibot(1:jdim)	_real +gridgen
      # array of un-normalized pol. mag. flux values across both divertor plates
-iseqdskr	integer	/0/
+iseqdskr	integer	/0/ +gridgen
      # switch (=1) for reflecting eqdsk data about the midplane;
      # used with geometry='uppersn' and for upper half-mesh of geometry='dnull'
-kymesh		integer	/1/
+kymesh		integer	/1/ +gridgen
      # option flag for setting flux contour values that define radial mesh
      # =0 user sets arrays psitop (midplane) and psibot (div plates)
      # =1 psitop and psibot are analytic forms (see rho1); adjust via alfcy
      # =2 psitop and psibot are analytic forms (see rho5); uniform core
-xcutoff1	real	/0./	[m]
+xcutoff1	real	/0./	[m] +gridgen
      # inboard cutoff radius for flux contours
-ycutoff1	real	/0./	[m]
+ycutoff1	real	/0./	[m] +gridgen
      # lower vertical cutoff for flux contours
-mdsefit		integer	/0/
+mdsefit		integer	/0/ +gridgen
      # Set this flag to 1 if the data is read in from Mdsplus
      # Prevents inflx from calling readefit.
 
 ***** Workdn:
      # some working arrays for full double-null configurations
-psi0_mp_inner(0:nym)	_real
+psi0_mp_inner(0:nym)	_real +gridgen
 # normalized flux values at radial mesh points of inner midplane
-psi0_mp_outer(0:nym)	_real
+psi0_mp_outer(0:nym)	_real +gridgen
 # normalized flux values at radial mesh points of outer midplane
-psi0_dp_lower_inner(0:nym)	_real
+psi0_dp_lower_inner(0:nym)	_real +gridgen
 # normalized flux values at radial mesh points of lower inner divertor plate
-psi0_dp_lower_outer(0:nym)	_real
+psi0_dp_lower_outer(0:nym)	_real +gridgen
 # normalized flux values at radial mesh points of lower outer divertor plate
-psi0_dp_upper_inner(0:nym)	_real
+psi0_dp_upper_inner(0:nym)	_real +gridgen
 # normalized flux values at radial mesh points of upper inner divertor plate
-psi0_dp_upper_outer(0:nym)	_real
+psi0_dp_upper_outer(0:nym)	_real +gridgen
 # normalized flux values at radial mesh points of upper outer divertor plate
 
 ***** Inpf0:
@@ -193,14 +193,14 @@ yminf0(nsearch)      _real   [m]
      # vertical cutoff for contours at upper edge of efit domain
 ymaxf0(nsearch)      _real   [m]
      # vertical cutoff for contours at lower edge of efit domain
-istcvon		integer	/0/
+istcvon		integer	/0/ +gridgen
      # obsolete option istcvon=1; use altsearch=2 instead.
-altsearch	integer /0/
+altsearch	integer /0/ +gridgen
      # flag to change search path for private flux surfaces
      # altsearch=0	--> search vertically up toward x-point
      # altsearch=1	--> search vertically down from x-point
      # altsearch=2	--> search diagonally down and in from x-point
-isetpath     integer /0/
+isetpath     integer /0/ +gridgen
      # set path for finding flux surfaces in midplane
      # isetpath=0    --> search radially outward from left boundary
      # isetpath=1    --> search radially inward from magnetic axis
@@ -238,7 +238,7 @@ ncmax1  integer
      # flux contouring variables on the refined grid
 plflux(jdim)     _real
      # temporary array of poloidal flux values in a search region
-mrfac	integer	/4/
+mrfac	integer	/4/ +gridgen
      # mesh refinement factor relative to EFIT
 nx4     integer
      # number of grid surfaces in x-direction on refined grid
@@ -253,7 +253,7 @@ f(nx4,ny4)      _real
 ijumpf(jdim)	_integer
      # core/p.f. discontinuity on flux contour j occurs between
      # data points ijumpf(j) and ijumpf(j)+1
-dsjumpf		real	/0.1/	[m]
+dsjumpf		real	/0.1/	[m] +gridgen
      # criterion for "jump" discontinuity in core/p.f. contours
 ilast(jdim)     _integer
      # comment needed
diff --git a/grd/grd.v b/grd/grd.v
index b43c8d54..3fa8f8ae 100755
--- a/grd/grd.v
+++ b/grd/grd.v
@@ -46,47 +46,47 @@ integer niwdim	integer
 
 ***** Analgrd:
 # common block with parameters for cylindrical & rectangular (IDEAL) grid
-radm    real [m] /-1.e-4/   #minimum "radius" of cylinder or slab
-radx    real [m]  /0.04/    #maximum "radius" of cylinder or slab
-rad0    real [m]   /0./     #location of "radial" separ'x for cylinder or slab
-rscalcore real [ ] /1./     #scale fac to change radial dimen. of core region
-za0     real [m]   /0./     #position of left-hand axial boundary position
-zax     real [m]   /1./     #position of right-hand axial boundary position
-zaxpt   real [m]   /.75/    #position of x-point; uniform grid to here
-tiltang real [deg] /0./     #inc. tilt angle of the divertor plate from 90 deg.
-ixsnog  integer    /1/	    #poloidal ix where nonorthogonal mesh begins
-zxpt_reset real [m] /0./    #reset x-pt2 here if >0 for single-region mesh
-alfyt   real      /-2./     #exponent coeff. for y (radial) grid nonuiformity
-tnoty   real      /0./      #shift if r(t)~del_r*tanh radial mesh profile
-sratiopf real      /0./     #ratio of effec. alfyt in priv. flux region; calc
-                            #internally to give same expans. rate if =0.
-alfxt   real      /4.0/     #exponent coeff. for x (axial) grid nonuiformity
-isadjalfxt integer /0/      #=1 changes alfxt slightly for smooth dx at ixpt2 
-tctr    real      /0./      #relative location of dx maximum;0, left; 1., right
-bpolfix real [T]   /.3/     #poloidal B-field for cartesian grid
-btfix   real [T]   /5./     #total B-field for cartesian grid
-rmajfix real [m]   /1.0/    #reference major radius for cartesian/cylindrical grid
-sigma_bpol real []  /0.0/   #exponent for poloidal field for cartesian/cylindrical grid
-sigma_btor real []  /0.0/   #exponent for toroidal field for cartesian/cylindrical grid
-isgdistort integer /0/      #switch to distort poloidal grid
-agsindx real       /0./     #max amplitude shift of poloidal cell face linear
+radm    real [m] /-1.e-4/   +gridgen #minimum "radius" of cylinder or slab
+radx    real [m]  /0.04/    +gridgen #maximum "radius" of cylinder or slab
+rad0    real [m]   /0./     +gridgen #location of "radial" separ'x for cylinder or slab
+rscalcore real [ ] /1./     +gridgen #scale fac to change radial dimen. of core region
+za0     real [m]   /0./     +gridgen #position of left-hand axial boundary position
+zax     real [m]   /1./     +gridgen #position of right-hand axial boundary position
+zaxpt   real [m]   /.75/    +gridgen #position of x-point; uniform grid to here
+tiltang real [deg] /0./     +gridgen #inc. tilt angle of the divertor plate from 90 deg.
+ixsnog  integer    /1/	    +gridgen #poloidal ix where nonorthogonal mesh begins
+zxpt_reset real [m] /0./    +gridgen #reset x-pt2 here if >0 for single-region mesh
+alfyt   real      /-2./     +gridgen #exponent coeff. for y (radial) grid nonuiformity
+tnoty   real      /0./      +gridgen #shift if r(t)~del_r*tanh radial mesh profile
+sratiopf real      /0./     +gridgen #ratio of effec. alfyt in priv. flux region; calc
+                            +gridgen #internally to give same expans. rate if =0.
+alfxt   real      /4.0/     +gridgen #exponent coeff. for x (axial) grid nonuiformity
+isadjalfxt integer /0/      +gridgen #=1 changes alfxt slightly for smooth dx at ixpt2 
+tctr    real      /0./      +gridgen #relative location of dx maximum;0, left; 1., right
+bpolfix real [T]   /.3/     +gridgen #poloidal B-field for cartesian grid
+btfix   real [T]   /5./     +gridgen #total B-field for cartesian grid
+rmajfix real [m]   /1.0/    +gridgen #reference major radius for cartesian/cylindrical grid
+sigma_bpol real []  /0.0/   +gridgen #exponent for poloidal field for cartesian/cylindrical grid
+sigma_btor real []  /0.0/   +gridgen #exponent for toroidal field for cartesian/cylindrical grid
+isgdistort integer /0/      +gridgen #switch to distort poloidal grid
+agsindx real       /0./     +gridgen #max amplitude shift of poloidal cell face linear
  			    #linear in radial index iy
-agsrsp  real       /0./     #max amplitude shift of poloidal cell face linear
+agsrsp  real       /0./     +gridgen #max amplitude shift of poloidal cell face linear
                             #in real space - use either asgindx or asgrsp/not b
-iynod   integer    /0/      #iy about which asgindx distortion is centered
-rnod    real       /0./     #value of y about which asgrsp distortion centered
-ixdstar integer    /1/      #ix where poloidal distortion begins
+iynod   integer    /0/      +gridgen #iy about which asgindx distortion is centered
+rnod    real       /0./     +gridgen #value of y about which asgrsp distortion centered
+ixdstar integer    /1/      +gridgen #ix where poloidal distortion begins
 
 ***** Torannulus:
-acore	real [m]   /0.5/    #minor radius of core-edge bdry for mhdgeo=2
-rm0	real [m]   /2./     #major radius of annulus for mhdgeo=2
-edgewid real [m]   /0.1/    #width of simulated edge region for mhdgeo=2
-dthlim  real [rad] /1e-4/   #polodial angular width of limiter cell
-bpol0   real [T]   /0.2/    #poloidal B-field for mhdgeo=2 (annulus)
-btor0   real [T]   /2./     #toroidal B-field for mhdgeo=2 on axis
-radf(0:nym+1,0:4) _real [m] # minor radius of cells for mhdgeo=2
-thpf(1:nxm,0:4)   _real [m] # poloidal angle of cells for mhdgeo=2
-ibpmodel integer   /0/      #=0, Bpol=bpol0; =1, Bpol=bpol0*rm0/R
+acore	real [m]   /0.5/    +gridgen #minor radius of core-edge bdry for mhdgeo=2
+rm0	real [m]   /2./     +gridgen #major radius of annulus for mhdgeo=2
+edgewid real [m]   /0.1/    +gridgen #width of simulated edge region for mhdgeo=2
+dthlim  real [rad] /1e-4/   +gridgen #polodial angular width of limiter cell
+bpol0   real [T]   /0.2/    +gridgen #poloidal B-field for mhdgeo=2 (annulus)
+btor0   real [T]   /2./     +gridgen #toroidal B-field for mhdgeo=2 on axis
+radf(0:nym+1,0:4) _real [m] +gridgen # minor radius of cells for mhdgeo=2
+thpf(1:nxm,0:4)   _real [m] +gridgen # poloidal angle of cells for mhdgeo=2
+ibpmodel integer   /0/      +gridgen #=0, Bpol=bpol0; =1, Bpol=bpol0*rm0/R
  
 ***** Magmirror:
 zu(1:nxm,1:nym,0:4)   _real [m] #axial postions of vertices & center (0)
@@ -202,23 +202,23 @@ iwsla(niwdim)	_integer
 
 ***** Inmesh:
 # input data from user
-isspnew		integer		/0/
+isspnew		integer		/0/ +gridgen
 	# flag for source of strike-point data
 	# isspnew = 0 --> strike point data from eqdsk files
 	#         = 1 --> user-specified values (rstrike(1:2),zstrike(1:2))
-rstrike(1:2)	real	[m]
+rstrike(1:2)	real	[m] +gridgen
 	# radial position of inboard:outboard strike point
-zstrike(1:2)	real	[m]
+zstrike(1:2)	real	[m] +gridgen
 	# vertical position of inboard:outboard strike point
-istpnew		integer		/0/
+istpnew		integer		/0/ +gridgen
 	# flag for source of first-seed-point data (top of mesh)
 	# istpnew = 0 --> 1st seed point at midplane for "dnbot"
 	#         = 1 --> user-specified values (rtpnew(1:2),ztpnew(1:2))
-rtpnew(1:2)	real	[m]
+rtpnew(1:2)	real	[m] +gridgen
 	# radial position of first inboard:outboard seed point
-ztpnew(1:2)	real	[m]
+ztpnew(1:2)	real	[m] +gridgen
 	# vertical position of first inboard:outboard seed point
-istptest(1:2)	     integer	/2*0/
+istptest(1:2)	     integer	/2*0/ +gridgen
 	# flag for algorithm that defines top-of-mesh on inboard, (1), 
 	# and outboard, (2), separatrix flux contours:
 	# = 0  -->  test on R only
@@ -226,10 +226,10 @@ istptest(1:2)	     integer	/2*0/
 	# = 2  -->  test on Z only
 ilmax(1:2)	integer
 	# index of last angle surface ( at divertor plate ) in each region
-seedxp(idim,noregs)     _real
+seedxp(idim,noregs)     _real +gridgen
 	# normalized distance along core segment of separatrix
 	# measured from first seed point (=0.) to x-point (=100.)
-seedxpxl(idim,noregs)   _real
+seedxpxl(idim,noregs)   _real +gridgen
 	# normalized distance along divertor leg of separatrix measured from
 	# x-point (=0.) to last seed point (=100.) 
 seed(idim,noregs)	_real
@@ -252,7 +252,7 @@ y0g(noregs)      _real
 	# vertical position of the first seed point on the separatrix
 ylast(noregs)      _real
 	# vertical position of the last seed point on the separatrix
-isztest(1:2)	     integer	/2*0/
+isztest(1:2)	     integer	/2*0/ +gridgen
 	# flag for algorithm that defines end-of-mesh on inboard, (1), 
 	# and outboard, (2), separatrix flux contours:
 	# = 0  -->  test on R only
@@ -260,7 +260,7 @@ isztest(1:2)	     integer	/2*0/
 	# = 2  -->  test on Z only
 epslon_lim	real  /1.e-3/
 	# ratio of limiter guard-cell x-width to adjacent cell
-dalpha       real /5./
+dalpha       real /5./ +gridgen
         # fuzziness or overlap (in degrees) of angle limits associ. with alpha1
 
 ***** Transit:
@@ -302,7 +302,7 @@ iendc(noregs)    _integer
 
 ***** UEgrid:
 # input/output data for defining the grid in the UEDGE code
-ixtop   integer
+ixtop   integer +gridgen
 	# ix index of top "angle" surface opposite the x-point
 
 ***** Mmod:
@@ -359,11 +359,11 @@ rtop2(ntop2)	_real	[m]
 ztop2(ntop2)	_real	[m]
 	# vertical position of data points on the outboard top-of-mesh
 	# reference surface
-istream			integer	/0/
+istream			integer	/0/ +gridgen
 	# option parameter for defining fixed upstream reference surface
 	# istream=0	midplane+cut(ismmon=1) or top-of-mesh(ismmon=2)
 	# istream=1	user-defined upstream surface arrays
-isupstreamx			integer	/0/
+isupstreamx			integer	/0/ +gridgen
 	# option parameter for defining fixed upstream reference surface
 	# isupstreamx=0	midplane+cut(ismmon=1) or top-of-mesh(ismmon=2)
 	# isupstreamx=1	orthogonal surface (SOL and PF) through x-point
@@ -399,23 +399,23 @@ rdnstream2(ndnstream2)	_real	[m]
 zdnstream2(ndnstream2)	_real	[m]
 	# vertical position of data points on the outboard downstream
 	# reference surface
-iplate			integer	/0/
+iplate			integer	/0/ +gridgen
 	# option parameter for defining divertor plates
 	# iplate=0	orthogonal plates
 	# iplate=1	user-defined divertor plates
-nplate1	integer
+nplate1	integer +gridgen
 	# number of data points on the inboard divertor plate surface
-rplate1(nplate1)	_real	[m]
+rplate1(nplate1)	_real	[m] +gridgen
 	# radial position of data points on the inboard divertor plate surface
-zplate1(nplate1)	_real	[m]
+zplate1(nplate1)	_real	[m] +gridgen
 	# vertical position of data points on the inboard divertor plate
 	# surface
-nplate2	integer
+nplate2	integer +gridgen
 	# number of data points on the outboard divertor plate surface
-rplate2(nplate2)	_real	[m]
+rplate2(nplate2)	_real	[m] +gridgen
 	# radial position of data points on the outboard divertor plate
 	# surface
-zplate2(nplate2)	_real	[m]
+zplate2(nplate2)	_real	[m] +gridgen
 	# vertical position of data points on the outboard divertor plate
 	# surface
 ntop		integer
@@ -462,17 +462,17 @@ zplate0(nptmp)		_real	[m]
 	# temporary array for subroutine meshmod
 dsnorm(idim)		_real
 	# temporary array for subroutine meshmod2
-wtold	real	/0.5/
+wtold	real	/0.5/ +gridgen
 	# weight factor for spatial smoothing of angle-like mesh surfaces
 	# wtold=1.0 ==> no smoothing
 	# wtold=0.5 ==> (1,2,1) relative weighting of (j-1,j,j+1)
 	# wtold=0.0 ==> (1,0,1) relative weighting of (j-1,j,j+1)
-nsmooth	integer	/2/
+nsmooth	integer	/2/ +gridgen
 	# number of times to apply the smoothing algorithm to each
 	# angle-like surface after non-orthogonal plate construction
-fuzzm	real	[m]	/1.0e-08/
+fuzzm	real	[m]	/1.0e-08/ +gridgen
 	# a measure of the "fuzziness" in meshpoint coordinates  
-delmax	real	[m]	/1.0e-08/
+delmax	real	[m]	/1.0e-08/ +gridgen
 	# estimated maximum deviation of mesh points from exact flux
 	# surfaces (used only in subroutine smooth)
 wtmesh1	real	/0.5/
@@ -482,7 +482,7 @@ wtmesh1	real	/0.5/
 wtm1(idim)	_real
 	# temporary array of weight factors for merging limiter mesh
 	# with original (unmodified) mesh
-dmix0	real	/0./
+dmix0	real	/0./ +gridgen
 	# normalized poloidal mixing length for combining mesh0 with mesh12
 	# =0. --> abrupt  change from orthogonal mesh to mesh12 at upstream 
         #         position
@@ -516,20 +516,20 @@ dsmesh3(idim)	_real
 dsmeshff(idim)	_real
 	# temporary array for subroutine meshff
 	# distance from top-of-mesh to modified meshpoints (flamefront)
-cwtffu		real	/1./
+cwtffu		real	/1./ +gridgen
 	# exponent for weight function variation between x-point and flamefront
 	# wt(ix)=wtff*fac(ix)**cwtff where fac(ix) varies linearly from
 	# zero at xpoint to unity at flamefront.
-cwtffd		real	/1./
+cwtffd		real	/1./ +gridgen
 	# exponent for weight function variation between flamefront and plate
 	# wt(ix)=wtff*fac(ix)**cwtff where fac(ix) varies linearly from
 	# zero at plate to unity at flamefront.
-isxtform	integer	/1/
+isxtform	integer	/1/ +gridgen
 	# flag for choosing various forms of x(ix) near flamefront
 	# =1 --> specify slope factor at flamefront only (default)
 	# =2 --> specify slope factor at flamefront and upstream
 	# =3 --> specify slope factor at flamefront, upstream and downstream
-iswtform	integer /0/
+iswtform	integer /0/ +gridgen
 	# flag for choosing various forms of weight factors near flamefront
 	# =0 --> wt(ix)=wtff for all ix (default)
 	# =1 --> wt(ix)~wtff*abs(ix-ixlimit)**cwtff between flamefront and
@@ -550,7 +550,7 @@ slpxffd1	real
 	# slope factor at downstream limit (plate) of flamefront mesh
 	# slpxuu < 1  makes mesh finer
 	# slpxuu > 1  makes mesh coarser
-nxdff1		integer		/0/
+nxdff1		integer		/0/ +gridgen
 	# number of cells between flame front and divertor plate
 	# on inner leg (region 1)
 wtff2		real
@@ -575,26 +575,26 @@ nxdff2		integer		/0/
 
 ***** Refinex:
 # data used for mesh refinement near the x-point
-isrefxptn	integer	/1/
+isrefxptn	integer	/1/ +gridgen
 	# flag for choosing x-point mesh refinement algorithm
 	# =0  old interpolation method
 	# =1  new flux-surface-based method
-nxmod	integer	/2/
+nxmod	integer	/2/ +gridgen
 	# number of 'upstream' poloidal cells (per quadrant) in the
 	# original mesh that we modify by calling subroutine refinex
-alfxptl real /1./	# use as alfxpt for cells below(l) the x-pt;
+alfxptl real /1./ +gridgen	# use as alfxpt for cells below(l) the x-pt;
         # frac=(i/(nxxpt+nxmod))**alfxpt for extra x-pt grid spacing below x-pt
-alfxpt2l real /1./	# use as alfxpt2 for cells below(l) the x-pt;
+alfxpt2l real /1./ +gridgen	# use as alfxpt2 for cells below(l) the x-pt;
         # frac2=(i/(nxxpt+nxmod-1))**alfxpt2 for mixing fixed lngth & 
 	# flux-surface length in adding extra x-pt cells below x-pt
-alfxptu real /1./	# use as alfxpt for cells above(u) the x-pt;	
+alfxptu real /1./ +gridgen	# use as alfxpt for cells above(u) the x-pt;	
         # frac=(i/(nxxpt+nxmod))**alfxpt for extra x-pt grid spacing above x-pt
-alfxpt2u real /1./	# use as alfxpt2 for cells above(u) the x-pt;	
+alfxpt2u real /1./ +gridgen	# use as alfxpt2 for cells above(u) the x-pt;	
         # frac2=(i/(nxxpt+nxmod-1))**alfxpt2 for mixing fixed lngth & 
 	# flux-surface length in adding extra x-pt cells above x-pt
-alfxpt  real /1./	# work var for alfxptl,u for below(l)/above(u) x-pt
+alfxpt  real /1./ +gridgen	# work var for alfxptl,u for below(l)/above(u) x-pt
         # frac=(i/(nxxpt+nxmod))**alfxpt for setting extra x-pt grid spacing
-alfxpt2 real /1./	# work var for alfxptsl,u for below(l)/above(u) x-pt
+alfxpt2 real /1./ +gridgen	# work var for alfxptsl,u for below(l)/above(u) x-pt
         # frac2=(i/(nxxpt+nxmod-1))**alfxpt2 for mixing fixed lngth & 
 	# flux-surface length in adding extra x-pt cells
 rsu(0:nym+2)	_real	[m]
@@ -624,7 +624,7 @@ rmm(0:nym,0:nxm)	_real	[m]
 zmm(0:nym,0:nxm)	_real	[m]
 	# working array that contains z-coord's of angle-like surfaces
 	# in refined region near x-point
-nsmoothx	integer	/8/
+nsmoothx	integer	/8/ +gridgen
 	# number of times to apply the smoothing algorithm to each
 	# angle-like surface after mesh refinement near the x-point
 
@@ -636,21 +636,21 @@ xdat(ndat) 	_real	[m]
 	# data values for xfcn
 tdat(ndat) 	_real
 	# data values for t
-kxmesh  integer /1/
+kxmesh  integer /1/ +gridgen
 	# switch parameter for choosing model that defines x-mesh :
 	#       kxmesh=0        use old model (manual def. of seed points)
 	#       kxmesh=1        use linear*rational form for x(t)
 	#       kxmesh=2        use linear*exponential form for x(t)
 	#       kxmesh=3        use spline form for x(t)
 	#       kxmesh=4        use exponential+spline form for x(t)
-slpxt	real	/1.0/
+slpxt	real	/1.0/ +gridgen
 	# slope enhancement factor for x(t) near the "top" of the core
 	# plasma
-alfx(2)		real	/2*0.1/
+alfx(2)		real	/2*0.1/ +gridgen
 	# log( dx(n+1)/dx(n) ) for 'gas' cells near the divertor plates
-dxgas(2)	real	[m]
+dxgas(2)	real	[m] +gridgen
 	# poloidal size of first 'gas' cell at inboard and outboard plates
-nxgas(2)	integer
+nxgas(2)	integer +gridgen
 	# number of poloidal 'gas' cells at inboard and outboard plates
 dt1	real
 	# normalized-index distance (t) from inboard plate to 'extra' data
@@ -662,19 +662,19 @@ dt2	real
 	# point
 dx2	real	[m]
 	# physical distance (x) from outboard plate to 'extra' data point
-ileft	integer	/0/
+ileft	integer	/0/ +gridgen
 	# type of end condition at the left endpoint
 	#     = 1  first derivative specified by dleft
 	#     = 2  second derivative specified by dleft
-dleft	real	/0.0/	[m]
+dleft	real	/0.0/	[m] +gridgen
 	# derivative at left endpoint
-iright	integer	/0/
+iright	integer	/0/ +gridgen
 	# type of end condition at the right endpoint
 	#     = 1  first derivative specified by dright
 	#     = 2  second derivative specified by dright
-dright	real	/0.0/	[m]
+dright	real	/0.0/	[m] +gridgen
 	# derivative at right endpoint
-kord	integer	/4/	# order of spline (=4 for cubic interpolation)
+kord	integer	/4/ +gridgen	# order of spline (=4 for cubic interpolation)
 ndatp2	integer	/NDATP2/ 	# NDATP2 = NDAT+2
 kntopt	integer	/1/		# knot selection option flag
 tknt(ndatp2+4)	_real		# knot locations
@@ -704,15 +704,15 @@ iysptrxu	integer	# radial index of cells just inside the separatrix
 
 ***** Expseed:
         # variables to control exponential poloidal mesh in sub exponseed
-fraclplt(2)   real  /.6,.6/     #frac of divertor leg with near-plate spacing
-alfxdiv(2)    real /.18,.18/    #exponential factor for cell-size expansion
-alfxcore(2)   real  /.4,.4/     #exponential factor for cell-size expansion
-shift_seed_leg(2)  real /0.,0./ #shift in seed away from Xpt toward plate
-shift_seed_core(2) real /1.,1./ #shift in seed away from Xpt toward top
-nxlplt(2)   integer     /12,12/ #num poloidal cells in leg-plate region
-nxlxpt(2)   integer     /4,4/   #num pol cells in leg-xpt region; 
+fraclplt(2)   real  /.6,.6/  +gridgen    #frac of divertor leg with near-plate spacing
+alfxdiv(2)    real /.18,.18/ +gridgen    #exponential factor for cell-size expansion
+alfxcore(2)   real  /.4,.4/  +gridgen    #exponential factor for cell-size expansion
+shift_seed_leg(2)  real /0.,0./ +gridgen #shift in seed away from Xpt toward plate
+shift_seed_core(2) real /1.,1./ +gridgen #shift in seed away from Xpt toward top
+nxlplt(2)   integer     /12,12/ +gridgen #num poloidal cells in leg-plate region
+nxlxpt(2)   integer     /4,4/   +gridgen #num pol cells in leg-xpt region; 
 			        #note nxlplt+nxlxpt = nxleg (must check)
-fcorenunif  real        /0.8/   #frac pol core mesh with expon mesh
+fcorenunif  real        /0.8/   +gridgen #frac pol core mesh with expon mesh
 
 ***** Xfcn:
 	# contains various x-mesh functional forms
diff --git a/pyexamples/box2/box2_in.py b/pyexamples/box2/box2_in.py
index 83bd75b8..8eaa6b4b 100644
--- a/pyexamples/box2/box2_in.py
+++ b/pyexamples/box2/box2_in.py
@@ -4,6 +4,8 @@
 # This is a Python version of the box case from Andreas Holm
 ###########################################################################
 
+from uedge import bbb, com, grd
+
 
 #-Geometry
 bbb.mhdgeo=-1 #-set cartesian geometry
@@ -96,7 +98,7 @@
 
 
 #-Neutral gas propeties
-bbb.tfcx=5.;bbb.tfcy=5.         #Franck-Condon temperatures
+#bbb.tfcx=5.;bbb.tfcy=5.         #Franck-Condon temperatures
 bbb.cngfx=1.;bbb.cngfy=1.       #turn-on grad(T_g) flux if =1
 bbb.cngflox=1.;bbb.cngfloy=0.   #turn-on drift with ions if =1
 bbb.cngmom = 1.             #ion-gas momentum transfer
diff --git a/pyexamples/box2/plotcontour.py b/pyexamples/box2/plotcontour.py
index fd273279..559998a5 100644
--- a/pyexamples/box2/plotcontour.py
+++ b/pyexamples/box2/plotcontour.py
@@ -1,10 +1,12 @@
 import matplotlib
+import matplotlib.pyplot as plt
 import matplotlib.gridspec as gridspec
+from uedge import bbb, com
 gs=gridspec.GridSpec(2, 2)
 
 plt.figure(10)
 plt.subplot(gs[0,0])
-CS = plt.contour(com.zm[:,:,0], com.rm[:,:,0], bbb.te/ev)
+CS = plt.contour(com.zm[:,:,0], com.rm[:,:,0], bbb.te/bbb.ev)
 plt.clabel(CS, inline=1, fontsize=10)
 params = {'mathtext.default': 'regular' }          
 plt.rcParams.update(params)
@@ -14,7 +16,7 @@
 
 
 plt.subplot(gs[0,1])
-CS = plt.contour(com.zm[:,:,0], com.rm[:,:,0], bbb.ti/ev)
+CS = plt.contour(com.zm[:,:,0], com.rm[:,:,0], bbb.ti/bbb.ev)
 plt.clabel(CS, inline=1, fontsize=10)
 plt.title('T$\mathregular{_i}$ [ev]')
 plt.grid(True)
diff --git a/pyexamples/box2/runcase.py b/pyexamples/box2/runcase.py
index d0a39448..4d77e082 100644
--- a/pyexamples/box2/runcase.py
+++ b/pyexamples/box2/runcase.py
@@ -9,18 +9,21 @@
 import matplotlib.gridspec as gridspec
 import numpy as np
 import os
+from uedge.uedgeplots import *
+from uedge.rundt import rundt
 
 #-import some utilities for using OS
 ###execfile(os.path.join(os.environ['HOME'], 'utils/python/osfun.py'))
 
+def paws():
+    programPause = input("Press the <ENTER> key to continue...")
 
 ##-how to do this better?
 #-in .bashrc: "export PYLIB=/home/umansky1/PyUEDGE/uedge/pylib"
-execfile(os.environ['PYLIB']+"/plotmesh.py")
-execfile(os.environ['PYLIB']+"/plotcontour.py")
-execfile(os.environ['PYLIB']+"/plotvar.py")
-execfile(os.environ['PYLIB']+"/paws.py")
-execfile(os.environ['PYLIB']+"/osfun.py")
+#execfile(os.environ['PYLIB']+"/plotmesh.py")
+#execfile(os.environ['PYLIB']+"/plotcontour.py")
+#execfile(os.environ['PYLIB']+"/plotvar.py")
+#execfile(os.environ['PYLIB']+"/osfun.py")
 #execfile("../../plotmesh.py")
 #execfile("../../pylib/plotvar.py")
 #execfile("../../pylib/plotr.py")
@@ -32,7 +35,7 @@
 
 
 #-read UEDGE settings
-execfile("box2_in.py")
+from box2_in import *
 
 
 #-do a quick preliminary run to set all internals
@@ -41,7 +44,7 @@
 
 #-show grid
 plotmesh()
-wait = raw_input("PAUSING, PRESS ENTER TO CONTINUE...")
+wait = input("PAUSING, PRESS ENTER TO CONTINUE...")
 
 
 #-this should be done in uefacets
@@ -66,13 +69,13 @@
     bbb.isbcwdt=1
     bbb.dtreal = 1e-14; bbb.itermx=30; bbb.exmain()
     bbb.t_stop=1e0
-    bbb.rundt()
+    rundt()
     bbb.dtreal=1e20; bbb.isbcwdt=0; bbb.exmain()
     hdf5_save('mycase.h5')
 
 
     ###execfile('plotcontour.py')
-    plotcontour()
+    from plotcontour import *
     paws()
 
 
diff --git a/pyexamples/d3dHsm/runcase.py b/pyexamples/d3dHsm/runcase.py
index f1356b92..e8fe478f 100644
--- a/pyexamples/d3dHsm/runcase.py
+++ b/pyexamples/d3dHsm/runcase.py
@@ -9,23 +9,21 @@
 import matplotlib.gridspec as gridspec
 import numpy as np
 import os
+from uedge.uedgeplots import *
+from uedge.rundt import rundt
+
 
 #-import some utilities for using OS
 ###execfile(os.path.join(os.environ['HOME'], 'utils/python/osfun.py'))
 
 
 #-in .bashrc: "export PYLIB=/home/umansky1/PyUEDGE/uedge/pylib"
-execfile(os.environ['PYLIB']+"/plotmesh.py")
-execfile(os.environ['PYLIB']+"/plotcontour.py")
-execfile(os.environ['PYLIB']+"/plotvar.py")
-execfile(os.environ['PYLIB']+"/paws.py")
-execfile(os.environ['PYLIB']+"/osfun.py")
 
 plt.ion()
 
 
 #-read UEDGE settings
-execfile("rd_d3dHsm_in.py")
+from rd_d3dHsm_in import *
 
 
 #-do a quick preliminary run to set all internals
@@ -33,8 +31,8 @@
 
 
 #-show grid
-plotmesh(iso=1)
-wait = raw_input("PAUSING, PRESS ENTER TO CONTINUE...")
+plotmesh()
+wait = input("PAUSING, PRESS ENTER TO CONTINUE...")
 
 
 #-run to steady state
@@ -42,12 +40,13 @@
 bbb.isbcwdt=1
 bbb.dtreal = 1e-14; bbb.itermx=30; bbb.exmain()
 bbb.t_stop=1e0
-bbb.rundt()
+print(rundt)
+rundt.rundt()
 bbb.dtreal=1e20; bbb.isbcwdt=0; bbb.exmain()
 
 
 #-show some results
-plotvar(bbb.te/bbb.ev)
+plotmeshval(bbb.te/bbb.ev)
 
 #-export the solution in hdf5 file
 hdf5_save('mycase.h5')
diff --git a/pyscripts/double.py b/pyscripts/double.py
deleted file mode 100755
index d9c2be74..00000000
--- a/pyscripts/double.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from uedge import *
-
-def uedouble():
-    com.nxleg=2*com.nxleg
-    com.nxcore=2*com.nxcore
-    com.nycore=2*com.nycore
-    com.nysol=2*com.nysol
-    if com.nxomit > 0:
-        if com.geometry=="dnbot":
-            com.nxomit = com.nxleg[0,0]+com.nxcore[0,0] + 2*com.nxxptxx + 1
-        else:
-            com.nxomit=2*(com.nxomit-2*com.nxxptxx) + 2*com.nxxpt  # assumes com.nxomit removes 1/2 SOL
-    if com.nyomitmx == 1: com.nysol = 1
-    if grd.kxmesh == 4:
-        dxgasold=grd.dxgas
-        alfxold=grd.alfx
-        grd.alfx=alfxold/2.
-        grd.dxgas=dxgasold*(exp(grd.alfx)-1)/(exp(alfxold)-1)
-        grd.nxgas=2*grd.nxgas
-    bbb.restart=1
-    bbb.newgeo=1
-    bbb.gengrid=1
-    bbb.isnintp=1
-    grd.ixdstar = com.nxcore[0,1]+1
diff --git a/pyscripts/osfun.py b/pyscripts/osfun.py
deleted file mode 100644
index 0264e1f0..00000000
--- a/pyscripts/osfun.py
+++ /dev/null
@@ -1,17 +0,0 @@
-def date():
-    os.system("date")
-
-def ls(opts=""):
-    os.system("ls " + opts)
-
-def more(fname):
-    os.system("more " + fname)
-
-def pwd():
-    os.system("pwd")
-
-def cp(opts=""):
-    os.system("cp " + opts)
-
-def mv(opts=""):
-    os.system("mv " + opts)
diff --git a/pyscripts/paws.py b/pyscripts/paws.py
deleted file mode 100644
index 72837492..00000000
--- a/pyscripts/paws.py
+++ /dev/null
@@ -1,2 +0,0 @@
-def paws():
-    programPause = raw_input("Press the <ENTER> key to continue...")
diff --git a/pyscripts/rdcontdt.py b/pyscripts/rdcontdt.py
deleted file mode 100755
index 79773ad3..00000000
--- a/pyscripts/rdcontdt.py
+++ /dev/null
@@ -1,251 +0,0 @@
-# This file runs a time-dependent case using dtreal.  First, obtain a converged
-# solution for a (usually small) dtreal; xuedge must report iterm=1 at the end.
-# Then adjust control parameters in rdinitdt; read this file, which reads rdinitdt.
-# If a mistake is made, to restart this file without a Jacobian evaluation,
-# be sure to reset iterm=1 (=> last step was successful)
-
-# IMPORT UEDGE (assuming starting from ipython before any imports)
-from .uedge import *
-from .ruthere import *
-from .uexec import *
-from numpy import zeros
-        
-# IMPORT HDF5 routines for saving solutions below
-from .hdf5 import *
-
-# INITIALIZE PARAMS -- SHOULD BE DONE IN MASTER SCRIPT OR TERMINAL SESSION
-# BEFORE INVOKING THIS SCRIPT
-uexec("uedge.rdinitdt",returns=globals())
-no = 0;yes = 1
-echo = no
-
-# Set precisions of floating point output
-###import print_options
-###print_options.set_float_precision(4)
-
-# Check if successful time-step exists (bbb.iterm=1)
-if (bbb.iterm == 1):
-    print("Initial successful time-step exists")
-    bbb.dtreal = bbb.dtreal*bbb.mult_dt #compensates dtreal divided by mult_dt below
-else:
-    print("*---------------------------------------------------------*")
-    print("Need to take initial step with Jacobian; trying to do here")
-    print("*---------------------------------------------------------*")
-    bbb.icntnunk = 0
-    bbb.exmain()
-    ruthere()
-    bbb.dtreal = bbb.dtreal*bbb.mult_dt #compensates dtreal divided by mult_dt below
-
-if (bbb.iterm != 1):
-    print("*--------------------------------------------------------------*")
-    print("Error: converge an initial time-step first; then retry rdcontdt")
-    print("*--------------------------------------------------------------*")
-    exit()
- 
-nx=com.nx;ny=com.ny;nisp=com.nisp;ngsp=com.ngsp;numvar=bbb.numvar
-isteon=bbb.isteon
-if (i_stor==0):
-   ni_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1,nisp),"d")	# set time storage arrays
-   up_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1,nisp),"d")
-   te_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1),"d")
-   ti_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1),"d")
-   ng_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1,ngsp),"d")
-   tg_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1,ngsp),"d")
-   phi_stor = zeros((bbb.n_stor,nx+1+1,ny+1+1),"d")
-   tim_stor = zeros((bbb.n_stor),"d")
-   dtreal_stor = zeros((bbb.n_stor),"d")
-   nfe_stor = zeros((bbb.n_stor),"l")
-   dt_stor = (bbb.tstor_e - bbb.tstor_s)/(bbb.n_stor - 1)
-
-i_stor = max(i_stor,1)			# set counter for storage arrays
-bbb.dt_tot = max(bbb.dt_tot,0.)
-nfe_tot = max(nfe_tot,0)
-deldt_0 = bbb.deldt
-isdtsf_sav = bbb.isdtsfscal
-
-if (bbb.ipt==1 and bbb.isteon==1): 	# set ipt to te(nx,iysptrx+1) if no user value
-   ipt = bbb.idxte[nx-1,com.iysptrx]  #note: ipt is local, bbb.ipt global
-
-bbb.irev = -1         # forces second branch of irev in ii1 loop below
-if (bbb.iterm == 1):  # successful initial run with dtreal
-   bbb.dtreal = bbb.dtreal/bbb.mult_dt     # gives same dtreal after irev loop
-else:                 # unsuccessful initial run; reduce dtreal
-   bbb.dtreal = bbb.dtreal/(3*bbb.mult_dt) # causes dt=dt/mult_dt after irev loop
-   
-if (bbb.initjac == 0): bbb.newgeo=0
-dtreal_sav = bbb.dtreal
-bbb.itermx = bbb.itermxrdc
-bbb.dtreal = bbb.dtreal/bbb.mult_dt	#adjust for mult. to follow; mult_dt in rdinitdt
-bbb.dtphi = bbb.rdtphidtr*bbb.dtreal
-neq=bbb.neq
-svrpkg=bbb.svrpkg.tostring().strip()
-#
-bbb.ylodt = bbb.yl
-bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
-fnrm_old = sqrt(sum((bbb.yldot[0:neq]*bbb.sfscal[0:neq])**2))
-if (bbb.initjac == 1): fnrm_old=1.e20
-print("initial fnrm =",fnrm_old)
-
-for ii1 in range( 1, bbb.ii1max+1):
-   if (bbb.ismfnkauto==1): bbb.mfnksol = 3
-   # adjust the time-step
-   if (bbb.irev == 0):
-      # Only used after a dt reduc. success. completes loop ii2 for fixed dt
-      bbb.dtreal = min(3*bbb.dtreal,bbb.t_stop)	#first move forward after reduction
-      bbb.dtphi = bbb.rdtphidtr*bbb.dtreal
-      if (bbb.ismfnkauto==1 and bbb.dtreal > bbb.dtmfnk3): bbb.mfnksol = -3
-      bbb.deldt =  3*bbb.deldt
-   else:
-      # either increase or decrease dtreal; depends on mult_dt
-      bbb.dtreal = min(bbb.mult_dt*bbb.dtreal,bbb.t_stop)
-      bbb.dtphi = bbb.rdtphidtr*bbb.dtreal
-      if (bbb.ismfnkauto==1 and bbb.dtreal > bbb.dtmfnk3): bbb.mfnksol = -3
-      bbb.deldt =  bbb.mult_dt*bbb.deldt
-      
-   bbb.dtreal = min(bbb.dtreal,bbb.dt_max)
-   bbb.dtphi = bbb.rdtphidtr*bbb.dtreal
-   if (bbb.ismfnkauto==1 and bbb.dtreal > bbb.dtmfnk3): bbb.mfnksol = -3
-   bbb.deldt = min(bbb.deldt,deldt_0)
-   bbb.deldt = max(bbb.deldt,bbb.deldt_min)
-   nsteps_nk=1
-   print('--------------------------------------------------------------------')
-   print('--------------------------------------------------------------------')
-   print(' ')
-   print('*** Number time-step changes = ',ii1,' New time-step = ', bbb.dtreal)
-   print('--------------------------------------------------------------------')
-
-   bbb.itermx = bbb.itermxrdc
-   if (ii1>1  or  bbb.initjac==1):	# first time calc Jac if initjac=1
-      if (bbb.irev == 1):      # decrease in bbb.dtreal
-         if (bbb.numrev < bbb.numrevjmax and \
-            bbb.numrfcum < bbb.numrevjmax+bbb.numfwdjmax): #dont recom bbb.jac
-            bbb.icntnunk = 1	
-            bbb.numrfcum = bbb.numrfcum + 1
-         else:                          # force bbb.jac calc, reset numrev
-            bbb.icntnunk = 0
-            bbb.numrev = -1		      # yields api.zero in next statement
-            bbb.numrfcum = 0
-         bbb.numrev = bbb.numrev + 1
-         bbb.numfwd = 0
-      else:  # increase in bbb.dtreal
-         if (bbb.numfwd < bbb.numfwdjmax and \
-            bbb.numrfcum < bbb.numrevjmax+bbb.numfwdjmax): 	#dont recomp bbb.jac
-            bbb.icntnunk = 1
-            bbb.numrfcum = bbb.numrfcum + 1
-         else:
-            bbb.icntnunk = 0			#recompute jacobian for increase dt
-            bbb.numfwd = -1
-            bbb.numrfcum = 0
-         bbb.numfwd = bbb.numfwd + 1
-         bbb.numrev = 0			#bbb.restart counter for dt reversals
-      bbb.isdtsfscal = isdtsf_sav
-      bbb.ftol = min(bbb.ftol_dt, 0.01*fnrm_old)
-      bbb.ftol = max(bbb.ftol, bbb.ftol_min)
-      exmain() # take a single step at the present bbb.dtreal
-      ruthere()
-      if (bbb.iterm == 1):
-         bbb.dt_tot = bbb.dt_tot + bbb.dtreal
-         nfe_tot = nfe_tot + bbb.nfe[0,0]
-         bbb.ylodt = bbb.yl
-         bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
-         fnrm_old = sqrt(sum((bbb.yldot[0:neq-1]*bbb.sfscal[0:neq-1])**2))
-         if (bbb.dt_tot>=0.9999999*bbb.t_stop  or  fnrm_old<bbb.ftol_min):
-            print(' ')
-            print('*****************************************************')
-            print('**  SUCCESS: frnm < bbb.ftol; or dt_tot >= t_stop  **')
-            print('*****************************************************')
-            break
-
-   bbb.icntnunk = 1
-   bbb.isdtsfscal = 0
-   for ii2 in range( 1, bbb.ii2max+1): #take ii2max steps at the present time-step
-      if (bbb.iterm == 1):
-         bbb.itermx = bbb.itermxrdc
-         bbb.ftol = min(bbb.ftol_dt, 0.01*fnrm_old)
-         bbb.ftol = max(bbb.ftol, bbb.ftol_min)
-         bbb.exmain()
-         ruthere()
-         if (bbb.iterm == 1):
-            bbb.ylodt = bbb.yl
-            bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
-            fnrm_old = sqrt(sum((bbb.yldot[0:neq-1]*bbb.sfscal[0:neq-1])**2))
-            print("Total time = ",bbb.dt_tot,"; Timestep = ",bbb.dtreal)
-            print("variable index ipt = ",ipt, " bbb.yl[ipt] = ",bbb.yl[ipt])
-            dtreal_sav = bbb.dtreal
-            bbb.dt_tot = bbb.dt_tot + bbb.dtreal
-            nfe_tot = nfe_tot + bbb.nfe[0,0]
-            hdf5_save(savefn)
-            if (bbb.dt_tot>=0.999999999999*bbb.t_stop  or  fnrm_old<bbb.ftol_min):
-               print(' ')
-               print('*****************************************************')
-               print('**  SUCCESS: frnm < bbb.ftol; or dt_tot >= t_stop  **')
-               print('*****************************************************')
-               break
-            print(" ")
-##       Store variables if a storage time has been crossed
-            if (bbb.dt_tot >= dt_stor*i_stor and i_stor<=bbb.n_stor):
-               i_stor1 = i_stor-1
-               ni_stor[i_stor1,:,:,:] = ni
-               up_stor[i_stor1,:,:,:] = up
-               te_stor[i_stor1,:,:] = te
-               ti_stor1[i_stor1,:,:] = ti
-               ng_stor[i_stor1,:,:,:] = ng
-               phi_stor1[i_stor1,:,:] = phi
-               tim_stor[i_stor1] = bbb.dt_tot
-               nfe_stor[i_stor1] = nfe_tot
-               dtreal_stor[i_stor1] = bbb.dtreal
-               i_stor = i_stor + 1
-   ##          End of storage section
-      
-   if (bbb.dt_tot>=bbb.t_stop  or  fnrm_old<bbb.ftol_min): break   # need for both loops
-   bbb.irev = bbb.irev-1
-   if (bbb.iterm != 1):	#print bad eqn, cut dtreal by 3, set irev flag
-            ####### a copy of idtroub script ########################
-      oldecho=echo
-      echo=no
-      # integer ii
-      # real8 ydmax 
-      scalfac = bbb.sfscal
-      if (svrpkg != "nksol"): scalfac = 1/(bbb.yl + 1.e-30)  # for time-dep calc.
-      ydmax = 0.999999999*max(abs(bbb.yldot*scalfac))
-      itrouble = 0
-      for ii in range(neq):
-         if (abs(bbb.yldot[ii]*scalfac[ii]) > ydmax):
-            itrouble=ii
-            print("** Fortran index of trouble making equation is:")
-            print(itrouble+1)
-            break
-      print("** Number of variables is:")
-      print("numvar = ", numvar)
-      print(" ")
-      iv_t = (itrouble).__mod__(numvar) + 1
-      print("** Troublemaker equation is:")
-      print("iv_t = ",iv_t)
-      print(" ")
-      print("** Troublemaker cell (ix,iy) is:")
-      print(bbb.igyl[itrouble,])
-      print(" ")
-      print("** Timestep for troublemaker equation:")
-      print(bbb.dtuse[itrouble])
-      print(" ")
-      print("** yl for troublemaker equation:")
-      print(bbb.yl[itrouble])
-      print(" ")
-      echo=oldecho
-      ######## end of idtroub script ##############################
-
-      if (bbb.dtreal < bbb.dt_kill):
-          print(' ')
-          print('*************************************')
-          print('**  FAILURE: time-step < dt_kill   **')
-          print('*************************************')
-          break
-      bbb.irev = 1
-      print('*** Converg. fails for bbb.dtreal; reduce time-step by 3, try again')
-      print('----------------------------------------------------------------- ')
-      bbb.dtreal = bbb.dtreal/(3*bbb.mult_dt)
-      bbb.dtphi = bbb.rdtphidtr*bbb.dtreal
-      if (bbb.ismfnkauto==1 and bbb.dtreal > bbb.dtmfnk3): bbb.mfnksol = -3
-      bbb.deldt =  bbb.deldt/(3*bbb.mult_dt) 
-      bbb.iterm = 1
-echo = yes
diff --git a/pyscripts/rdinitdt.py b/pyscripts/rdinitdt.py
deleted file mode 100755
index db60867c..00000000
--- a/pyscripts/rdinitdt.py
+++ /dev/null
@@ -1,37 +0,0 @@
-# Setup file to run time-dependently using dtreal
-# Change dtreal for starting dt and savefname to change pfb file name
-# Once variables are set, read rdrundt to execute a time-dependent run
-from uedge import *
-
-i_stor = 0
-nfe_tot = 0
-savefn = "savedt.hdf5"  # name of hdf5 savefile written every timestep
-
-bbb.rdtphidtr = 1e20	# ratio dtphi/dtreal
-bbb.ismfnkauto = 1		# if =1, mfnksol=3 for dtreal<dtmfnk3, otherwise=-3
-bbb.dtmfnk3 = 5.e-4		# dtreal for mfnksol sign change if ismfnkauto=1
-bbb.mult_dt = 3.4		# factor expanding dtreal after ii2max steps
-bbb.ii1max = 500		# number of changes to dtreal
-bbb.ii2max = 5		    # number of timesteps at current dtreal
-bbb.itermxrdc = 7	    # value of itermx used by rdcontdt
-bbb.incpset = 7		    # iterations until Jacobian is recomputed
-bbb.ftol_dt = 1.e-5		# fnrm tolerance for the time-dependent steps
-bbb.ftol_min = 1e-9		# value of fnrm where time advance will stop
-bbb.dt_tot = 0.		    # tot time accumulated for run (output, not input)
-bbb.t_stop = 100.		# value of dt_tot (sec) where calculation will stop
-bbb.dt_max = 100.		# maximum time step for dtreal
-bbb.dt_kill = 1e-14		# min allowed time step; rdcontdt stops if reached
-bbb.deldt_min = 0.04	# minimum relative change allowed for model_dt > 0
-bbb.initjac = 0		    # if=1, calc initial Jac upon reading rdcontdt
-bbb.numrevjmax = 2		# number of dt reductions before Jac recalculated
-bbb.numfwdjmax = 1		# number of dt increases before Jac recalculated
-###bbb.ismmaxuc = 1		   # =1 for intern calc mmaxu; =0,set mmaxu & dont chng
-bbb.irev = -1		    # flag to allow reduced dt advance after cutback
-bbb.rlx = 0.9		    # max. change in variable at each linear iteration
-bbb.itermx = 7	 	    # max. number of linear iterations allowed
-bbb.tstor_s = 1e-5		# beginning time for storing solution
-bbb.tstor_e = 1e-3		# ending time for storing solution
-bbb.n_stor = 0		    # number of linearly spaced storage points
-bbb.ipt = 1		   	    # index of variable; value printed at step
-			            # if ipt not reset from unity, ipt=idxte(nx,iysptrx+1)
-
diff --git a/pyscripts/rundt.py b/pyscripts/rundt.py
index 94085935..2e60512c 100644
--- a/pyscripts/rundt.py
+++ b/pyscripts/rundt.py
@@ -16,35 +16,28 @@
 
 class UeRun():
     ''' Class containing information on run '''
-    def __init__(self, n_stor = False):
-        from time import time
+    def __init__(self, *args, n_stor = False, **kwargs):
         from numpy import array        
         from uedge import bbb, com
         # TODO: Add restore/recover from timeslice
         # TODO: Add plot timeslice directly
         # NOTE: No -> Utilize direct I/O from file instead
-        self.tstart = time()
-        self.numvar = bbb.numvar
-        self.nx = com.nx
-        self.ny = com.ny
-        self.ixpt1 = com.ixpt1[0]
-        self.ixpt2 = com.ixpt2[0]
-        self.iysptrx = com.iysptrx
         self.equationkey = array([b'te', b'ti', b'phi', b'up', b'ni', b'ng', 
             b'tg'])
 
-        self.classvars = ['slice_ni', 'slice_ng', 'slice_up', 'slice_te', 
-            'slice_ti', 'slice_tg', 'slice_phi', 'slice_dttot', 'time', 
-            'fnorm', 'nfe', 'dt_tot', 'dtreal', 'ii1', 'ii2', 'ii1fail', 
-            'ii2fail', 'dtrealfail', 'itrouble', 'troubleeq', 'troubleindex',
-            'ylfail', 'isteon', 'istion', 'isupon', 'isphion', 'isupgon',
-            'isngon', 'istgon', 'ishymol', 'nisp', 'ngsp', 'nhsp', 'nhgsp', 
-            'nzsp', 'b0', 'ncore', 'pcoree', 'pcorei', 'internaleq',
-            'internalspecies', 'yldotsfscalfail']
-
-        # Intiialize all variables to empty lists in class
-        for var in self.classvars:
-            self.__setattr__(var, [])
+        self.setupvars = {}
+        for var in [ 'numvar', 'isteon', 'istion', 'isupon', 'isphion', 
+            'isupgon', 'isngon', 'istgon', 'ishymol', 'nisp', 'ngsp', 'nhsp', 
+            'nhgsp', 'nzsp', 'b0', 'ncore', 'pcoree', 'pcorei', 'nx', 'ny',
+            'iysptrx', 'ixpt1', 'ixpt2', 'neq'
+            ]:
+            try:
+                self.setupvars[var] = getattr(bbb, var)
+            except:
+                self.setupvars[var] = getattr(com, var)
+        self.setupvars['ixpt1'] = self.setupvars['ixpt1'][0]
+        self.setupvars['ixpt2'] = self.setupvars['ixpt2'][0]        
+        super().__init__(*args, **kwargs)
 
     def itroub(self):
         ''' Function that displays information on the problematic equation '''
@@ -58,88 +51,79 @@ def itroub(self):
             'Ion momentum', 'Ion density', 'Gas density', 'Gas temperature']
 
         # Find the fortran index of the troublemaking equation
-        self.neq = bbb.neq
-        self.itrouble.append(deepcopy(argmax(abs(bbb.yldot*\
+        self.classvars['itrouble'].append(deepcopy(argmax(abs(bbb.yldot*\
             bbb.sfscal)[:bbb.neq])+1))
         print("** Fortran index of trouble making equation is:\n{}".format(\
-            self.itrouble[-1]))
+            self.classvars['itrouble'][-1]))
         # Print equation information
         print("** Number of equations solved per cell:\n    numvar = {}\n"\
-            .format(self.numvar))
+            .format(bbb.numvar))
 
-        self.troubleeq.append(mod(self.itrouble[-1]-1, bbb.numvar)+1)
+        self.classvars['troubleeq'].append(mod(self.classvars['itrouble'][-1]-1, bbb.numvar)+1)
 
         species = ''
-        self.internaleq.append([abs(x - self.itrouble[-1]).min() for x in \
+        self.classvars['internaleq'].append([abs(x - self.classvars['itrouble'][-1]).min() for x in \
             self.equations].index(0))
-        if self.equations[self.internaleq[-1]].ndim == 3:
-            self.internalspecies.append( where(\
-                self.equations[self.internaleq[-1]] == self.itrouble[-1])\
+        if self.equations[self.classvars['internaleq'][-1]].ndim == 3:
+            self.classvars['internalspecies'].append( where(\
+                self.equations[self.classvars['internaleq'][-1]] == self.classvars['itrouble'][-1])\
                 [-1][0] + 1)
-            species = ' of species {}'.format(self.internalspecies[-1])
+            species = ' of species {}'.format(self.classvars['internalspecies'][-1])
         else:
-            self.internalspecies.append(0)
+            self.classvars['internalspecies'].append(0)
 
 
         print('** Troublemaker equation is:\n{} equation{}: iv_t={}\n'\
-            .format(equationsdescription[self.internaleq[-1]], species, 
-            self.troubleeq[-1]))
+            .format(equationsdescription[self.classvars['internaleq'][-1]], species, 
+            self.classvars['troubleeq'][-1]))
 
         # Display additional information about troublemaker cell
-        self.troubleindex.append(deepcopy(bbb.igyl[self.itrouble[-1]-1,]))
-        self.dtrealfail.append(deepcopy(bbb.dtreal))
-        self.ylfail.append(deepcopy(bbb.yl[self.itrouble[-1]-1]))
-        self.yldotsfscalfail.append(deepcopy((bbb.yldot*bbb.sfscal)\
-            [self.itrouble[-1]-1]))
+        self.classvars['troubleindex'].append(deepcopy(bbb.igyl[self.classvars['itrouble'][-1]-1,]))
+        self.classvars['dtrealfail'].append(deepcopy(bbb.dtreal))
+        self.classvars['ylfail'].append(deepcopy(bbb.yl[self.classvars['itrouble'][-1]-1]))
+        self.classvars['yldotsfscalfail'].append(deepcopy((bbb.yldot*bbb.sfscal)\
+            [self.classvars['itrouble'][-1]-1]))
         print('** Troublemaker cell (ix,iy) is:\n' + \
-            '{}\n'.format(self.troubleindex[-1]))
+            '{}\n'.format(self.classvars['troubleindex'][-1]))
         print('** Timestep for troublemaker equation:\n' + \
-            '{:.4e}\n'.format(self.dtrealfail[-1]))
+            '{:.4e}\n'.format(self.classvars['dtrealfail'][-1]))
         print('** yl for troublemaker equation:\n' + \
-            '{:.4e}\n'.format(self.ylfail[-1]))
-        print('** yl*sfscal for troublemaker equation:\n' + \
-            '{:.4e}\n'.format(self.yldotsfscalfail[-1]))
+            '{:.4e}\n'.format(self.classvars['ylfail'][-1]))
+        print('** yldot*sfscal for troublemaker equation:\n' + \
+            '{:.4e}\n'.format(self.classvars['yldotsfscalfail'][-1]))
     
-    def savesuccess(self, ii1, ii2, savedir, savename, fnrm=None):
+    def savesuccess(self, savename, fnrm=None):
         from time import time
         from uedge import bbb
         from copy import deepcopy
 
-        self.time.append(time())
-        if fnrm is None:
-            bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
-            self.fnorm.append(deepcopy((sum((bbb.yldot[:bbb.neq]*\
-                bbb.sfscal[:bbb.neq])**2))**0.5))
-        else:
-            self.fnorm.append(fnrm)
-        self.nfe.append(deepcopy(bbb.nfe))
-        self.dt_tot.append(deepcopy(bbb.dt_tot))
-        self.dtreal.append(deepcopy(bbb.dtreal))
-        self.ii1.append(ii1)
-        self.ii2.append(ii2)
-        self.neq = bbb.neq
         try:
-            self.save('{}_UeCase.hdf5'.format(savefname.split('.')[0]))
+            self.classvars['time'].append(time())
         except:
             pass
-
-        self.save_intermediate(savedir, savename)
+        if 'fnorm' in self.classvars.keys():
+            if fnrm is None:
+                bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
+                self.classvars['fnorm'].append(deepcopy((sum((bbb.yldot[:bbb.neq]*\
+                    bbb.sfscal[:bbb.neq])**2))**0.5))
+            else:
+                self.classvars['fnorm'].append(fnrm)
+        for var in ['nfe', 'dt_tot', 'dtreal']:
+            if var in self.classvars:
+                self.classvars[var].append(deepcopy(getattr(bbb, var)))
+        self.save_intermediate(savename)
 
     def store_timeslice(self):
         from copy import deepcopy
         from uedge import bbb
 
-        self.slice_ni.append(deepcopy(bbb.ni))
-        self.slice_ng.append(deepcopy(bbb.ng))
-        self.slice_up.append(deepcopy(bbb.up))
-        self.slice_te.append(deepcopy(bbb.te))
-        self.slice_ti.append(deepcopy(bbb.ti))
-        self.slice_tg.append(deepcopy(bbb.tg))
-        self.slice_phi.append(deepcopy(bbb.phi))
-        self.slice_dttot.append(deepcopy(bbb.dt_tot))
+        for var in ['ni', 'ng', 'up', 'te', 'ti', 'tg', 'phi', 'dt_tot']:
+            self.classvars['slice_{}'.format(var)].append(deepcopy(getattr(bbb, var)))
+
 
-    def save_intermediate(self, savedir, savename):
+    def save_intermediate(self, savename):
         from uedge.hdf5 import hdf5_save
+        from os.path import exists
         from uedge import bbb, com
         from h5py import File
 
@@ -149,56 +133,39 @@ def save_intermediate(self, savedir, savename):
         for var in [ 'nisp', 'ngsp', 'nhsp', 'nhgsp', 'nzsp']:
             self.__setattr__(var, com.__getattribute__(var))
 
-        try:
-            hdf5_save('{}/{}_last_ii2.hdf5'.format(savedir,savename))
-        except:
+
+
+        if not exists('/'.join(savename.split('/')[:-1])):
             print('Folder {} not found, saving output to cwd...'\
-                .format(savedir))
-            hdf5_save('{}_last_ii2.hdf5'.format(savename))
+                .format(savename.split('/')[0]))
+            hdf5_save(savename)
+            
+    
 
-        # Try to store ready-made Case-file, if possible
         try:
-            self.save('{}/{}_last_ii2_Case.hdf5'.format(savedir,savename))
+            self.save(savename)#.replace('.hdf5', '_UeCase.hdf5'))
         except:
-            pass
+            hdf5_save(savename)
 
-        try:
-            file = File('{}/{}_last_ii2.hdf5'.format(savedir, savename), 'r+')
-        except:
-            file = File('{}_last_ii2.hdf5'.format(savename), 'r+')
-
-        file.require_group('convergence')
-        group = file['convergence']
-        group.create_dataset('t_start', data=self.tstart)
-        group.create_dataset('numvar', data=self.numvar)
-        group.create_dataset('neq', data=self.neq)
-        group.create_dataset('nx', data=self.nx)
-        group.create_dataset('ny', data=self.ny)
-        group.create_dataset('ixpt1', data=self.ixpt1)
-        group.create_dataset('ixpt2', data=self.ixpt2)
-        group.create_dataset('iysptrx', data=self.iysptrx)
-        group.create_dataset('equationkey', data=self.equationkey)
-        group.create_dataset('itermx', data=self.itermx)
-        group.create_dataset('incpset', data=self.incpset)
-        group.create_dataset('ii1max', data=self.ii1max)
-        group.create_dataset('ii2max', data=self.ii1max)
-        group.create_dataset('numrevjmax', data=self.numrevjmax)
-        group.create_dataset('numfwdjmax', data=self.numfwdjmax)
-        group.create_dataset('numtotjmax', data=self.numtotjmax)
-        group.create_dataset('rdtphidtr', data=self.rdtphidtr)
-        group.create_dataset('deldt_min', data=self.deldt_min)
-        group.create_dataset('rlx', data=self.rlx)
-
-        for var in self.classvars:
-            group.create_dataset(var, data=self.__getattribute__(var))
-
-        file.close()
-    
-    def convergenceanalysis(savefname, savedir='../solutions', fig=None,
+        with File(savename, 'r+') as file:
+            file.require_group('convergence')
+            group = file['convergence']
+            group.create_dataset('t_start', data=self.tstart)
+            group.create_dataset('equationkey', data=self.equationkey)
+            for var, value in self.setupvars.items():
+                group.create_dataset(var, data=value)
+            for var, value in self.classsetup.items():
+                group.create_dataset(var, data=value)
+            for var in self.classvars:
+                group.create_dataset(var, data=self.classvars[var])
+        print('Intermediate solution written to {}'.format(savename))
+
+    def convergenceanalysis(self, savefname, fig=None,
         xaxis = 'exmain', logx = False, color='k', label=None,
         ylim = (None, None)):
         from h5py import File
         from matplotlib.pyplot import subplots
+        from os.path import exists
         from datetime import timedelta
         from matplotlib.ticker import FuncFormatter
         from numpy import cumsum, ones
@@ -210,49 +177,49 @@ def convergenceanalysis(savefname, savedir='../solutions', fig=None,
                 print('Three subplots required for plots! Aborting...')
                 return
             f = fig
-        try:
-            file = File('{}/{}'.format(savedir, savefname), 'r')
-        except:
-            print('File {}/{} not found. Aborting!'.format(savedir, 
-                savefname))
+
+        if not exists(savefname):
+            print('File {} not found. Aborting!'.format(savefname))
             return
-        data = file['convergence']
-        try:
+
+        with File(savefname, 'r') as file:
             data = file['convergence']
-        except:
-            print('Convergence data not found in {}/{}. Aborting!'.format(\
-                savedir, savefname))
-            return
-        
-        if xaxis == 'exmain':
-            xlabel = 'Exmain calls'
-            xones = ones(data['ii2'][()].shape)
-            x = cumsum(xones)
-        elif xaxis == 'nfe':
-            xlabel = 'nfe internal iterations'
-            x = cumsum(data['nfe'][()][:, 0, 0])
-        elif xaxis == 'time':
-            xlabel = 'Total wall-clock time [HH:MM]'
-            x = [timedelta(t - data['t_start'][()]) for t in data['time'][()]]
-            x = data['time'][()] - data['t_start'][()]
+            try:
+                data = file['convergence']
+            except:
+                print('Convergence data not found in {}. Aborting!'.format(\
+                    savefname))
+                return
             
-        if logx is True:
-            ax[0].loglog(x, data['fnorm'][()], '-', color=color, label=label)
-            ax[1].loglog(data['dt_tot'][()], data['fnorm'][()], '-', 
-                color=color, label=label)
-            ax[2].loglog(x, data['dtreal'][()], '-', color=color, label=label)
-        else:
-            ax[0].semilogy(x, data['fnorm'][()], '-', color=color, label=label)
-            ax[1].semilogy(data['dt_tot'][()], data['fnorm'][()], '-', 
-                color=color, label=label)
-            ax[2].semilogy(x, data['dtreal'][()], '-', color=color, 
-                label=label)
+            if xaxis == 'exmain':
+                xlabel = 'Exmain calls'
+                xones = ones(data['ii2'][()].shape)
+                x = cumsum(xones)
+            elif xaxis == 'nfe':
+                xlabel = 'nfe internal iterations'
+                x = cumsum(data['nfe'][()][:, 0, 0])
+            elif xaxis == 'time':
+                xlabel = 'Total wall-clock time [HH:MM]'
+                x = [timedelta(t - data['t_start'][()]) for t in data['time'][()]]
+                x = data['time'][()] - data['t_start'][()]
+                
+            if logx is True:
+                ax[0].loglog(x, data['fnorm'][()], '-', color=color, label=label)
+                ax[1].loglog(data['dt_tot'][()], data['fnorm'][()], '-', 
+                    color=color, label=label)
+                ax[2].loglog(x, data['dtreal'][()], '-', color=color, label=label)
+            else:
+                ax[0].semilogy(x, data['fnorm'][()], '-', color=color, label=label)
+                ax[1].semilogy(data['dt_tot'][()], data['fnorm'][()], '-', 
+                    color=color, label=label)
+                ax[2].semilogy(x, data['dtreal'][()], '-', color=color, 
+                    label=label)
+            ax[1].set_title('Total exmain evaluations: {}'.format\
+                (len(data['dtreal'][()])))
 
         ax[0].set_xlabel(xlabel)
         ax[1].set_xlabel('Accumulated plasma simualtion time [s]')
         ax[2].set_xlabel(xlabel)
-        ax[1].set_title('Total exmain evaluations: {}'.format\
-            (len(data['dtreal'][()])))
         ax[0].set_ylabel('Initial fnorm')
         ax[1].set_ylabel('Initial fnorm')
         ax[2].set_ylabel('Time-step (dtreal) [s]')
@@ -269,105 +236,169 @@ def convergenceanalysis(savefname, savedir='../solutions', fig=None,
         return f
 
 
-    def failureanalysis(savefname, savedir='../solutions', equation=None):
+    def failureanalysis(self, savefname, equation=None, N=slice(None), geometry=False):
         from h5py import File
+        from os.path import exists
         from matplotlib.pyplot import subplots
         from numpy import histogram, zeros
         from matplotlib.collections import PolyCollection
         
-        f, ax = subplots(2,1, figsize=(10, 7))
-        try:
-            file = File('{}/{}'.format(savedir, savefname), 'r')
-        except:
-            print('File {}/{} not found. Aborting!'.format(savedir, 
-                savefname))
-        try:
-            data = file['convergence']
-        except:
-            print('Convergence data not found in {}/{}. Aborting!'.format(\
-                savedir, savefname))
+        # TODO: add option for plotting offending cell on geometric grid
+        if geometry is True:
+            f, ax = subplots(1,2, figsize=(12, 8), 
+                gridspec_kw={'width_ratios': [1, 1.2]})
+            f.subplots_adjust(top=0.98)
+        else:
+            f, ax = subplots(2,1, figsize=(10, 7))
+
+        if not exists(savefname):
+            print('File {} not found. Aborting!'.format(savefname))
             return
+        
+        with File(savefname, 'r') as file:
+            try:
+                data = file['convergence']
+            except:
+                print('Convergence data not found in {}. Aborting!'.format(\
+                    savefname))
+                return
 
-        if equation is not None:
-            iequation = [x.decode('UTF-8') for x in data['equationkey']]\
-                .index(equation)
-        # Bin the equation errors
-        nspecies = 1/(data['nisp'][()] + 1)
-        nbins = 7*data['nisp'][()]
-        counts, bins = histogram((data['internaleq'][()]+\
-            data['internalspecies']*nspecies)-0.5, bins=nbins, 
-            range=(-0.5,6.5))
-        h, e = histogram(data['internaleq'][()] - 0.5, bins=7, 
-            range=(-0.5,6.5))
-        ax[0].bar([x for x in range(7)], h, width=1, edgecolor='k',
-            color=(0, 87/255, 183/255))
-        ax[0].hist(bins[3*data['nisp'][()]:-1], bins[3*data['nisp'][()]:], 
-            weights=counts[3*data['nisp'][()]:], edgecolor='k', 
-            color=(255/255, 215/255, 0))
-        ax[0].set_xticks(range(7))
-        ax[0].set_xticklabels([x.decode('UTF-8') for x in \
-            data['equationkey'][()]])
-        ax[0].grid(linestyle=':', linewidth=0.5, axis='y')
-        ax[0].set_xlim((-0.5,6.5))
-        ax[0].set_ylabel('Counts')
-        for i in range(7):
-            ax[0].axvline(i-0.5, linewidth=1, color='k')
-
-        # Visualize error locations
-        nx = data['nx'][()]        
-        ny = data['ny'][()]        
-        ixpt1 = data['ixpt1'][()]
-        ixpt2 = data['ixpt2'][()]
-        iysptrx = data['iysptrx'][()]
-        frequency = zeros((nx+2, ny+2))
-
-        cells = []
-        for i in range(nx+2):
-            for j in range(ny+2):
-                cells.append([[i-.5, j-.5], [i+.5, j-.5], 
-                    [i+.5, j+.5], [i-.5, j+.5]])
-
-        polys = PolyCollection(cells, edgecolors='k', linewidth=0.5, 
-            linestyle=':')
-            
-        for i in range(len(data['itrouble'])):
-            coord = data['troubleindex'][()][i]
-            if equation is None:
-                frequency[coord[0], coord[1]] += 1
-            elif iequation == data['internaleq'][()][i]:
-                frequency[coord[0], coord[1]] += 1
-
-        polys.set_cmap('binary')
+            if equation is not None:
+                iequation = [x.decode('UTF-8') for x in data['equationkey']]\
+                    .index(equation)
+            # Bin the equation errors
+            nspecies = 1/(data['nisp'][()] + 1)
+            nbins = 7*data['nisp'][()]
+            counts, bins = histogram((data['internaleq'][N]+\
+                data['internalspecies'][N]*nspecies)-0.5, bins=nbins, 
+                range=(-0.5,6.5))
+            h, e = histogram(data['internaleq'][N] - 0.5, bins=7, 
+                range=(-0.5,6.5))
+            ax[0].bar([x for x in range(7)], h, width=1, edgecolor='k',
+                color=(0, 87/255, 183/255))
+            ax[0].hist(bins[3*data['nisp'][()]:-1], bins[3*data['nisp'][()]:], 
+                weights=counts[3*data['nisp'][()]:], edgecolor='k', 
+                color=(255/255, 215/255, 0))
+            ax[0].set_xticks(range(7))
+            ax[0].set_xticklabels([x.decode('UTF-8') for x in \
+                data['equationkey'][()]])
+            ax[0].grid(linestyle=':', linewidth=0.5, axis='y')
+            ax[0].set_xlim((-0.5,6.5))
+            ax[0].set_ylabel('Counts')
+            for i in range(7):
+                ax[0].axvline(i-0.5, linewidth=1, color='k')
+
+            # Visualize error locations
+            nx = data['nx'][()]        
+            ny = data['ny'][()]        
+            ixpt1 = data['ixpt1'][()]
+            ixpt2 = data['ixpt2'][()]
+            iysptrx = data['iysptrx'][()]
+            frequency = zeros((nx+2, ny+2))
+
+            cells = []
+            if geometry is True:
+                try:
+                    rm = file['grid/com/rm'][()] 
+                    zm = file['grid/com/zm'][()] 
+                except:
+                    raise KeyError('Grid data not found in {}'.format(\
+                        savefname))
+                for i in range(nx+2):
+                    for j in range(ny+2):
+                        cell = []
+                        for k in [1, 2, 4, 3]:
+                            cell.append((rm[i, j, k], zm[i, j, k]))
+                        cells.append(cell)
+            else:
+                for i in range(nx+2):
+                    for j in range(ny+2):
+                        cells.append([[i-.5, j-.5], [i+.5, j-.5], 
+                            [i+.5, j+.5], [i-.5, j+.5]])
+
+            polys = PolyCollection(cells, edgecolors='k', 
+                linewidth=0.5-0.45*geometry, linestyle=':')
+                
+            for i in range(len(data['itrouble'][N])):
+                coord = data['troubleindex'][N][i]
+                if equation is None:
+                    frequency[coord[0], coord[1]] += 1
+                elif iequation == data['internaleq'][N][i]:
+                    frequency[coord[0], coord[1]] += 1
+
+        if geometry is False:
+            polys.set_cmap('binary')
+        else:
+            polys.set_cmap('binary')
         polys.set_array(frequency.reshape(((nx+2)*(ny+2),)))
 
         cbar = f.colorbar(polys, ax=ax[1])
         cbar.ax.set_ylabel('N trouble'+' for {}'.format(equation)*\
             (equation is not None), va='bottom', labelpad=20)
 
-        ax[1].plot([.5, nx+.5, nx+.5, .5, .5], [.5, .5, ny+.5, ny+.5, .5], 
-            'k-', linewidth=1)
 
         ax[1].set_xlabel('Poloidal index')
         ax[1].set_ylabel('Radial index')
         ax[1].add_collection(polys)
-        ax[1].plot([.5, nx+.5],[iysptrx+.5, iysptrx+.5], 'k-', 
-            linewidth=1)
-        ax[1].plot([ixpt1+.5, ixpt1+.5], [.5, iysptrx+.5], 'k-', 
-            linewidth=1)
-        ax[1].plot([ixpt2+.5, ixpt2+.5], [.5, iysptrx+.5], 'k-', 
-            linewidth=1)
-
-        file.close()
+        if geometry is False:
+            ax[1].plot([.5, nx+.5, nx+.5, .5, .5], [.5, .5, ny+.5, ny+.5, .5], 
+                'k-', linewidth=1)
+            ax[1].plot([.5, nx+.5],[iysptrx+.5, iysptrx+.5], 'k-', 
+                linewidth=1)
+            ax[1].plot([ixpt1+.5, ixpt1+.5], [.5, iysptrx+.5], 'k-', 
+                linewidth=1)
+            ax[1].plot([ixpt2+.5, ixpt2+.5], [.5, iysptrx+.5], 'k-', 
+                linewidth=1)
+        else:
+            ax[1].set_aspect('equal')
+            ax[1].set_ylim((0.95*zm.min(), 1.05*zm.max()))
+            ax[1].set_xlim((0.95*rm.min(), 1.05*rm.max()))
+
         return f
 
 
+    def restorevalues(self):
+        ''' Restores the original UEDGE values '''
+        from uedge import bbb
+        for key, value in self.orig.items():
+            bbb.__setattr__(key, value)
+
+    def exmain_isaborted(self):
+        ''' Checks if abort is requested '''
+        from uedge import bbb
+        bbb.exmain()
+        # Abort flag set, abort case
+        if bbb.exmain_aborted == 1: 
+            # Reset flag
+            bbb.exmain_aborted == 0 
+            # Restore parameters modified by script
+            try:
+                self.restorevalues(self)
+            except:
+                self.restorevalues()
+            return True
+
+    def message(self, string, separator='-', pad='', seppad = '', 
+        nseparator=1):
+        ''' Prints formatted self.message to stdout '''
+        # TODO: add formatting for len>75 strings
+        msg = pad.strip() + ' ' + string.strip() + ' ' + pad.strip()
+        for i in range(nseparator):
+            print(seppad + separator*(len(msg)-2*len(seppad)) + seppad)
+        print(msg)
+        print(seppad + separator*(len(msg)-2*len(seppad)) + seppad)
+
+
+
 
     def converge(self, dtreal=2e-9, ii1max=5000, ii2max=5, itermx=7, ftol=1e-5,
         dt_kill=1e-14, t_stop=100, dt_max=100, ftol_min = 1e-9, incpset=7,
         n_stor=0, storedist='lin', numrevjmax=2, numfwdjmax=1, numtotjmax=0, 
         tstor=(1e-3, 4e-2), ismfnkauto=True, dtmfnk3=5e-4, mult_dt=3.4, 
-        reset=True, initjac=False, rdtphidtr=1e20, deldt_min=0.04, rlx=0.9,
-        tsnapshot=None, savedir='../solutions', ii2increase=0):
+        reset=True, initjac=True, rdtphidtr=1e20, deldt_min=0.04, rlx=0.9,
+
+        tsnapshot=None, savedir='../solutions', ii2increase=0, savefname=None,
+        message=None):
 
         ''' Converges the case by increasing dt 
         dtreal : float [1e-9]
@@ -438,8 +469,11 @@ def converge(self, dtreal=2e-9, ii1max=5000, ii2max=5, itermx=7, ftol=1e-5,
         from numpy import linspace, logspace, log10, append
         from copy import deepcopy
         from uedge import bbb
+        from time import time
         from os.path import exists
 
+        self.tstart = time()
+        # TODO: add kwarg savename
 
         # Check if requested save-directory exists: if not, write to cwd
         if not exists(savedir):
@@ -447,68 +481,52 @@ def converge(self, dtreal=2e-9, ii1max=5000, ii2max=5, itermx=7, ftol=1e-5,
                 savedir))
             savedir = '.'        
 
+        if savefname is None:
+            autoname = True
+            try:
+                savefname = self.casename
+            except:
+                savefname = 'dtrun'
+        else:
+            autoname = False
+        
+        savefname = '{}/{}'.format(savedir, savefname)
 
-        self.orig = {}
-        self.orig['itermx'] = deepcopy(bbb.itermx)
-        self.orig['dtreal'] = deepcopy(bbb.dtreal)
-        self.orig['icntnunk'] = deepcopy(bbb.icntnunk)
-        self.orig['ftol'] = deepcopy(bbb.ftol)
-        self.orig['mfnksol'] = deepcopy(bbb.mfnksol)
-        self.orig['rlx'] = deepcopy(bbb.rlx)
-        self.orig['deldt'] = deepcopy(bbb.deldt)
-        self.orig['isdtsfscal'] = deepcopy(bbb.isdtsfscal)
-        self.orig['incpset'] = deepcopy(bbb.incpset)
+        if autoname is True:
+            if exists('{}_last_ii2.hdf5'.format(savefname)):
+                i = 2
+                while exists('{}_{}_last_ii2.hdf5'.format(savefname, i)):
+                    i += 1
+                savefname = '{}_{}'.format(savefname, i)
+        savefname = '{}_last_ii2.hdf5'.format(savefname)
+             
+        self.classvars = {}
+        for  var in ['slice_ni', 'slice_ng', 
+            'slice_up', 'slice_te', 'slice_ti', 'slice_tg', 'slice_phi', 
+            'slice_dt_tot', 'time', 'fnorm', 'nfe', 'dt_tot', 'dtreal', 'ii1', 
+            'ii2', 'ii1fail', 'ii2fail', 'dtrealfail', 'itrouble', 'troubleeq',
+            'troubleindex', 'ylfail', 'internaleq', 'internalspecies', 
+            'yldotsfscalfail']:
+            self.classvars[var] = []
 
+        self.orig = {}
+        for var in ['itermx', 'dtreal', 'icntnunk', 'ftol', 'mfnksol', 'rlx',
+            'deldt', 'isdtsfscal', 'incpset']:
+            self.orig[var] = deepcopy(getattr(bbb, var))
         if numtotjmax == 0:
             numtotjmax = numrevjmax + numfwdjmax
-
-
-        self.itermx = itermx
-        self.incpset = incpset
-        self.ii1max = ii1max
-        self.ii2max = ii2max
-        self.numrevjmax = numrevjmax
-        self.numfwdjmax = numfwdjmax
-        self.numtotjmax = numtotjmax
-        self.rdtphidtr = rdtphidtr
-        self.deldt_min = deldt_min
-        self.rlx = rlx
-
+        self.classsetup = {}
+        for var in ['itermx', 'incpset', 'ii1max', 'ii2max', 'numrevjmax',
+            'numfwdjmax', 'numtotjmax', 'rdtphidtr', 'deldt_min', 'rlx']:
+            self.classsetup[var] = locals()[var]
 # TODO: Add variable to control reduciton factor?
 # TODO: Should dtreal = min(x, t_stop) actually be t_stop or dt_max?
 
-        def restorevalues(self):
-            ''' Restores the original UEDGE values '''
-            for key, value in self.orig.items():
-                bbb.__setattr__(key, value)
-
-        def message(string, separator='-', pad='', seppad = '', 
-            nseparator=1):
-            ''' Prints formatted message to stdout '''
-            # TODO: add formatting for len>75 strings
-            message = pad.strip() + ' ' + string.strip() + ' ' + pad.strip()
-            for i in range(nseparator):
-                print(seppad + separator*(len(message)-2*len(seppad)) + seppad)
-            print(message)
-            print(seppad + separator*(len(message)-2*len(seppad)) + seppad)
-
         def scale_timestep(scaling):
             ''' Increases/decreases time-step ''' 
             bbb.dtreal *= scaling
 
-        def exmain_isaborted(self):
-            ''' Checks if abort is requested '''
-            from uedge import bbb
-            bbb.exmain()
-            # Abort flag set, abort case
-            if bbb.exmain_aborted == 1: 
-                # Reset flag
-                bbb.exmain_aborted == 0 
-                # Restore parameters modified by script
-                restorevalues(self)
-                return True
-
-        def issuccess(self, t_stop, ftol_min):
+        def issuccess(self, t_stop, ftol_min, savefname):
             ''' Checks if case is converged '''
             from datetime import timedelta
             from time import time
@@ -518,25 +536,32 @@ def issuccess(self, t_stop, ftol_min):
                 bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
                 self.fnrm_old = sum((bbb.yldot[:bbb.neq-1]*\
                     bbb.sfscal[:bbb.neq-1])**2)**0.5
-                self.savesuccess(ii1, ii2, savedir, bbb.label[0].strip(\
-                    ).decode('UTF-8'), self.fnrm_old)
+                self.savesuccess(savefname,
+                    #bbb.label[0].strip(\).decode('UTF-8'), 
+                    self.fnrm_old)
                 if (bbb.dt_tot>=t_stop  or  self.fnrm_old<ftol_min):
                     print('')
-                    message('SUCCESS: ' + 'fnrm < bbb.ftol'\
+                    self.message('SUCCESS: ' + 'fnrm < bbb.ftol'\
                         *(self.fnrm_old<ftol_min) + \
                         'dt_tot >= t_stop'*(bbb.dt_tot >= t_stop), pad='**', 
                         separator='*')
                     print('Total runtime: {}'.format(timedelta(
                         seconds=round(time()-self.tstart))))
-                    restorevalues(self)
+                    try:
+                        self.restorevalues(self)
+                    except:
+                        self.restorevalues()
                     return True
     
         def isfail(dt_kill):
             ''' Checks whether to abandon case '''
             if (bbb.dtreal < dt_kill):
-                message('FAILURE: time-step < dt_kill', pad='**', 
+                self.message('FAILURE: time-step < dt_kill', pad='**', 
                 separator='*')
-                restorevalues(self)
+                try:
+                    self.restorevalues(self)
+                except:
+                    self.restorevalues()
                 return True
 
         def setmfnksol(ismfnkauto, dtmfnk3):
@@ -570,22 +595,29 @@ def calc_fnrm():
         bbb.rlx = rlx
         bbb.dtreal = dtreal
         bbb.ftol = ftol
+        ii1 = 0
+        ii2 = 0
         if (bbb.iterm == 1) and (bbb.ijactot > 0):
-            message('Initial successful time-step exists', separator='')
+            self.message('Initial successful time-step exists', separator='')
         else:
-            message('Need to take initial step with Jacobian; ' + \
+            self.message('Need to take initial step with Jacobian; ' + \
                 'trying to do here', seppad='*')
             # Ensure time-step is taken
             bbb.icntnunk = 0
+            if message is not None:
+                print(message)
             # Take timestep and see if abort requested
-            if exmain_isaborted(self):
+            if self.exmain_isaborted():
                 return
             # Increase time
             # Verify time-step was successful
             if (bbb.iterm != 1):
-                restorevalues(self)
-                message('Error: converge an initial time-step first; then ' + \
-                    're-execute command', seppad='*')
+                try:
+                    self.restorevalues(self)
+                except:
+                    self.restorevalues()
+                self.message('Error: converge an initial time-step first; '
+                    'then re-execute command', seppad='*')
                 return
         bbb.incpset = incpset
         bbb.itermx = itermx
@@ -626,7 +658,7 @@ def calc_fnrm():
             bbb.dtreal = min([bbb.dtreal, dt_max]) 
             bbb.dtphi = rdtphidtr*bbb.dtreal
             bbb.deldt =  min([bbb.deldt, deldt_0, deldt_min])
-            message('Number of time-step changes = ''{} New time-step: {:.2E}\n'\
+            self.message('Number of time-step changes = ''{} New time-step: {:.2E}\n'\
                 .format((ii1+1), bbb.dtreal), pad='***', nseparator=1)
 
             # Enter for every loop except first, unless intijac == True
@@ -659,9 +691,14 @@ def calc_fnrm():
                 # Dynamically decrease ftol as the initial ftol decreases
                 bbb.ftol = max(min(ftol, 0.01*self.fnrm_old),ftol_min)
                 # Take timestep and see if abort requested
-                if exmain_isaborted(self):
+                if message is not None:
+                    print(message)
+                if self.exmain_isaborted():
                     return
-                if issuccess(self, t_stop, ftol_min):
+                if bbb.iterm == 1:
+                    self.classvars['ii1'].append(ii1)
+                    self.classvars['ii2'].append(ii2)
+                if issuccess(self, t_stop, ftol_min, savefname):
                     return
             bbb.icntnunk = 2
             bbb.isdtsfscal = 0
@@ -673,13 +710,18 @@ def calc_fnrm():
                 if (bbb.iterm == 1):
                     bbb.ftol = max(min(ftol, 0.01*self.fnrm_old),ftol_min)
                     # Take timestep and see if abort requested
-                    message("Inner iteration #{}".format(ii2+1), nseparator=0,
+                    self.message("Inner iteration #{}".format(ii2+1), nseparator=0, 
                         separator='')
-                    if exmain_isaborted(self):
+                    if message is not None:
+                        print(message)
+                    if self.exmain_isaborted():
                         return
-                    if issuccess(self, t_stop, ftol_min):
+                    if bbb.iterm == 1:
+                        self.classvars['ii1'].append(ii1)
+                        self.classvars['ii2'].append(ii2)
+                    if issuccess(self, t_stop, ftol_min, savefname):
                         return
-                    message("Total time = {:.4E}; Timestep = {:.4E}".format(\
+                    self.message("Total time = {:.4E}; Timestep = {:.4E}".format(\
                         bbb.dt_tot-bbb.dtreal,bbb.dtreal), nseparator=0, 
                         separator='')
 # TODO: replace with more useful information
@@ -702,19 +744,528 @@ def calc_fnrm():
                 self.itroub()
                 ''' ISFAIL '''
                 if isfail(dt_kill):
-                    self.save_intermediate(savedir, bbb.label[0].strip()\
-                        .decode('UTF-8'))
+                    self.save_intermediate(savefname)
+#                        bbb.label[0].strip().decode('UTF-8'))
                     break
                 irev = 1
-                message('Converg. fails for bbb.dtreal; reduce time-step by '+\
+                self.message('Converg. fails for bbb.dtreal; reduce time-step by '+\
                     '3, try again', pad = '***', nseparator=0)
                 scale_timestep(1/(3*mult_dt))
                 bbb.dtphi = rdtphidtr*bbb.dtreal
                 bbb.deldt *=  1/(3*mult_dt) 
                 setmfnksol(ismfnkauto, dtmfnk3)
 #                bbb.iterm = 1
-#        bbb.iterm = -1 # Ensure subsequent repetitions work as intended
+        # ii1max iterations completed without convergence
+        # Indicate solver failure regardless of whether last solve was completer
+        # or not.
+        bbb.iterm = -1 # Ensure subsequent repetitions work as intended
+        # Return False to signal fail
+        return False
+
+
+    def continuation_solve(self, 
+        var, 
+        target=None, 
+        savedir=None,
+        index=None, 
+        dt=0.02,
+        dtreal=1e-5, 
+        ftol=1e-5,
+        iicont_max=7,
+        iicont_fail_max=3,
+        cutoff=1e6,
+        itermx=5,
+        incpset=8,
+        initres=1000,
+        deltafac=2,
+        dtdeltafac=2,
+        staticiter_max=3,
+        dtlim=1e4,
+        ii1max=150,
+        saveres=7,
+        **kwargs):
+        """ Solves var up to target using continuation method
+        var - string for variable, or nested dict of variables and targets
+                If nested dict, top level is variable name and subdict contains
+                keys 'target' and optionally 'index'. These values override the 
+                kwargs of the solver. If index is not set, defaults to None
+        target - target value for variable
+        index - tuple containing index of var if var is array.
+                In case of extended array slicing, e.g. setting ranges of
+                var, index must be defined as tuples of indices and/or 
+                slice objects. E.g. to set var[1:4,:,0], one would use
+                index = (slice(1,4), slice(None), 0). If ranges of var is
+                set, ensure target has the matching, appropriate dimensions
+                or is a float
+        dt - time-step used when solving using continuation
+        staticiter_max - maximum consequtive static iterations before callong 
+                time-depenent run
+        dtreal - time-step used when resorting to time-dependent solve
+        ftol - ftol to be attained
+        iicont_max - iterations in continuation loop
+        iicont_fail_max - max fails in continuation loop before going time-dependent
+        cutoff - cutoff value for required interations at current delta to attain target
+        itermx - max number of iterations to take within time-step
+        incpset - max iterations before re-calculating jacobian
+        initres - inital resolution, i.e. delta = target-var/initres
+        deltafac - factor by which delta is increased after iicont_max increases
+        dtdeltafac - factor by which delta is increased by for time-dependent run
+        dtlim - Cutoff on (target-var)/delta for which a time-dependent run is triggered
+        ii1max - maximum number of dt iterations to take
+        saveres - how many successful iterations are allowed between saves are dumped
+        kwargs passed to rundt
+        """
+        from uedge import bbb
+        from time import time
+        from os import makedirs
+        from copy import deepcopy
+        from shutil import rmtree
+        from os.path import exists
+        from numpy import array
+        from Forthon import package, packageobject
+        # TODO: icntnunk=0 on fail only?
+
+        self.tstart = time()
+        # ==== HELPERS ====
+        def changevar():
+            """ Changes var by delta """
+            setvar(min(self.lastsuccess + self.delta, 1))
+           
+        def setvar(value):
+            """ Sets var to value """
+            for key, subdict in self.var.items():
+                newvar = subdict['origvar'] + value * subdict['deltavar']
+                if subdict['index'] is None:
+                    setattr(subdict['pkgobj'], key, newvar)
+                else:
+                    getattr(subdict['pkgobj'], key)[subdict['index']] = newvar
+
+        def getvar(key, subdict):
+            """ Returns current value of var """
+            # Variable is array: only set requested index
+            if 'index' not in subdict:
+                return getattr(subdict['pkgobj'], key)
+            else:
+                try:
+                    return getattr(subdict['pkgobj'], key)[subdict['index']]
+                except:
+                    return getattr(subdict['pkgobj'], key)
+
+        def issuccess():
+            """ Checks whether case is converged at target value of var """
+            from time import time
+            from datetime import timedelta
+            self.lastsuccess += min(self.delta, 1-self.lastsuccess)
+            if self.lastsuccess >= 1:
+                print('\n===== TARGET VALUE ACHIEVED: REDUCE FNORM ====')
+                staticiter()
+                bbb.dtreal = 1e20
+
+                print('++++++++++++++++++++++++++++++++++++++++')
+                print('+++++ CONTINUATION SOLVE SUCCEEDED +++++')
+                print('++++++++++++++++++++++++++++++++++++++++')
+                print('Total runtime: {}'.format(timedelta(
+                        seconds=round(time()-self.tstart))))
+                self.savesuccess('SUCCESS_{}.hdf5'.format(self.savedir))
+                self.restorevalues()
+                return True
+            else:
+                if self.isave >= self.saveres:
+                    self.isave = 0
+                    self.savesuccess(self.savefname.format('{:.3f}'.format(self.lastsuccess).replace('.','p')))
+                else:
+                    self.isave += 1
+
+        def printinfo(printdelta=True):
+            """ Print current solve status """
+            # TODO: add printing of indices?
+            ljust = 42
+            print('    -Variable(s) being solved:')
+            for key, _ in self.var.items():
+                print(' '.ljust(ljust-3), '-',key)
+            print('{}{:.3f}%'.format('    -Progress'.ljust(ljust),
+                        self.lastsuccess*100
+            ))
+            if printdelta is not False:
+                print('{}{:.3f}%'.format('    -Advancing by'.ljust(ljust),
+                        self.delta*100
+                ))
+                print('{}{}'.format('    -Steps to target at current delta:'.ljust(ljust), 
+                    (int((1 - self.lastsuccess)/self.delta))))
+            print('')
+
+        def isdeltatoosmall():
+            """ Returns True if delta is below cutoff """
+            if self.delta < 1/self.cutoff:
+                return True
+            return False
+
+        def dostaticiter():
+            """ Returns True if delta is above dt-run threshold """
+            if self.delta > 1/self.dtlim:
+                return True
+            return False
+                    
+
+        def staticiter():
+            """ Tries to reduce initial fnrm by iterating at constant var """
+            from uedge import bbb
+            from copy import deepcopy
+            # TODO: always dump save on successful steady-state solution?
+            printinfo(False)
+            setvar(self.lastsuccess)
+            dtreal_orig = deepcopy(bbb.dtreal)
+            ftol_orig = deepcopy(bbb.ftol)
+            bbb.dtreal = dtreal_orig/100
+            while bbb.dtreal < 1e5:
+                ftol_old = deepcopy(bbb.ftol)
+                # Dynamically decreasing fnorm
+                bbb.pandf1 (-1, -1, 0, bbb.neq, 1., bbb.yl, bbb.yldot)
+                fnorm_old = (sum((bbb.yldot[:bbb.neq]*\
+                    bbb.sfscal[:bbb.neq])**2))**0.5
+                if bbb.dtreal > 1:
+                    bbb.dtreal = 1e20
+                print('\n===== STATIC ITERATION AT DTREAL={:.2e} ====='.format(bbb.dtreal))
+                bbb.ftol = max(min(bbb.ftol, 0.01*fnorm_old), 1e-9)
+                # Take a converging step
+                if self.exmain_isaborted():
+                    setvar(self.lastsuccess)
+                    bbb.dtreal = dtreal_orig
+                    bbb.ftol = ftol_orig
+                    return None
+                # Temporary fix to avoid Segfault when using icntnunk=1!
+                bbb.ijactot = 2
+                bbb.icntnunk = 1
+                bbb.ftol = ftol_old
+                bbb.dtreal = bbb.dtreal*5
+                # Assert steady-state
+                if bbb.iterm != 1:
+                    bbb.dtreal = dtreal_orig
+                    setvar(self.lastsuccess)
+                    bbb.ftol = ftol_orig
+                    print('\n===== STATIC FNRM REDUCTION FAILED =====\n')
+                    return False
+            self.savesuccess(self.savefname.format('{:.3f}_staticiter'.format(\
+                    self.lastsuccess).replace('.','p')
+                ))
+            print('===== CONVERGED AT STEADY STATE: RETURNING TO MAIN LOOP =====')
+            bbb.dtreal = dtreal_orig
+            bbb.ftol = ftol_orig
+            return True
+
+        def dtsolve(dtdeltafac):
+            """ Perform a time-dependent solve """
+            from uedge import bbb
+            printinfo(False)
+            bbb.icntnunk = 0
+            # Make backup of original values before entering dt run
+            # TODO: compress the storing/setting/resetting of vars
+            tstart_cont = deepcopy(self.tstart)
+            incpset_cont = deepcopy(bbb.incpset)
+            itermx_cont = deepcopy(bbb.itermx)
+            dtreal_cont = deepcopy(bbb.dtreal)
+            ftol_cont = deepcopy(bbb.ftol)
+            orig_cont = deepcopy(self.orig)
+            classvars_cont = deepcopy(self.classvars)
+            classsetup_cont = deepcopy(self.classsetup)
+            bbb.incpset = 5
+            bbb.itermx = 30
+            bbb.dtreal = 1e-5
+            bbb.ftol = 1e-8
+            abort = False
+            # Ensure a first time-step can be taken
+            dtdelta = self.lastsuccess + dtdeltafac/100
+            while bbb.iterm != 1:
+                dtdelta = self.lastsuccess + dtdeltafac/100
+                setvar(dtdelta)
+                if self.exmain_isaborted():
+                    setvar(self.lastsuccess)
+                    return False
+                # If the iteration does not succeed, reduce the time-step
+                if bbb.iterm != 1:
+                    # Advancing less than .5% dt is probably an indication of a failure
+                    if dtdeltafac < 0.5:
+                        abort = True
+                        break
+                    dtdeltafac /=2
+            if abort is False:
+                self.converge(dtreal=dtreal, savedir='.', 
+                    savefname=self.savefname.format('{:.3f}_dtrun'.format(\
+                    dtdelta).replace('.','p')).replace('.hdf5',''), 
+                    message='Solving for delta={:.3f}%'.format(dtdelta*100),
+                    ii1max=ii1max, **kwargs)
+                if bbb.iterm == 1:
+                    self.lastsuccess = dtdelta
+                # Ensure original values are still being kept track of
+                self.orig = orig_cont
+                bbb.incpset = incpset_cont 
+                bbb.itermx = itermx_cont 
+                bbb.dtreal = dtreal_cont 
+                bbb.ftol = ftol_cont 
+                orig_cont = deepcopy(self.orig)
+                self.classvars = classvars_cont
+                self.classsetup = classsetup_cont
+                self.tstart = tstart_cont
+                bbb.dtreal = dt
+            if bbb.iterm != 1:
+                print('=====================================')
+                print('===== CONTINUATION SOLVE FAILED =====')
+                print('=====================================')
+                setvar(self.lastsuccess)
+                print('Progress upon abortion: {:.3f}%'.format(
+                    self.lastsuccess*100)
+                )
+                return False
+            else:
+                return True
+
+        if isinstance(var, str): 
+            if target is None:
+                raise KeyError("Keyword argument 'target' must be set"
+                    " when evaluating a single variable!"
+                )
+        elif isinstance(var, dict):
+            if savedir is None: 
+                raise KeyError("Must define save directory name when "
+                    "evalauting multiple variables!"
+                )
+        self.savedir = savedir
+        if self.savedir is None:
+            self.savedir = bbb.label[0].decode('UTF-8').strip()
+            autosavedir = True
+        else:
+            autosavedir = False
+        if len(self.savedir) == 0:
+            self.savedir = '{}_solve'.format(var)
+            autosavedir = True
+        if autosavedir:
+            if exists(self.savedir):
+                i=2
+                while exists(self.savedir+'_{}'.format(i)):
+                    i += 1
+                print('Run-folder {} exists: saving to {}_{}'.format(\
+                    self.savedir, self.savedir, i)
+                )
+                self.savedir = '{}_{}'.format(self.savedir, i)
+            else:
+                print('Saving intermediate saves to {}'.format(self.savedir))
+        else:
+            if exists(self.savedir):
+                rmtree(self.savedir)
+        # Finalize savename w/ placeholder
+        self.savefname = '{}/progress{{}}.hdf5'.format(self.savedir)
+        makedirs(self.savedir)
+        # Additional variables to be stored in save files
+        self.classvars = {}
+        for dictkeys in ['delta', 'progress', 'delta_fail', 'progress_fail']:
+            self.classvars[dictkeys] = []
+        # Find package variable
+        # TODO: Use dict to set one or multiple variables instead of string?
 
+        # Set up variables that need to be accessed by helpers
+        self.dtlim = dtlim
+        self.cutoff = cutoff
+        # Set up control flags
+        start = True
+        nstaticiter = 0
+        iicont = 0
+        iicont_fail = 0
+        dtiter = 0
+        self.isave = saveres
+        self.saveres = saveres
+        self.delta = 1/initres
+        self.lastsuccess = 0
+
+        # Set up dictionary with variables and targets
+        self.var = {}
+        # Construct the variable dictionary based on the user input
+        if isinstance(var, str):
+            self.var = {    var: {
+                            'index': index,
+                            'target': target
+                    }}
+        else:
+            self.var = var
+            for key, subdict in self.var.items():
+                if 'target' not in subdict.keys():
+                    raise KeyError("Target not set for variable {}!".format(key))
+                elif 'index' not in subdict.keys():
+                    self.var[key]['index'] = None
+        # Complement the user input with gradients for each variable
+        for key, subdict in self.var.items():
+            if isinstance(subdict['target'], list):
+                subdict['target'] = array(subdict['target'])
+            for pkg in package():
+                pkgobj = packageobject(pkg)
+                if key in pkgobj.varlist():
+                    subdict['pkg'] = pkg
+                    subdict['pkgobj'] = pkgobj
+            if subdict['index'] is not None:
+                try:
+                    getattr(subdict['pkgobj'], key)[subdict['index']]
+                except:
+                    raise ValueError('{} does not accommodate requested indices!'.format(key))
+            subdict['origvar'] = deepcopy(getvar(key, subdict))
+            subdict['deltavar'] = deepcopy(subdict['target'] - subdict['origvar'])
+            try:
+                dist = abs(subdict['deltavar']).max()
+            except:
+                dist = abs(subdict['deltavar'])
+            if dist < 1e-10:
+                raise ValueError('Target equals current value for {}, aborting!'.format(key))
+                
+        self.classsetup = {}
+        for key, subdict in self.var.items():
+            self.setupvars[key] = getattr(subdict['pkgobj'], key)
+            self.classsetup['initial_{}'.format(key)] = getvar(key, subdict)
+            self.classsetup['delta_{}'.format(key)] = subdict['deltavar']
+            self.classsetup['target_{}'.format(key)] = subdict['target']
+            if isinstance(subdict['index'], (tuple, slice)):
+                self.classsetup['index_{}'.format(key)] = str(subdict['index']).encode("ascii", "ignore")
+            elif subdict['index'] is not None:
+                self.classsetup['index_{}'.format(key)] = subdict['index']
+            else:
+                self.classsetup['index_{}'.format(key)] = False
+
+        # Record original solver settings            
+        self.orig = {}
+        for ovar in ['itermx', 'dtreal', 'icntnunk', 'ftol', 'incpset',
+            'ismmaxuc', 'mmaxu'        
+        ]:
+            self.orig[ovar] = deepcopy(getattr(bbb, ovar))
+        # Take the initial time-step
+        changevar()
+        # Set remaining solver settings
+        bbb.dtreal = dt
+        bbb.ftol = ftol
+        bbb.incpset = incpset
+        bbb.itermx = itermx
+#        bbb.ismmaxuc = 0
+#        bbb.mmaxu = 70
+        if (bbb.iterm == 1) and (bbb.ijactot > 0):
+            self.message('Initial successful time-step exists', separator='')
+        else:
+            self.message('Need to take initial step with Jacobian; ' + \
+                'trying to do here', seppad='*')
+            printinfo()
+            # Ensure preconditioner is calculated
+            bbb.icntnunk = 0
+            # Take timestep and see if abort requested
+            if self.exmain_isaborted():
+                setvar(self.lastsuccess)
+                return
+            # Increase time
+            # Verify time-step was successful
+            if (bbb.iterm != 1):
+                self.restorevalues()
+                setvar(self.lastsuccess)
+                self.message('Error: converge an initial time-step first; then ' + \
+                    're-execute command', seppad='*')
+                return
+        # Start outer loop
+        while True:
+            # Ensure we don't exceed the target value
+            # Re-eval preconditioner: omit first step
+            if start is False:
+                bbb.icntnunk = 0
+            else: 
+                bbb.icntnunk = 1
+                start = False
+            # Reset counters
+            iicont = 0
+            iicont_fail = 0
+            # Start inner loop
+            while iicont < iicont_max:
+                print('===== MAIN LOOP {}/{} ====='.format(iicont+1, iicont_max))
+                printinfo()
+                # TODO: how to get intial fnrm rather than last fnorm?
+                fnorm_old = (sum((bbb.yldot[:bbb.neq]*\
+                    bbb.sfscal[:bbb.neq])**2))**0.5
+                bbb.ftol = min(max(fnorm_old/100, 1e-6), ftol)
+                # Take step and check whether abort is requested
+                if self.exmain_isaborted():
+                    setvar(self.lastsuccess)
+                    return
+                bbb.ftol = ftol
+                bbb.icntnunk = 1
+                # Failure to take time-step
+                if bbb.iterm != 1:
+                    # Check whether an excorbant number of iterations are necessary to converge: fail if yes
+                    self.classvars['delta_fail'].append(self.delta)
+                    self.classvars['progress_fail'].append(self.lastsuccess)
+                    if isdeltatoosmall():
+                        print('=====================================')
+                        print('===== CONTINUATION SOLVE FAILED =====')
+                        print('=====================================')
+                        print('Last successful step for {}: {:.4e}'.format(\
+                            self.var, self.lastsuccess)
+                        )
+                        return
+                    # Start trying to reset convergence
+                    else:
+                        # Reset success counter
+                        iicont = 0
+                        iicont_fail += 1
+                        # Delta has been reduced too many times: do some moves to knock the case loose
+                        if iicont_fail >= iicont_fail_max:
+                            print('===== RECOVERY LOOP ENTERED =====')
+                            # Iterate the case at the last successful 
+                            bbb.icntnunk = 0
+                            if dostaticiter():
+                                staticstatus = staticiter()
+                                # Flag for abortion
+                                if staticstatus is None:
+                                    return 
+                                elif staticstatus is False:
+                                    dtcall=True
+                                else:
+                                    dtcall=False
+                                nstaticiter += 1
+                            # Enter loop for time-dependent simulations
+                            if (bbb.iterm != 1) or (dtcall is True) or (nstaticiter==staticiter_max):
+                                print('===== ENTER TIME-DEPENDENT SOLVE =====')
+                                if dtsolve(dtdeltafac) is False:
+                                    return
+                                else:
+                                    # Force-break inner loop
+                                    iicont = 1e5
+                                    dtcall = False
+                                    bbb.icntnunk = 0
+                                    if issuccess():
+                                        return
+                                    changevar()
+                            # Initial fnrm successfully reduced, continue increasing var
+                            else:
+                                iicont_fail = 0
+                                changevar()
+                        # Try to attain convergence again by decreasing change in var
+                        else:
+                            print('\n===== FAIL {}/{} ====='.format(iicont_fail, iicont_fail_max))
+                            print('===== DECREASE DELTA AND TRY AGAIN =====')
+                            # Reset to last successful step
+                            setvar(self.lastsuccess)
+                            # Decrease change in variable
+                            self.delta /= deltafac
+                            # Set to new, decreased change
+                            changevar()
+                            bbb.icntnunk = 0
+                # Success: update counter and last successful value
+                else:
+                    self.classvars['delta'].append(self.delta)
+                    self.classvars['progress'].append(self.lastsuccess)
+                    if issuccess():
+                        return
+                    # Check whether to increment time-step
+                    if iicont == iicont_max-1:
+                        print('\n===== INNER LOOP COMPLETED: ADVANCING DELTA =====')
+                        nstaticiter = 0
+                        self.delta *= 1.1*deltafac
+                    else:
+                        print('\n===== SUCCESS: ADVANCING VARIABLE =====')
+                    iicont += 1
+                    changevar()
+        print('EXITED LOOP: YOU SHOULD NOT BE HERE...')
+        return
 
 def rundt(**kwargs):
     runcase=UeRun()
diff --git a/pyscripts/ruthere.py b/pyscripts/ruthere.py
deleted file mode 100755
index 7b42c2d3..00000000
--- a/pyscripts/ruthere.py
+++ /dev/null
@@ -1,66 +0,0 @@
-from numpy import *
-import time
-import signal
-import sys
- 
-#############################################################################
-# From Dave Grote:
-# --- Setup signal handler to capture Control-C
-# --- To use, first call arminterrupt(). Then at the place where the interrupt
-# --- is allowed, call ruthere(). This will raise a KeyboardInterrupt if
-# --- Control-C had been pressed.
-# --- When a interrupt request is received, all this handler does is set a
-# --- flag to that effect. Then, a subsequent call to ruthere will check
-# --- that flag, and if set, raise an exception. This allows a graceful
-# --- stop with the current time step completed.
-# --- Set the following two in case ruthere is called before arminterrupt.
-_defaultcontrolC = signal.getsignal(signal.SIGINT)
-_controlCrecieved = False
-savetracebacklimit = 0
-
-def _handlecontrolC(signum, frame):
-    global _controlCrecieved
-    _controlCrecieved = True
- 
-def ruthere(reset=True):
-    """
-Checks if an interrupt was requested (usually control-C). If so, then raise
-an exception. If reset is True, restore the original interrupt handler so that the
-calling code does not have to, and so that, if there is an exception, it gets
-restored (since the calling code is not returned to).
-    """
-    global _controlCrecieved
-    global _defaultcontrolC
-    global savetracebacklimit
-    if _controlCrecieved:
-        if reset:
-            signal.signal(signal.SIGINT, _defaultcontrolC)
-        _controlCrecieved = False
-        raise KeyboardInterrupt("Interrupt requested")
- 
-def arminterrupt():
-    global _controlCrecieved
-    global _defaultcontrolC
-    global savetracebacklimit
-    _controlCrecieved = False
-    _defaultcontrolC = signal.getsignal(signal.SIGINT)
-    try:
-       savetracebacklimit = sys.tracebacklimit
-    except:
-       savetracebacklimit = None       
-    signal.signal(signal.SIGINT, _handlecontrolC)
-    sys.tracebacklimit = 0
-
-def disarminterrupt():
-    global _defaultcontrolC
-    global savetracebacklimit
-    signal.signal(signal.SIGINT, _defaultcontrolC)
-    sys.tracebacklimit = savetracebacklimit
-  
-  
-#=========================================================================
-
-arminterrupt()
-
-
- 
diff --git a/pyscripts/uedgeplots.py b/pyscripts/uedgeplots.py
index 502dfb86..ce1aa8db 100755
--- a/pyscripts/uedgeplots.py
+++ b/pyscripts/uedgeplots.py
@@ -44,13 +44,16 @@ def plotmesh(ixmin=None, ixmax=None, iymin=None, iymax=None,
 
        The plot axis limits may be specified with r_rmin,r_max,z_min,z_max.
     """
-    zrefl = com.zm
-    zlim = com.ylim
-    zreflbdry = com.zbdry
-    if str(com.geometry) == str([b'uppersn         ']):
-       zrefl = 2.0 * com.zmid - com.zm
-       zlim = 2.0 * com.zmid - com.ylim
-       zreflbdry = 2.0 * com.zmid - com.zbdry
+    try:
+        zrefl = com.zm
+        zlim = com.ylim
+        zreflbdry = com.zbdry
+        if str(com.geometry) == str([b'uppersn         ']):
+           zrefl = 2.0 * com.zmid - com.zm
+           zlim = 2.0 * com.zmid - com.ylim
+           zreflbdry = 2.0 * com.zmid - com.zbdry
+    except:
+        pass
 
     if ixmin == None:
         ixmin = com.nxomit
@@ -112,13 +115,16 @@ def plotanymesh(verts, r_min=None, r_max=None, z_min=None, z_max=None, title=Non
 
        The plot axis limits may be specified with r_rmin,r_max,z_min,z_max.
     """
-    zrefl = com.zm
-    zlim = com.ylim
-    zreflbdry = com.zbdry
-    if str(com.geometry) == str([b'uppersn         ']):
-       zrefl = 2.0 * com.zmid - com.zm
-       zlim = 2.0 * com.zmid - com.ylim
-       zreflbdry = 2.0 * com.zmid - com.zbdry
+    try:
+        zrefl = com.zm
+        zlim = com.ylim
+        zreflbdry = com.zbdry
+        if str(com.geometry) == str([b'uppersn         ']):
+           zrefl = 2.0 * com.zmid - com.zm
+           zlim = 2.0 * com.zmid - com.ylim
+           zreflbdry = 2.0 * com.zmid - com.zbdry
+    except:
+        pass
 
     if r_min == None:
         r_min = np.min(verts[:,:,:,0])
@@ -181,13 +187,16 @@ def plotmeshval(val, ixmin=None, ixmax=None, iymin=None, iymax=None,
 
        The plot axis limits may be specified with r_rmin,r_max,z_min,z_max.
     """
-    zrefl = com.zm
-    zlim = com.ylim
-    zreflbdry = com.zbdry
-    if str(com.geometry) == str([b'uppersn         ']):
-       zrefl = 2.0 * com.zmid - com.zm
-       zlim = 2.0 * com.zmid - com.ylim
-       zreflbdry = 2.0 * com.zmid - com.zbdry
+    try:
+        zrefl = com.zm
+        zlim = com.ylim
+        zreflbdry = com.zbdry
+        if str(com.geometry) == str([b'uppersn         ']):
+           zrefl = 2.0 * com.zmid - com.zm
+           zlim = 2.0 * com.zmid - com.ylim
+           zreflbdry = 2.0 * com.zmid - com.zbdry
+    except:
+        pass
 
     if ixmin == None:
         ixmin = com.nxomit
@@ -263,13 +272,16 @@ def plotanymeshval(verts,z, r_min=None, r_max=None, z_min=None, z_max=None, titl
 
        The plot axis limits may be specified with r_rmin,r_max,z_min,z_max.
     """
-    zrefl = com.zm
-    zlim = com.ylim
-    zreflbdry = com.zbdry
-    if str(com.geometry) == str([b'uppersn         ']):
-       zrefl = 2.0 * com.zmid - com.zm
-       zlim = 2.0 * com.zmid - com.ylim
-       zreflbdry = 2.0 * com.zmid - com.zbdry
+    try:
+        zrefl = com.zm
+        zlim = com.ylim
+        zreflbdry = com.zbdry
+        if str(com.geometry) == str([b'uppersn         ']):
+           zrefl = 2.0 * com.zmid - com.zm
+           zlim = 2.0 * com.zmid - com.ylim
+           zreflbdry = 2.0 * com.zmid - com.zbdry
+    except:
+        pass
 
     if r_min == None:
         r_min = com.rm.min()
@@ -333,13 +345,16 @@ def mkdensityfile(filename, ival, renmin=None, renmax=None, samples=[500, 500, 5
           about 1cm r resolution and .6cm in z.
 
     """
-    zrefl = com.zm
-    zlim = com.ylim
-    zreflbdry = com.zbdry
-    if str(com.geometry) == str([b'uppersn         ']):
-       zrefl = 2.0 * com.zmid - com.zm
-       zlim = 2.0 * com.zmid - com.ylim
-       zreflbdry = 2.0 * com.zmid - com.zbdry
+    try:
+        zrefl = com.zm
+        zlim = com.ylim
+        zreflbdry = com.zbdry
+        if str(com.geometry) == str([b'uppersn         ']):
+           zrefl = 2.0 * com.zmid - com.zm
+           zlim = 2.0 * com.zmid - com.ylim
+           zreflbdry = 2.0 * com.zmid - com.zbdry
+    except:
+        pass
 
     if renmin == None:
         renmin = np.min(ival)
diff --git a/pyscripts/uexec.py b/pyscripts/uexec.py
deleted file mode 100755
index e5e51522..00000000
--- a/pyscripts/uexec.py
+++ /dev/null
@@ -1,30 +0,0 @@
-
-
-import sys
-try:
-     from importlib import reload,import_module
-except:
-     from importlib import import_module
-
-
-import builtins
-
-
-def uexec(mname,returns=globals()):
-    if mname in sys.modules:
-       _m = reload(sys.modules[mname])
-    else:
-       _m = import_module(mname)
-
-    # is there an __all__?  if so respect it
-    if "__all__" in _m.__dict__:
-        names = _m.__dict__["__all__"]
-    else:
-        # otherwise we import all names that don't begin with _
-        names = [x for x in _m.__dict__ if not x.startswith("_")]
-
-    # now drag them in
-    for k in names:
-        #print k,getattr(_m,k) 
-        returns[k] = getattr(_m,k)
-
diff --git a/wdf/wdf.m b/wdf/wdf.m
index 7fc10e0b..0e98847e 100755
--- a/wdf/wdf.m
+++ b/wdf/wdf.m
@@ -5,7 +5,7 @@
 Use(Xpoint_indices)     # ixpt1,ixpt2 from com package
 Use(Share)              # geometry from com package
 Use(Dimwdf)             # nptsvb,nptshb,nptskb,nptsw,npsegxz
-Use(Auxw)               # ixpt1b,ixpt2b,ixtop1b,ixtop2b,
+Use(Auxw)               # ixpt1b_wdf,ixpt2b_wdf,ixtop1b,ixtop2b,
                         # nohzsb,novzsb,nosegsxzb
 Use(Options)            # iswdfon
 
@@ -21,10 +21,10 @@ call xerrab("")
 
 c     allocate arrays for DEGAS
 
-      ixpt1b  = ixpt1(1)
-      ixtop1b = ixpt1b  + (ixpt2(1)-ixpt1(1))/2
+      ixpt1b_wdf  = ixpt1(1)
+      ixtop1b = ixpt1b_wdf  + (ixpt2(1)-ixpt1(1))/2
       ixtop2b = ixtop1b + 1
-      ixpt2b  = ixpt2(1)
+      ixpt2b_wdf  = ixpt2(1)
       if (geometry .eq. "dnbot") then
 	 ixtop1b=ixtop1b-1	# we omit guard cells at the midplane
 	 ixtop2b=ixtop2b+1	# of up/down symmetric double nulls
@@ -151,7 +151,7 @@ subroutine rdgrd3 (iunit)
 Use(RZ_grid_info)  # rm,zm from com package
 Use(Linkbbb)       # nxbbb,nybbb from com package
 Use(Dimwdf)
-Use(Auxw)          # ixpt1b,ixpt2b,ixtop1b,ixtop2b
+Use(Auxw)          # ixpt1b_wdf,ixpt2b_wdf,ixtop1b,ixtop2b
 Use(Linkgrd)
 Use(Degas1)
 Use(Degas2)
@@ -167,7 +167,7 @@ subroutine rdgrd3 (iunit)
          i = 1
          gridx(j,i,1) = rm(ixtop1b,iy,4) - rgrid1w
          gridz(j,i,1) = zm(ixtop1b,iy,4)
-         do ix = ixtop1b, ixpt1b+1, -1
+         do ix = ixtop1b, ixpt1b_wdf+1, -1
             i = i + 1
             gridx(j,i,1) = rm(ix,iy,3) - rgrid1w
             gridz(j,i,1) = zm(ix,iy,3)
@@ -176,9 +176,9 @@ subroutine rdgrd3 (iunit)
          gridx(j,i,1) = gridx(j,i-1,1)
          gridz(j,i,1) = gridz(j,i-1,1)
          i = i + 1
-         gridx(j,i,1) = rm(ixpt1b,iy,4) - rgrid1w
-         gridz(j,i,1) = zm(ixpt1b,iy,4)
-         do ix = ixpt1b, 1, -1
+         gridx(j,i,1) = rm(ixpt1b_wdf,iy,4) - rgrid1w
+         gridz(j,i,1) = zm(ixpt1b_wdf,iy,4)
+         do ix = ixpt1b_wdf, 1, -1
             i = i + 1
             gridx(j,i,1) = rm(ix,iy,3) - rgrid1w
             gridz(j,i,1) = zm(ix,iy,3)
@@ -198,7 +198,7 @@ subroutine rdgrd3 (iunit)
          i = 1
          gridx(j,i,1) = rm(ixtop2b,iy,3) - rgrid1w
          gridz(j,i,1) = zm(ixtop2b,iy,3)
-         do ix = ixtop2b, ixpt2b
+         do ix = ixtop2b, ixpt2b_wdf
             i = i + 1
             gridx(j,i,1) = rm(ix,iy,4) - rgrid1w
             gridz(j,i,1) = zm(ix,iy,4)
@@ -207,9 +207,9 @@ subroutine rdgrd3 (iunit)
          gridx(j,i,1) = gridx(j,i-1,1)
          gridz(j,i,1) = gridz(j,i-1,1)
          i = i + 1
-         gridx(j,i,1) = rm(ixpt2b+1,iy,3) - rgrid1w
-         gridz(j,i,1) = zm(ixpt2b+1,iy,3)
-         do ix = ixpt2b+1, nxbbb
+         gridx(j,i,1) = rm(ixpt2b_wdf+1,iy,3) - rgrid1w
+         gridz(j,i,1) = zm(ixpt2b_wdf+1,iy,3)
+         do ix = ixpt2b_wdf+1, nxbbb
             i = i + 1
             gridx(j,i,1) = rm(ix,iy,4) - rgrid1w
             gridz(j,i,1) = zm(ix,iy,4)
@@ -225,11 +225,11 @@ subroutine rdgrd3 (iunit)
       endwhile
 c Finally, the "magnetic axis" for core and private flux regions
       j = nybbb + 2
-      do i = 1, ixtop1b-ixpt1b+2
+      do i = 1, ixtop1b-ixpt1b_wdf+2
          gridx(j,i,1) = rmagxw - rgrid1w
          gridz(j,i,1) = zmagxw
       enddo
-      do i = ixtop1b-ixpt1b+3, nptshb
+      do i = ixtop1b-ixpt1b_wdf+3, nptshb
          gridx(j,i,1) = 0.5*(gridx(j-1,nptshb,1)+gridx(j+1,nptshb,1))
          gridz(j,i,1) = 0.5*(gridz(j-1,nptshb,1)+gridz(j+1,nptshb,1))
       enddo
@@ -277,13 +277,13 @@ subroutine rdgrd3 (iunit)
       xwall(itot,2)=gridx(j,i,1)
       zwall(itot,2)=gridz(j,i,1)
       j=j-1                             # jump to inboard half of p.f.
-      do i=ixtop1b+3,ixtop1b-ixpt1b+3,-1
+      do i=ixtop1b+3,ixtop1b-ixpt1b_wdf+3,-1
          itot=itot+1
          xwall(itot,2)=gridx(j,i,1)
          zwall(itot,2)=gridz(j,i,1)
       enddo
       j=j+2                             # jump to outboard half of p.f.
-      do i=ixpt2b-ixtop2b+4,nxbbb-ixtop2b+4
+      do i=ixpt2b_wdf-ixtop2b+4,nxbbb-ixtop2b+4
          itot=itot+1
          xwall(itot,2)=gridx(j,i,1)
          zwall(itot,2)=gridz(j,i,1)
@@ -302,13 +302,13 @@ subroutine rdgrd3 (iunit)
 c Third, clockwise around the core
       itot=0
       j=nybbb+1
-      do i=ixtop1b-ixpt1b+2,1,-1
+      do i=ixtop1b-ixpt1b_wdf+2,1,-1
          itot=itot+1
          xwall(itot,3)=gridx(j,i,1)
          zwall(itot,3)=gridz(j,i,1)
       enddo
       j=j+2
-      do i=1,ixtop1b-ixpt1b+2
+      do i=1,ixtop1b-ixpt1b_wdf+2
          itot=itot+1
          xwall(itot,3)=gridx(j,i,1)
          zwall(itot,3)=gridz(j,i,1)
@@ -365,7 +365,7 @@ call xerrab("**** bbb-wdf file not found")
 Use(Xpoint_indices)     # from com package
 Use(Linkbbb)
 Use(Dimwdf)
-Use(Auxw)               # ixpt1b,ixpt2b,ixtop1b,ixtop2b,nosegsxzb,novzsb
+Use(Auxw)               # ixpt1b_wdf,ixpt2b_wdf,ixtop1b,ixtop2b,nosegsxzb,novzsb
 Use(Linkgrd)
 Use(Degas1)
 Use(Degas2)
@@ -376,16 +376,16 @@ call xerrab("**** bbb-wdf file not found")
       do ix=1,nxbbb
 	 do iy=1,nybbb
 c translate UEDGE cell index (ix,iy) to DEGAS cell index (iv,jh)
-	    if ((1 .le. ix) .and. (ix .le. ixpt1b)) then
+	    if ((1 .le. ix) .and. (ix .le. ixpt1b_wdf)) then
 	       jh = nybbb + 1 - iy
 	       iv = ixtop1b + 3 - ix
-	    elseif ((ixpt1b+1 .le. ix) .and. (ix .le. ixtop1b)) then
+	    elseif ((ixpt1b_wdf+1 .le. ix) .and. (ix .le. ixtop1b)) then
 	       jh = nybbb + 1 - iy
 	       iv = ixtop1b + 1 - ix
-	    elseif ((ixtop2b .le. ix) .and. (ix .le. ixpt2b)) then
+	    elseif ((ixtop2b .le. ix) .and. (ix .le. ixpt2b_wdf)) then
 	       jh = nybbb + 2 + iy
 	       iv = ix - ixtop2b + 1
-	    elseif ((ixpt2b+1 .le. ix) .and. (ix .le. nxbbb)) then
+	    elseif ((ixpt2b_wdf+1 .le. ix) .and. (ix .le. nxbbb)) then
 	       jh = nybbb + 2 + iy
 	       iv = ix - ixtop2b + 3
 	    endif
@@ -410,12 +410,12 @@ c translate UEDGE plate index (nxm,iy) to DEGAS wall segment index (iseg)
 
 c translate UEDGE private flux wall index (ix) to DEGAS private region
 c wall segment index (iseg) on wall number 2
-      do ix=1,ixpt1b
+      do ix=1,ixpt1b_wdf
 	 iseg = 1 + ix
 	 currxzt(iseg,1,2,1) = - abs(fngysibbb(ix))# NOTE negative for puffing
       enddo
-      do ix=ixpt2b+1,nxbbb
-	 iseg = 1 + ixpt1b + 1 + (ix-ixpt2b)
+      do ix=ixpt2b_wdf+1,nxbbb
+	 iseg = 1 + ixpt1b_wdf + 1 + (ix-ixpt2b_wdf)
 	 currxzt(iseg,1,2,1) = - abs(fngysibbb(ix))
       enddo
 
@@ -438,7 +438,7 @@ c wall segment index (iseg) on wall number 1
       subroutine defaultz
       integer jb,jj,ib,ii
 Use(Dimwdf)
-Use(Auxw)               # ixpt1b
+Use(Auxw)               # ixpt1b_wdf
 Use(Degas1)
 Use(Degas2)
 Use(Eqdsk)
@@ -468,7 +468,7 @@ c wall segment index (iseg) on wall number 1
       novbs = ib
       novzs = novbs - 1
 
-      ivnull = ixtop1b - ixpt1b + 2     # vertical index of non-physical zone
+      ivnull = ixtop1b - ixpt1b_wdf + 2     # vertical index of non-physical zone
                                         # between core and private flux
 
 c.....set kzone arrays
diff --git a/wdf/wdf.v b/wdf/wdf.v
index b4c1036a..b2c5417d 100755
--- a/wdf/wdf.v
+++ b/wdf/wdf.v
@@ -51,10 +51,10 @@ nixw     integer
  
 ***** Auxw:
      # some parameters used to transform UEDGE indices to DEGAS indices
-ixpt1b     integer  # ix index of pf cell just below x-point on inboard half
+ixpt1b_wdf integer  # ix index of pf cell just below x-point on inboard half
 ixtop1b    integer  # ix index of cell at top of inboard half mesh
 ixtop2b    integer  # ix index of cell at top of outboard half mesh
-ixpt2b     integer  # ix index of core cell just above x-point on outboard half
+ixpt2b_wdf integer  # ix index of core cell just above x-point on outboard half
 nohzsb     integer  # number of DEGAS horizontal zones
 novzsb     integer  # number of DEGAS vertical zones
 nosegsxzb  integer  # number of DEGAS wall segments
@@ -258,9 +258,9 @@ sndspd  real
      # plasma flow mach number where sound speed = sqrt((te+ti)/mi)
 t0puff(npns)    _real    [eV]	/.025/
      # energy of puffed source of neutrals
-te0     real    [eV]
+te0_wdf real    [eV]
      # electron temperature in the case of a constant plasma
-ti0(npis)       _real    [eV]
+ti0_wdf(npis)       _real    [eV]
      # ion temperature in the case of a constant plasma
 wtmin0  real
      # minimum test flight weight