diff --git a/Makefile b/Makefile
index 73f5763bc..47970cc8f 100644
--- a/Makefile
+++ b/Makefile
@@ -10,11 +10,13 @@ all:
 	cd tgyro ; make
 	cd profiles_gen ; make
 	cd f2py ; make
+	cd qlgyro ; make
 	@echo "GACODE build done"
 
 clean:
 	rm -f .VERSION
 	cd shared ; make clean
+	cd shared/hybridtest ; make clean
 	cd neo ; make clean
 	cd vgen ; make clean
 	cd tglf ; make clean
@@ -23,6 +25,7 @@ clean:
 	cd tgyro ; make clean
 	cd profiles_gen ; make clean
 	cd f2py ; make clean
+	cd qlgyro ; make clean
 	rm -f f2py/*/*.pyc
 	rm -f f2py/*.pyc
 	rm -f f2py/pygacode/*/*.pyc
@@ -43,6 +46,7 @@ distclean:
 	cd tgyro ; make clean
 	cd profiles_gen ; make clean
 	cd f2py ; make clean
+	cd qlgyro ; make clean
 	rm -f python/*/*.pyc
 	rm -f python/*.pyc
 	rm -f modules/*genmod*
diff --git a/README.rst b/README.rst
index 45d8697ae..5767740f3 100644
--- a/README.rst
+++ b/README.rst
@@ -1,4 +1,4 @@
 GACODE repository
 =================
 
-For documentation, please refer to the `GACODE website <http://gafusion.github.io/doc/>`_.
+For documentation, please refer to the `GACODE website <http://gacode.io>`_.
diff --git a/cgyro/src/cgyro_write_initdata.f90 b/cgyro/src/cgyro_write_initdata.f90
index 47e4f84e6..f58ec9f60 100644
--- a/cgyro/src/cgyro_write_initdata.f90
+++ b/cgyro/src/cgyro_write_initdata.f90
@@ -13,7 +13,7 @@ subroutine cgyro_write_initdata
   implicit none
 
   integer :: p,in,is,it
-  real :: kymax,kyrat,dn
+  real :: kymax,kyrat,dn,dt
   real, external :: spectraldiss
   character(len=50) :: msg
 
@@ -120,13 +120,25 @@ subroutine cgyro_write_initdata
 
      write(io,*)
      write(io,'(a)') &
-          ' i  z  n/n_norm   T/T_norm   m/m_norm     a/Ln       a/Lt       nu        s(a/Ln)    s(a/Lt)'
+          ' i  z  n/n_norm   T/T_norm   m/m_norm     a/Ln       a/Lt       nu'
      do is=1,n_species
         write(io,'(t1,i2,1x,i2,3(2x,1pe9.3),2(1x,1pe10.3),(2x,1pe9.3),2(1x,1pe10.3))') &
-             is,int(z(is)),dens(is),temp(is),mass(is),dlnndr(is),dlntdr(is),nu(is),&
-             sdlnndr(is),sdlntdr(is)
+             is,int(z(is)),dens(is),temp(is),mass(is),dlnndr(is),dlntdr(is),nu(is)
      enddo
 
+     ! Profile shear
+     if (profile_shear_flag == 1) then
+        write(io,*)
+        write(io,'(a)') ' i  s(a/Ln)  (a/Ln)_L  (a/Ln)_R  |  s(a/Lt)  (a/Lt)_L  (a/Lt)_R ' 
+        do is=1,n_species
+           dn = sdlnndr(is)*length/rho/4
+           dt = sdlntdr(is)*length/rho/4
+           write(io,'(t1,i2,3(1x,1pe9.3),2x,3(1x,1pe9.3))') &
+             is,sdlnndr(is),dlnndr(is)-dn,dlnndr(is)+dn,sdlntdr(is),dlntdr(is)-dt,dlntdr(is)+dt
+        enddo
+     endif
+
+     ! Running from input.gacode
      if (profile_model == 2) then
         dn = rho/(rhos/a_meters)
         kyrat = abs(q/rmin*rhos/a_meters)
diff --git a/f2py/expro/expro.f90 b/f2py/expro/expro.f90
index fa7409d75..522abcba2 100644
--- a/f2py/expro/expro.f90
+++ b/f2py/expro/expro.f90
@@ -180,6 +180,7 @@ module expro
   integer :: expro_ctrl_quasineutral_flag 
   integer :: expro_ctrl_numeq_flag
   integer :: expro_error=0
+  integer :: expro_jerr=0
 
   ! Header information
   character(len=70) :: expro_head_original =  '#  *original : null'
diff --git a/f2py/expro/expro_util.f90 b/f2py/expro/expro_util.f90
index 4543ea77b..8b0210f3b 100644
--- a/f2py/expro/expro_util.f90
+++ b/f2py/expro/expro_util.f90
@@ -208,7 +208,7 @@ subroutine expro_compute_derived
 
   ! r_min = a [m]
   r_min = expro_rmin(expro_n_exp)
-
+  
   do i=2,expro_n_exp
 
      ! Parameters to be passed to geo library   
@@ -262,9 +262,11 @@ subroutine expro_compute_derived
         geo_fourier_in(1:4,0:geo_nfourier_in) = expro_geo(:,:,i)/r_min
         geo_fourier_in(5:8,0:geo_nfourier_in) = expro_dgeo(:,:,i)
      endif
+
      call geo_interp(1,theta,.true.)
      if (minval(geov_jac_r) <= 0d0) then
-        print '(a,i3,a)','WARNING: (expro_util) Negative Jacobian for i =',i,' in input.gacode'
+        print '(a,i3,a,f5.2)','WARNING: (expro_util) J < 0 for i=',i,' in input.gacode: ',minval(geov_jac_r)
+        expro_jerr = 1
      endif
 
      ! V, dV/dr and S (note that S=dV/dr only in a circle)
@@ -415,9 +417,9 @@ subroutine expro_compute_derived
         expro_ni_new(:) = expro_ni_new(:)+expro_z(is)*expro_ni(is,:)
         expro_dlnnidr_new(:) = expro_dlnnidr_new(:)+expro_z(is)*expro_ni(is,:)*expro_dlnnidr(is,:)
      enddo
-     
+
      ! New quasineutral ion 1 profiles:
-     
+
      ! density  
      expro_ni_new(:) = (expro_ne(:)-expro_ni_new(:))/expro_z(1)
      ! gradient scale length 1/L_ni = -dln(ni)/dr (1/m)
@@ -427,7 +429,7 @@ subroutine expro_compute_derived
      call bound_deriv(expro_sdlnnidr_new(:),expro_ni_new(:)*expro_dlnnidr_new(:),&
           expro_rmin,expro_n_exp)
      expro_sdlnnidr_new(:) = expro_sdlnnidr_new(:)/expro_ni_new(:)*expro_rhos(:)
-     
+
      if (minval(expro_ni_new(:)) <= 0d0) expro_error = 1
 
   else
@@ -498,7 +500,7 @@ subroutine expro_compute_derived
 
   ! Reset geo variables to standard values to prevent expro from leaving
   ! geo in a "mysterious" state
-  
+
   geo_rmin_in      = 1d0
   geo_rmaj_in      = 0.5d0
   geo_drmaj_in     = 3d0
diff --git a/f2py/pygacode/cgyro/data.py b/f2py/pygacode/cgyro/data.py
index 14a353fc8..51e083de5 100644
--- a/f2py/pygacode/cgyro/data.py
+++ b/f2py/pygacode/cgyro/data.py
@@ -201,10 +201,7 @@ def getxflux(self):
 
    def xfluxave(self,w,moment,e=0.2,nscale=0):
 
-      """
-      Do complicated spatial averages for xflux
-      RESULT: self.lky_flux_ave
-      """
+      # Averaging functionfor global fluxes
 
       print('INFO: (xfluxave) Computing partial-domain averages')
 
@@ -221,41 +218,39 @@ def xfluxave(self,w,moment,e=0.2,nscale=0):
       else:
          sc[:] = 1.0
 
+      # Sum moments over fields (3) and toroidal modes (4)
+      # NOTE: lky_flux_n[2,ng,ns,nfield,n_n,nt]
       if moment == 'n':
          z = np.sum(self.lky_flux_n,axis=(3,4))
       elif moment == 'e':
          z = np.sum(self.lky_flux_e,axis=(3,4))
       elif moment == 'v':
          z = np.sum(self.lky_flux_v,axis=(3,4))
-      else:
-         raise ValueError('(xfluxave) Invalid moment.')
-
+         
       #--------------------------------------------
-      # Useful arrays required outside this routine
-      self.lky_xr = np.zeros((ns,ng))
-      self.lky_xi = np.zeros((ns,ng))
-      self.lky_flux_ave = np.zeros((ns,2))
+      # Arrays required outside this routine
+      self.lky_xr = np.zeros([ng,ns])
+      self.lky_xi = np.zeros([ng,ns])
+      self.lky_flux_ave = np.zeros([ns,2])
       #--------------------------------------------
 
-      imin,imax=time_index(self.t,w)
-      
-      for ispec in range(ns):
-         for l in range(ng):
-            self.lky_xr[ispec,l] = time_average(z[0,l,ispec,:],self.t,imin,imax)*sc[ispec]
-            self.lky_xi[ispec,l] = time_average(z[1,l,ispec,:],self.t,imin,imax)*sc[ispec]
+      imin,imax = time_index(self.t,w)
+
+      # Time averages of real and imaginary parts
+      self.lky_xr[:,:] = time_average(z[0,:,:,:],self.t,imin,imax)
+      self.lky_xi[:,:] = time_average(z[1,:,:,:],self.t,imin,imax)
 
+      l = np.arange(1,ng)
+      u = (2*np.pi*e)*l
+      for ispec in range(ns):
          # Flux partial average over [-e,e]
-         g0 = self.lky_xr[ispec,0]
-         g1 = g0
-         for l in range(1,ng):
-            u = 2*np.pi*l*e
-            g0 = g0+2*np.sin(u)*self.lky_xr[ispec,l]/u
-            g1 = g1+2*np.sin(u)*self.lky_xr[ispec,l]/u*(-1)**l
+         g0 = self.lky_xr[0,ispec]+2*np.sum(np.sin(u)*self.lky_xr[l,ispec]/u)
+         g1 = self.lky_xr[0,ispec]+2*np.sum(np.sin(u)*self.lky_xr[l,ispec]/u*(-1)**l)
 
          # Average over true (positive) interval
-         self.lky_flux_ave[ispec,0] = g0
+         self.lky_flux_ave[ispec,0] = g0*sc[ispec]
          # Average over negative interval
-         self.lky_flux_ave[ispec,1] = g1
+         self.lky_flux_ave[ispec,1] = g1*sc[ispec]
 
    def getbigfield(self):
 
diff --git a/f2py/pygacode/cgyro/data_plot.py b/f2py/pygacode/cgyro/data_plot.py
index 1eec7c5e7..248fd3475 100644
--- a/f2py/pygacode/cgyro/data_plot.py
+++ b/f2py/pygacode/cgyro/data_plot.py
@@ -1006,6 +1006,7 @@ def plot_xflux(self,xin):
       nscale = xin['nscale']
       ymin   = xin['ymin']
       ymax   = xin['ymax']
+      mirror = xin['abs']
 
       if xin['fig'] is None:
          fig = plt.figure(MYDIR,figsize=(xin['lx'],xin['ly']))
@@ -1013,33 +1014,21 @@ def plot_xflux(self,xin):
       self.getxflux()
       
       ns = self.n_species
-      nl = self.n_global+1
+      ng = self.n_global+1
       t  = self.t
 
-      ky  = self.ky
-      ave = np.zeros((self.n_n,ns))
-
       if moment == 'phi':
          moment = 'e'
-
-      # NOTE: lky_flux_* -> [ 2, nl , ns , n_n , nt ]
-      #                       0  1    2     3    4 
-
+         
       if moment == 'n':
          ntag = 'Density~flux'
          mtag = '\Gamma'
-         z = np.sum(self.lky_flux_n,axis=3)
-         ftag = 'xflux_n'
       elif moment == 'e':
          ntag = 'Energy~flux'
          mtag = 'Q'
-         z = np.sum(self.lky_flux_e,axis=3)
-         ftag = 'xflux_e'
       elif moment == 'v':
          ntag = 'Momentum~flux'
          mtag = '\Pi'
-         z = np.sum(self.lky_flux_v,axis=3)
-         ftag = 'xflux_v'
       else:
          print('ERROR: (plot_xflux) Invalid moment.')
          sys.exit()
@@ -1055,7 +1044,6 @@ def plot_xflux(self,xin):
       else:
          mnorm = ''
 
-
       #============================================================
       # Otherwise plot
       ax = fig.add_subplot(111)
@@ -1065,51 +1053,53 @@ def plot_xflux(self,xin):
 
       color = ['k','m','b','c','g','r']
 
-      imin,imax=time_index(t,w)
+      imin,imax = time_index(t,w)
       mpre,mwin = wintxt(imin,imax,t)
 
       ax.set_title(r'$\mathrm{'+ntag+'} \quad $'+mwin)
-    
-      a = -np.pi+2*np.pi*np.arange(0.0,1.0,0.001)
+
+      na = 128
+      a  = np.linspace(-np.pi,np.pi,na)
+      ah = np.linspace(0,-2*np.pi,na)
 
       for ispec in range(ns):
 
          u = specmap(self.mass[ispec],self.z[ispec])
 
-         # Flux curve
-         g = np.zeros(len(t))
-         g = self.lky_xr[ispec,0] 
-         for l in range(1,nl):
-            g = g+2*(np.cos(l*a)*self.lky_xr[ispec,l]-np.sin(l*a)*self.lky_xi[ispec,l])
+         #---------------------------------
+         # Global flux versus x
+         g = np.zeros(na) ; g[:] = self.lky_xr[0,ispec]          
+         for l in range(1,ng):
+            g[:] = g[:]+2*(np.cos(l*a)*self.lky_xr[l,ispec]-np.sin(l*a)*self.lky_xi[l,ispec])
          ax.plot(a/(2*np.pi),g,color=color[ispec])
-
+         g = np.zeros(na) ; g[:] = self.lky_xr[0,ispec]          
+         for l in range(1,ng):
+            g[:] = g[:]+2*(np.cos(l*ah)*self.lky_xr[l,ispec]-np.sin(l*ah)*self.lky_xi[l,ispec])
+         ax.plot(a/(2*np.pi),g,color=color[ispec],linestyle='--')
          #---------------------------------
-         # Flux partial average over [-e,e]
+   
+         #---------------------------------
+         # Flux partial average over "positive" [-e,e] interval
          g0 = self.lky_flux_ave[ispec,0]
          label = r'$'+mtag+mnorm+'_'+u+'/'+mtag+'_\mathrm{GB}: '+str(round(g0,3))+'$'
          ax.plot([-e,e],[g0,g0],'o-',color=color[ispec],alpha=0.2,linewidth=3,label=label)
          #---------------------------------
 
          #---------------------------------
-         # Flux partial average over "negative" interval
+         # Flux partial average over "negative" [-e,e] interval
          g1 = self.lky_flux_ave[ispec,1]
          ax.plot([0.5-e,0.5],[g1,g1],'o--',color=color[ispec],alpha=0.2,linewidth=3)
          ax.plot([-0.5,-0.5+e],[g1,g1],'o--',color=color[ispec],alpha=0.2,linewidth=3)
          #---------------------------------
-
-         #---------------------------------
-         # Flux spectral average
-         gs = self.lky_xr[ispec,0]+2*np.pi/4*self.lky_xr[ispec,1]
-         #---------------------------------
-         
+        
          #---------------------------------
          # Flux domain average
-         ga = self.lky_xr[ispec,0]
+         ga = self.lky_xr[0,ispec]
          ax.plot([-0.5,0.5],[ga,ga],color=color[ispec],alpha=0.5)
          #---------------------------------
 
-         print('INFO: (plot_xflux) Ave [inner/inner_spec, outer, domain] = '
-               '{:.2f}/{:.2f}, {:.2f}, {:.2f}'.format(g0,gs,g1,ga)) 
+         print('INFO: (plot_xflux) Ave [inner-e, outer-e, domain] = '
+               '{:.2f}, {:.2f}, {:.2f}'.format(g0,g1,ga)) 
 
          if ymax != 'auto':
             ax.set_ylim(top=float(ymax))
diff --git a/f2py/pygacode/profiles_gen/prgen_shapeprofile.py b/f2py/pygacode/profiles_gen/prgen_shapeprofile.py
index 5b19c6162..cf13e3f14 100644
--- a/f2py/pygacode/profiles_gen/prgen_shapeprofile.py
+++ b/f2py/pygacode/profiles_gen/prgen_shapeprofile.py
@@ -8,18 +8,14 @@
 from .prgen_contour import *
 from .prgen_shape import *
 
-if len(sys.argv) > 1:
-   gfile   = sys.argv[1]
-   mag     = sys.argv[2]
-   narc    = int(sys.argv[3])
-   npsi    = int(sys.argv[4])
-   nharm   = int(sys.argv[5])
-   nfourier = int(sys.argv[6])
-   plotpng = bool(int(sys.argv[7]))
-   psinorm = float(sys.argv[8])
-else:
-   print('Usage: python prgen_shapeprofile.py <gfile> <mag> <narc> <npsi> <nfourier>')
-   sys.exit()
+gfile = sys.argv[1]
+mag   = sys.argv[2]
+narc  = int(sys.argv[3])
+npsi  = int(sys.argv[4])
+nharm = int(sys.argv[5])
+nfourier = int(sys.argv[6])
+plotpng  = bool(int(sys.argv[7]))
+psinorm  = float(sys.argv[8])
 
 efit = prgen_geqdsk(gfile)
 psi0 = efit['SIMAG']
diff --git a/neo/src/neo_make_profiles.f90 b/neo/src/neo_make_profiles.f90
index 628af7ff1..baf4e13d2 100644
--- a/neo/src/neo_make_profiles.f90
+++ b/neo/src/neo_make_profiles.f90
@@ -441,6 +441,7 @@ subroutine neo_make_profiles
      enddo
      close(io)
 
+     ! JC: New file, introduced in Dec 2023 for neo_nice
      open(unit=io,file=trim(path)//'out.neo.species',status='replace')
      do is=1,n_species
         write (io,'(e16.8)',advance='no') mass(is)
diff --git a/platform/build/make.inc.CORG b/platform/build/make.inc.CORG
index be63527e4..b60aa3908 100644
--- a/platform/build/make.inc.CORG
+++ b/platform/build/make.inc.CORG
@@ -1,5 +1,5 @@
 #---------------------------------------------------
-# Linux Mint 
+# CORG (Ubuntu server)
 #---------------------------------------------------
 
 IDENTITY="corg.gat.com gfortran+mpich+OpenBLAS (/usr)"
diff --git a/platform/build/make.inc.OSX_CATALINA b/platform/build/make.inc.OSX_CATALINA
index f1d4606de..7b98a8295 100644
--- a/platform/build/make.inc.OSX_CATALINA
+++ b/platform/build/make.inc.OSX_CATALINA
@@ -17,7 +17,7 @@
 
 # Compilers and flags
 
-FC  = mpif90-mpich-gcc9 -I$(GACODE_ROOT)/modules -J$(GACODE_ROOT)/modules -fPIC -framework Accelerate
+FC  = mpif90-mpich-gcc11 -I$(GACODE_ROOT)/modules -J$(GACODE_ROOT)/modules -fPIC -framework Accelerate
 F77 = mpif77 -std=legacy
 CC  = ${FC}
 
diff --git a/platform/exec/exec.MINT b/platform/exec/exec.MINT
index d38fc632a..1d8cb2480 100755
--- a/platform/exec/exec.MINT
+++ b/platform/exec/exec.MINT
@@ -9,5 +9,5 @@ numa=${5}
 mpinuma=${6}
 
 cd $simdir
-mpiexec -env OMP_NUM_THREADS $nomp -n $nmpi $exec
+mpiexec -env OMP_NUM_THREADS $nomp -n $nmpi $exec 
 
diff --git a/platform/qsub/qsub.AZURE_GPU b/platform/qsub/qsub.AZURE_GPU
index 01ef3f670..2d0b4ca17 100644
--- a/platform/qsub/qsub.AZURE_GPU
+++ b/platform/qsub/qsub.AZURE_GPU
@@ -11,8 +11,15 @@ fi
 # Note: Will always put 32 mpi ranks per node
 #
 
+if [ -n $MEMPERCPU ] 
+then
+  echo "Error: Azure GPU does not accept mem per cpu"
+elif [ -z $MEMPERNODE ]
+  MEMPERNODE=400G
+fi
+
 bfile=$SIMDIR/batch.src
 echo "#!/bin/bash " > $bfile
-echo "#SBATCH --time $WALLTIME -p hpc --ntasks-per-node=32 --mem=400G -n $nmpi" >> $bfile
+echo "#SBATCH --time $WALLTIME -p hpc --ntasks-per-node=32 --mem=$MEMPERNODE -n $nmpi" >> $bfile
 
 echo "$CODE -e $LOCDIR -n $nmpi -nomp $nomp -numa $numa -mpinuma $mpinuma -p $SIMROOT" >> $bfile
diff --git a/platform/qsub/qsub.OMEGA b/platform/qsub/qsub.OMEGA
index f72e02c9a..4a8cca730 100644
--- a/platform/qsub/qsub.OMEGA
+++ b/platform/qsub/qsub.OMEGA
@@ -7,11 +7,13 @@ echo "#SBATCH -e $SIMDIR/batch.err" >> $bfile
 echo "#SBATCH -t $WALLTIME" >> $bfile
 echo "#SBATCH -n $cores_used" >> $bfile
 
-if [ -n $MEMNODE ] 
+if [ -n $MEMPERNODE ] 
 then
   echo "#SBATCH --mem $MEMNODE" >> $bfile
 elif [ -n $MEMPERCPU ]
   echo "#SBATCH --mem-per-cpu $MEMPERCPU" >> $bfile
+else
+  echo "#SBATCH --mem-per-cpu 16GB" >> $bfile
 fi
 
 if [ "$QUEUE" = "null_queue" ]
diff --git a/platform/qsub/qsub.PPPL b/platform/qsub/qsub.PPPL
index a19c75b6b..48364c22b 100644
--- a/platform/qsub/qsub.PPPL
+++ b/platform/qsub/qsub.PPPL
@@ -7,7 +7,7 @@ echo "#SBATCH -e $SIMDIR/batch.err" >> $bfile
 echo "#SBATCH -t $WALLTIME" >> $bfile
 echo "#SBATCH -n $cores_used" >> $bfile
 
-if [ -n $MEMNODE ] 
+if [ -n $MEMPERNODE ] 
 then
   echo "#SBATCH --mem $MEMNODE" >> $bfile
 elif [ -n $MEMPERCPU ]
@@ -19,6 +19,8 @@ then
   echo "#SBATCH -p general" >> $bfile
 else
   echo "#SBATCH -p $QUEUE" >> $bfile
+else
+  echo "#SBATCH --mem-per-cpu 4GB" >> $bfile
 fi
 
 echo "$CODE -e $LOCDIR -n $nmpi -nomp $nomp -numa $numa -mpinuma $mpinuma -p $SIMROOT" >> $bfile
diff --git a/platform/qsub/qsub.PPPL_gcc b/platform/qsub/qsub.PPPL_gcc
index d3d0e037c..a47805fc5 100644
--- a/platform/qsub/qsub.PPPL_gcc
+++ b/platform/qsub/qsub.PPPL_gcc
@@ -6,7 +6,16 @@ echo "#SBATCH -o $SIMDIR/batch.out" >> $bfile
 echo "#SBATCH -e $SIMDIR/batch.err" >> $bfile
 echo "#SBATCH -t $WALLTIME" >> $bfile
 echo "#SBATCH -n $cores_used" >> $bfile
-echo "#SBATCH --mem=4GB" >> $bfile
+
+if [ -n $MEMPERNODE ] 
+then
+  echo "#SBATCH --mem $MEMNODE" >> $bfile
+elif [ -n $MEMPERCPU ]
+  echo "#SBATCH --mem-per-cpu $MEMPERCPU" >> $bfile
+else
+  echo "#SBATCH --mem-per-cpu 4GB" >> $bfile
+fi
+
 if [ "$QUEUE" = "null_queue" ]
 then
   echo "#SBATCH -p general" >> $bfile
diff --git a/platform/qsub/qsub.SATURN_GCC b/platform/qsub/qsub.SATURN_GCC
index 042633db0..9095b9b0d 100644
--- a/platform/qsub/qsub.SATURN_GCC
+++ b/platform/qsub/qsub.SATURN_GCC
@@ -6,7 +6,19 @@ echo "#SBATCH -o $SIMDIR/batch.out" >> $bfile
 echo "#SBATCH -e $SIMDIR/batch.err" >> $bfile
 echo "#SBATCH -t $WALLTIME" >> $bfile
 echo "#SBATCH -n $cores_used" >> $bfile
-echo "#SBATCH --mem 45G" >> $bfile
+
+if [ -n $MEMPERNODE ] 
+then
+  echo "#SBATCH --mem $MEMNODE" >> $bfile
+elif [ -n $MEMPERCPU ]
+  echo "#SBATCH --mem-per-cpu $MEMPERCPU" >> $bfile
+else
+  echo "#SBATCH --mem 45GB" >> $bfile
+fi
+
+
+
+
 if [ "$QUEUE" = "null_queue" ]
 then
   echo "#SBATCH -p medium" >> $bfile
diff --git a/profiles_gen/bin/gacode_type_autodetect b/profiles_gen/bin/gacode_type_autodetect
index 0b0a1a4d5..41713d1ef 100755
--- a/profiles_gen/bin/gacode_type_autodetect
+++ b/profiles_gen/bin/gacode_type_autodetect
@@ -26,6 +26,10 @@ if [ "$1" == "null" ] ; then
    echo "null"
    exit 0
 fi
+if [ "$1" == "manual" ] ; then
+   echo "manual"
+   exit 0
+fi
 if [ ! -f $1 ] ; then
    echo "NOT_FOUND"
    exit 1
diff --git a/profiles_gen/bin/profiles_gen b/profiles_gen/bin/profiles_gen
index db15b84c4..b6e8a2d4b 100755
--- a/profiles_gen/bin/profiles_gen
+++ b/profiles_gen/bin/profiles_gen
@@ -254,7 +254,7 @@ N_NULL=128
 IPCCW=0
 BTCCW=0
 
-# OMFIT mapper variables
+# Mapper variables
 EFIT=0
 MAG=auto
 NPSI=256
@@ -448,14 +448,14 @@ if [ "$itype" == "GACODE" ] && [ $INFO_FLAG == 1 ] ; then
     exit 0
 fi
 #=============================================================
-# Managing input file (also catches UFILE mode)
+# Managing input file 
 
 if [ "$itype" == "null" ] ; then
 
    # gfile-only mode
    echo "INFO: (profiles_gen) Parsing GFILE only."
 
-else
+else 
 
    echo "INFO: (profiles_gen) $FILE is autodetected as $itype."
 
@@ -687,7 +687,13 @@ fi
 $EXEC
 
 if [ -f "success" ] ; then
-   echo "INFO: (profiles_gen) Done."
+   if [ `cat success` -eq "1" ] ; then
+      echo "INFO: (profiles_gen) Done."
+   else
+      m=0.001
+      r=$(echo "($PSINORM-$m)"| bc -l)
+      echo "ERROR: (profiles_gen) Rerun with -psinorm $r"
+   fi
 else
    echo "ERROR: (profiles_gen) *Failed*. Try running with -V option"
 fi
diff --git a/profiles_gen/bin/ufile2.py b/profiles_gen/bin/ufile2.py
new file mode 100755
index 000000000..0531e4945
--- /dev/null
+++ b/profiles_gen/bin/ufile2.py
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+# Usage:
+#
+#   python ufile2.py <datafile> <time>
+#
+#   NOTES:
+#   - DOC: http://tokamak-profiledb.ccfe.ac.uk/DOCS/PR08MAN/pdbman.html
+
+import sys
+import numpy as np
+
+def extract2d(infile):
+
+    vt = np.zeros(1)
+    data_region = 0
+    for line in open(infile,'r').readlines():
+        if line.count("END-OF-DATA") == 1:
+            data_region = 0
+            # Compute average if time-point in range
+            fxt  = vy.reshape((nx,nt),order='F')
+            print('Converting '+var)
+            # Write the averaged data for current profile (var)
+            # Output filename: "out.TAG.ave"
+            np.savetxt(var+'.txt',np.transpose((vx,fxt[:,0])),fmt='%1.6e')
+
+        if data_region == 0:
+
+            if line.count("-DEP") == 1:
+                # Extract current variable name
+                var=line.split('  ')[0].strip()
+
+            if line.count("X PTS") == 1:
+                # Get length of radial grid
+                nx=int(line.split(";-# OF X")[0].strip())
+                vx = np.zeros(nx)
+
+            if line.count("Y PTS") == 1:
+                # Get size of time grid
+                nt=int(line.split(";-# OF Y")[0].strip())
+                vy = np.zeros(nx*nt)
+                vt = np.zeros(nt)
+                # Signal header end
+                data_region = 1
+                ix = 0
+                it = 0
+                iy = 0
+                # Write dimensions
+                #if var=="NE":
+                f=open('out.dim','w')
+                f.write(str(nx)+'\n')
+                f.close()
+
+        else:
+
+            # Here we are reading numbers
+
+            # Number of columns
+            n = np.max([line.count("E"),line.count("e")])
+
+            if ix < nx:
+                # Read the radial grid [nx points]
+                for i in range(n):
+                    vx[ix]=float(line[1+13*i:1+13*i+13])
+                    ix = ix+1
+            elif it < nt:
+                # Read the time grid [nt points]
+                vt[0]=float(line)
+                it = 1
+            else:
+                # Read the radial-time grid [(nx+1)*ny points]
+                for i in range(n):
+                    vy[iy]=float(line[1+13*i:1+13*i+13])
+                    iy = iy+1
+
+#----------------------------------------------------------------------------
+# Manage input parameters
+
+# <datafile>
+try:
+    infile=sys.argv[1]
+except:
+    print('Usage: python ufile2.py <datafile> <time>')
+    sys.exit()
+
+varlist = []
+t0 = -1.0
+# Generate list of included profiles (tags)
+for line in open(infile,'r').readlines():
+    if line.count("-DEP") == 1:
+        # Extract current variable name
+        var=line.split('  ')[0].strip()
+        varlist.append(var)
+# Print list of included profiles (tags) in blocks of 10
+print('INFO: (ufile2) tags ->')
+for i in np.arange(start=0,stop=len(varlist),step=10):
+    print('       '+' '.join(varlist[i:i+10]))
+
+extract2d(infile)
diff --git a/profiles_gen/src/Makefile b/profiles_gen/src/Makefile
index ef2bfa3cd..f37b06202 100644
--- a/profiles_gen/src/Makefile
+++ b/profiles_gen/src/Makefile
@@ -18,6 +18,7 @@ OBJECTS = prgen_globals.o \
           prgen_geometry.o \
           prgen_ion_name.o \
           prgen_map_iterdb.o \
+          prgen_map_manual.o \
           prgen_map_null.o \
           prgen_map_plasmastate.o \
 	  prgen_map_peqdsk.o \
@@ -27,6 +28,7 @@ OBJECTS = prgen_globals.o \
           prgen_read_ti.o \
           prgen_read_iterdb.o \
           prgen_read_iterdb_nc.o \
+          prgen_read_manual.o \
           prgen_read_plasmastate.o \
 	  prgen_read_peqdsk.o \
 	  prgen_read_genf.o \
diff --git a/profiles_gen/src/prgen.f90 b/profiles_gen/src/prgen.f90
index 252539474..499b2b356 100644
--- a/profiles_gen/src/prgen.f90
+++ b/profiles_gen/src/prgen.f90
@@ -12,6 +12,7 @@
 !   SWIM        (plasmastate)
 !   PFILE       (peqdsk)
 !   GENF        (General Fusion)
+!   MANUAL      (Auto-import of text files)
 !
 !  Autodetected geometry formats:
 !   GFILE       (geqdsk equilibrium data)
@@ -96,6 +97,12 @@ program prgen
      format_type = 4
      call prgen_read_genf
 
+  case ('manual') ! MANUAL import
+     print '(a)','INFO: (prgen) Assuming MANUAL file import.'
+
+     format_type = 5
+     call prgen_read_manual
+
   case('GACODE') ! Note (we may or may not have gmerge_flag == 1)
      print '(a)','INFO: (prgen) Assuming input.gacode (GACODE) format.'
 
@@ -150,6 +157,8 @@ program prgen
      call prgen_map_peqdsk
   case (4)
      call prgen_map_genf
+  case (5)
+     call prgen_map_manual
   case (7,8)
      call prgen_map_inputgacode
   end select
@@ -157,9 +166,4 @@ program prgen
   call prgen_swap
   call prgen_write
 
-  ! Successful completion
-  open(unit=1,file='success',status='replace')
-  write(1,*) 1
-  close(1)
-
 end program prgen
diff --git a/profiles_gen/src/prgen_allocate.f90 b/profiles_gen/src/prgen_allocate.f90
index 315bb2855..7c94d74f6 100644
--- a/profiles_gen/src/prgen_allocate.f90
+++ b/profiles_gen/src/prgen_allocate.f90
@@ -20,6 +20,7 @@ subroutine prgen_allocate(ftype)
   allocate(ti_kev(nx))
   allocate(ne_e19m3(nx))
   allocate(ni_e19m3(nx))
+  allocate(nz_e19m3(nx))
   allocate(zeff(nx))
 
   allocate(jtot(nx))
diff --git a/profiles_gen/src/prgen_geometry.f90 b/profiles_gen/src/prgen_geometry.f90
index 0946efbec..e87687530 100644
--- a/profiles_gen/src/prgen_geometry.f90
+++ b/profiles_gen/src/prgen_geometry.f90
@@ -57,13 +57,21 @@ subroutine prgen_geometry
   read(1) efit_zmaj
   close(1)
 
+  ! Get rho on efit mesh (so have psi,rho,q)
+  call prgen_get_chi(npsi,efit_q,efit_psi,efit_rho,torfluxa)
+
+  efit_psi = efit_psi-efit_psi(1)
+
   ! PFILE only contains normalized flux
   if (format_type == 3) then
      dpsi = (psi1-psi0)*dpsi
   endif
-  
-  efit_psi = efit_psi-efit_psi(1)
 
+  ! manual method needs dpsi on statefile grid
+  if (format_type == 5) then
+     call bound_interp(efit_rho,efit_psi,npsi,rho,dpsi,nx)
+  endif
+ 
   ! Deal with null statefile
   if (format_type == 0) then
      nx = npsi
@@ -90,13 +98,11 @@ subroutine prgen_geometry
   endif
   !--------------------------------------------------------------------------------------
 
-  ! Get rho on efit mesh (so have psi,rho,q)
-  call prgen_get_chi(npsi,efit_q,efit_psi,efit_rho,torfluxa)
   ! Get q
   call cub_spline(efit_psi,efit_q,npsi,dpsi,q,nx)
   ! Get rho
   call prgen_get_chi(nx,q,dpsi,rho,torfluxa)
-
+   
   call bound_interp(efit_rho,efit_rmin,npsi,rho,rmin,nx)
   call bound_interp(efit_psi,efit_q,npsi,dpsi,q,nx)
   call bound_interp(efit_psi,efit_p,npsi,dpsi,p_tot,nx)
diff --git a/profiles_gen/src/prgen_globals.f90 b/profiles_gen/src/prgen_globals.f90
index 178e96253..227b73cfe 100644
--- a/profiles_gen/src/prgen_globals.f90
+++ b/profiles_gen/src/prgen_globals.f90
@@ -57,6 +57,7 @@ module prgen_globals
   real, dimension(:), allocatable :: ti_kev
   real, dimension(:), allocatable :: ne_e19m3
   real, dimension(:), allocatable :: ni_e19m3
+  real, dimension(:), allocatable :: nz_e19m3
   real, dimension(:), allocatable :: zeff
 
   real, dimension(:), allocatable :: jtot
diff --git a/profiles_gen/src/prgen_map_manual.f90 b/profiles_gen/src/prgen_map_manual.f90
new file mode 100644
index 000000000..d853a9bb4
--- /dev/null
+++ b/profiles_gen/src/prgen_map_manual.f90
@@ -0,0 +1,45 @@
+!------------------------------------------------------------
+! prgen_map_manual.f90
+!
+! PURPOSE:
+!  Map MANUAL data
+!------------------------------------------------------------
+
+subroutine prgen_map_manual
+
+  use prgen_globals
+  use expro
+  
+  implicit none
+
+  !---------------------------------------------------------
+  ! Map profile data onto single array:
+  !
+  expro_n_exp = nx
+  expro_n_ion = 2
+  call expro_init(1)
+  !
+  expro_rho(:)   = rho(:)
+  expro_rmin(:)  = rmin(:)
+  expro_rmaj(:)  = rmaj(:)
+  expro_te(:)    = te_kev(:)
+  expro_ne(:)    = ne_e19m3(:)
+  expro_w0(:)    = omega0(:)
+
+  expro_mass(1) = 2.0
+  expro_z(1) = 1.0
+  expro_name(1) = 'D'
+  expro_type(1) = type_therm
+  
+  expro_ni(1,:) = ni_e19m3(:)
+  expro_ti(1,:) = ti_kev(:)
+
+  expro_mass(2) = 12.0
+  expro_z(2) = 6.0
+  expro_name(2) = 'C'
+  expro_type(2) = type_therm
+  
+  expro_ni(2,:) = nz_e19m3(:)
+  expro_ti(2,:) = ti_kev(:)
+  
+end subroutine prgen_map_manual
diff --git a/profiles_gen/src/prgen_read_manual.f90 b/profiles_gen/src/prgen_read_manual.f90
new file mode 100644
index 000000000..afec6b8c6
--- /dev/null
+++ b/profiles_gen/src/prgen_read_manual.f90
@@ -0,0 +1,90 @@
+!--------------------------------------------------------------
+! prgen_read_genf.f90
+!
+! PURPOSE:
+!  Read profiles from General Fusion Statefile
+!--------------------------------------------------------------
+
+subroutine prgen_read_manual
+
+  use prgen_globals
+
+  implicit none
+
+  integer :: i,n0
+  
+  character(len=1) :: a
+  real, dimension(:,:), allocatable :: x
+  real, dimension(:), allocatable :: rho0
+
+  ! Number of resampled points
+  nx = 64
+  call prgen_allocate('')
+  
+  call getlen('TE.txt',n0)
+  
+  allocate(x(2,n0))
+  allocate(rho0(n0))
+
+  ! te
+  open(unit=1,file='TE.txt',status='old')
+  read(1,*) x(:,:)
+  close(1)
+  rho0 = x(1,:)
+  do i=1,nx
+     rho(i) = rho0(1)+(i-1.0)/(nx-1.0)*(rho0(n0)-rho0(1))
+  enddo
+  call bound_interp(rho0,x(2,:)*1e-3,n0,rho,te_kev,nx)
+
+  ! ti (eV)
+  open(unit=1,file='TI.txt',status='old')
+  read(1,*) x(:,:)
+  close(1)
+  call bound_interp(rho0,x(2,:)*1e-3,n0,rho,ti_kev,nx)
+
+  ! ne (1/m^3)
+  open(unit=1,file='NE.txt',status='old')
+  read(1,*) x(:,:)
+  close(1)
+  call bound_interp(rho0,x(2,:)*1e-19,n0,rho,ne_e19m3,nx)
+
+  ! ni (1/m^3)
+  open(unit=1,file='NI.txt',status='old')
+  read(1,*) x(:,:)
+  close(1)
+  call bound_interp(rho0,x(2,:)*1e-19,n0,rho,ni_e19m3,nx)
+
+  ! nz (1/m^3)
+  open(unit=1,file='NZ.txt',status='old')
+  read(1,*) x(:,:)
+  close(1)
+  call bound_interp(rho0,x(2,:)*1e-19,n0,rho,nz_e19m3,nx)
+
+  ! omega (rad/s)
+  open(unit=1,file='VROT.txt',status='old')
+  read(1,*) x(:,:)
+  close(1)
+  call bound_interp(rho0,x(2,:)*1e-3,n0,rho,omega0,nx)
+
+end subroutine prgen_read_manual
+
+subroutine getlen(infile,n)
+
+  implicit none
+  
+  character(len=*), intent(in) :: infile
+  integer, intent(inout) :: n
+  character(len=1) :: a
+  integer :: ios
+  
+  open(unit=1,file=trim(infile),status='old')
+  n = -1
+  do
+     read(1,*,iostat=ios) a
+     if (ios < 0) exit
+     n = n+1
+  enddo
+  close(1)
+  
+end subroutine getlen
+
diff --git a/profiles_gen/src/prgen_read_peqdsk.f90 b/profiles_gen/src/prgen_read_peqdsk.f90
index 223bfcfb9..5d481012d 100644
--- a/profiles_gen/src/prgen_read_peqdsk.f90
+++ b/profiles_gen/src/prgen_read_peqdsk.f90
@@ -20,7 +20,6 @@ subroutine prgen_read_peqdsk
   !----------------------------------------------------
   ! Read the peqdsk file
   !
-
   open(unit=1,file='pfile.ne',status='old')
   read(1,*) i
   nx = i
diff --git a/profiles_gen/src/prgen_write.f90 b/profiles_gen/src/prgen_write.f90
index 6228ae3ab..1517273cf 100644
--- a/profiles_gen/src/prgen_write.f90
+++ b/profiles_gen/src/prgen_write.f90
@@ -48,7 +48,7 @@ subroutine prgen_write
      expro_shape_cos6 = shape_cos(6,:)
 
      expro_z_eff = zeff
-     
+
      ! EFIT passthrough functions
      expro_ptot = p_tot
      expro_fpol = fpol
@@ -63,9 +63,20 @@ subroutine prgen_write
   expro_head_gfile     = '#     *gfile : '//trim(file_g)
   expro_head_cerfile   = '#   *cerfile : '//trim(file_cer)
 
-  call expro_write('input.gacode')
-  print '(a)','INFO: (prgen_write) Wrote input.gacode.'
-  !-------------------------------------------------------------------------------------
-   
+  ! Run check for Jacobian
+  call expro_compute_derived
+
+  ! Use unit=2 since expro use unit=1
+  open(unit=2,file='success',status='replace')
+  if (expro_jerr == 0) then
+     call expro_write('input.gacode')
+     print '(a)','INFO: (prgen_write) Wrote input.gacode.'
+     ! Successful completion
+     write(2,*) 1
+  else
+     write(2,*) 2
+  endif
+  close(2)
+
 end subroutine prgen_write
 
diff --git a/qlgyro/Makefile b/qlgyro/Makefile
new file mode 100644
index 000000000..e3dfd7ef5
--- /dev/null
+++ b/qlgyro/Makefile
@@ -0,0 +1,30 @@
+#-----------------------------
+# Toplevel makefile for qlgyro
+#-----------------------------
+
+include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
+
+export EXTRA_LIBS = \
+       ${GACODE_ROOT}/neo/src/neo_lib.a \
+       ${GACODE_ROOT}/shared/nclass/nclass_lib.a \
+       ${GACODE_ROOT}/tglf/src/tglf_lib.a \
+       ${GACODE_ROOT}/cgyro/src/cgyro_lib.a \
+       ${GACODE_ROOT}/f2py/expro/expro_lib.a \
+       ${GACODE_ROOT}/f2py/geo/geo_lib.a \
+       ${GACODE_ROOT}/shared/math/math_lib.a \
+       ${GACODE_ROOT}/shared/UMFPACK/UMFPACK_lib.a
+
+all:
+	gacode_getversion > .VERSION
+	cd ${GACODE_ROOT}/shared ; make
+	cd ${GACODE_ROOT}/f2py ; make
+	cd ${GACODE_ROOT}/neo ; make
+	cd ${GACODE_ROOT}/tglf ; make
+	cd ${GACODE_ROOT}/cgyro ; make
+	cd src ; make
+
+clean:
+	cd src ; make clean
+	rm -rf .VERSION
+
+.IGNORE:
diff --git a/qlgyro/bin/qlgyro b/qlgyro/bin/qlgyro
new file mode 100755
index 000000000..4c6d0b958
--- /dev/null
+++ b/qlgyro/bin/qlgyro
@@ -0,0 +1,392 @@
+#!/bin/bash
+#=============================================================
+# qlgyro
+#
+# PURPOSE:
+#  Top-level script controlling execution of QLGYRO.
+#=============================================================
+
+#=============================================================
+# Syntax validity check and help message
+#
+n=$#
+
+if [ $n -eq 0 ]
+then
+  echo
+  echo "Usage:   qlgyro [options]"
+  echo
+  echo "         -p <path>"
+  echo "         Set optional path to simulation directory."
+  echo "         [The default path is the current directory]"
+  echo
+  echo "EXECUTE MODE"
+  echo
+  echo "         -e <simdir>" 
+  echo "         Run QLGYRO using input data in <simdir>."
+  echo
+  echo "         -n <MPI tasks>" 
+  echo "         Number of MPI tasks."
+  echo
+  echo "         -nomp <threads>" 
+  echo "         Number of OpenMP threads per MPI task."
+  echo
+  echo "         -numa <n>" 
+  echo "         NUMAs active per node."
+  echo
+  echo "         -mpinuma <n>" 
+  echo "         MPI tasks per active NUMA."
+  echo
+  echo "STARTUP CONTROL"
+  echo
+  echo "         -start <mode>"  
+  echo "         Mode for start/restart control"
+  echo "         <mode>=nosave (start new, don't save restart data),"
+  echo "                new    (start new, save restart data) [DEFAULT],"
+  echo "                cont   (continue simulation with restart data, save restart data),"
+  echo "                retry  (continue simulation with restart data, don't save restart data),"
+  echo "                init   (continue simulation with restart data, reset time to t=0)."
+  echo
+  echo "TEST MODE"
+  echo
+  echo "         -t <simdir>"  
+  echo "         Sanity test for INPUT data in <simdir>."
+  echo
+  echo "INITIALIZE ONLY"
+  echo
+  echo "         -i <simdir>" 
+  echo "         Process input.qlgyro only."
+  echo
+  echo "HALT"
+  echo
+  echo "         -K <simdir>" 
+  echo "         Set non-persistent halt signal in <simdir>."
+  echo 
+  echo "         -k <simdir>" 
+  echo "         Set persistent halt signal in <simdir>."
+  echo 
+  echo "         -c <simdir>" 
+  echo "         Clear persistent halt signal from <simdir>."
+  echo 
+  echo "REGRESSION TESTING"
+  echo
+  echo "         -rc <simdir>"
+  echo "         Check <simdir> for regression pass/fail."
+  echo 
+  echo "         -r"
+  echo "         Auto-run the full regression suite."
+  echo 
+  echo "         -reset"
+  echo "         Reset regression data."
+  echo 
+  echo "TEMPLATE GENERATION"
+  echo
+  echo "         -g"
+  echo "         List available simulation templates."
+  echo
+  echo "         -g <template>"
+  echo "         Copy <template> into simulation path."
+  echo
+  echo "UTILITIES"
+  echo 
+  echo "         -s <simdir>" 
+  echo "         Create small portable copy of <simdir>."
+  echo 
+  echo "         -h" 
+  echo "         Version and platform information."
+
+  exit 1
+fi
+#=============================================================
+
+#=============================================================
+# Define variables for flag capture
+#
+RUNBASE='out.qlgyro.run'
+VERBASE='out.qlgyro.version'
+#
+# Default simulation root and qlgyro directory
+SIMROOT=$PWD
+QLGYRO_DIR=$GACODE_ROOT/qlgyro
+GYRO_DIR=$GACODE_ROOT/gyro
+CGYRO_DIR=$GACODE_ROOT/cgyro
+CGYRO=0
+GYRO=0
+# Parallelization parameters
+NPROC=1
+NOMP=1
+NUMA=0
+MPINUMA=0
+# Execute/test mode flags
+EXEC_FLAG=0
+TEST_FLAG=0
+INIT_FLAG=0
+GENERATE_FLAG=0
+REGRESS=0
+REGRESS_RESET=0
+SCOPY_FLAG=0
+KILL_STATUS=2
+START=new
+#=============================================================
+
+#=============================================================
+# Parse command line options
+#
+while [ $# -gt 0 ] ; do
+  case "$1" in
+
+  -p) shift ; SIMROOT=$1 ;;
+
+  -e) shift ; LOCDIR=$1 ; EXEC_FLAG=1 ;;
+
+  -t) shift ; LOCDIR=$1 ; TEST_FLAG=1 ;;
+
+  -i) shift ; LOCDIR=$1 ; INIT_FLAG=1 ;;
+
+  -g) shift ; LOCDIR=$1 ; GENERATE_FLAG=1 ;;
+
+  -r) REGRESS=1 ;;
+
+  -rc) shift ; LOCDIR=$1 ; REGRESS=2 ;;
+
+  -reset) REGRESS_RESET=1 ;;
+
+  -s) shift ; LOCDIR=$1 ; SCOPY_FLAG=1 ;;
+
+  -n) shift ; NPROC=$1 ;;
+
+  -nomp) shift ; NOMP=$1 ;;
+
+  -numa) shift ; NUMA=$1 ;;
+
+  -mpinuma) shift ; MPINUMA=$1 ;;
+
+  -h) gacode_printversion QLGYRO ; exit 0 ;;
+
+  -K) shift ; KILL_STATUS=1 ; LOCDIR=$1 ;;
+
+  -k) shift ; KILL_STATUS=-1 ; LOCDIR=$1 ;;
+
+  -c) shift ; KILL_STATUS=0 ; LOCDIR=$1 ;;
+
+  -start) shift ; START=$1 ;;
+
+  *) echo "ERROR: incorrect qlgyro syntax." ; exit 1 ;;
+ 
+  esac
+  shift
+done
+#=============================================================
+
+if [ "$LOCDIR" == "." ]
+then
+   LOCDIR=`basename $PWD`
+   cd .. ; SIMROOT=$PWD
+fi
+SIMDIR=$SIMROOT/$LOCDIR
+
+#=============================================================
+case "$KILL_STATUS" in
+  -1) qlgyro_sim_kill $SIMDIR -1 ; exit 0 ;;
+   0) qlgyro_sim_kill $SIMDIR 0  ; exit 0 ;;
+   1) qlgyro_sim_kill $SIMDIR 1  ; exit 0 ;;  
+esac
+#=============================================================
+ 
+#============================================================
+# Check for inconsistent flags:
+if [ $REGRESS -eq 0 ] ; then
+   REGRESS_FLAG=0
+else
+   REGRESS_FLAG=1
+fi
+FLAG_SUM=$[$EXEC_FLAG+$TEST_FLAG+$GENERATE_FLAG 
+                     +$REGRESS_FLAG+$INIT_FLAG]
+if [ $FLAG_SUM -gt 1 ]
+then
+   echo "ERROR: Can only specify one of -e, -t, -g, -r, -i"
+   exit 1
+fi
+#============================================================
+
+#============================================================
+# Generate simdir if -g set, then exit.
+#
+if [ $GENERATE_FLAG -eq 1 ]
+then
+   if [ ! -f "${QLGYRO_DIR}/tools/input/$LOCDIR/input.gyro" ]
+   then
+      cat ${QLGYRO_DIR}/tools/input/simdir_list
+   else
+      cp -ai ${QLGYRO_DIR}/tools/input/$LOCDIR $SIMDIR
+   fi
+   exit 0
+fi
+#============================================================
+
+#============================================================
+# Do the regression test if -r set, then exit.
+#
+if [ $REGRESS -eq 1 ] 
+then 
+   N2=$[ NPROC / 2 ]
+   if [ $[ NPROC - 2 * N2 ] -eq 1 ]
+   then
+      echo "ERROR: QLGYRO regression tool"
+      echo "       Number of processors must be multiple of 2." 
+      exit 1
+   fi   
+   gacode_reg_do $NPROC $NOMP $REGRESS_RESET gyro 1e-5
+   exit 0
+fi
+if [ $REGRESS -eq 2 ] 
+then 
+   gacode_reg $LOCDIR $GACODE_ROOT/gyro/tools/input out.gyro.prec 1e-5 
+   exit 0
+fi
+#============================================================
+
+#============================================================
+# Everything else must be done in $SIMDIR; so ensure existence 
+# of $SIMDIR (needed at this point) and go there: 
+#
+if ! gacode_sim_warn $SIMDIR
+then
+   exit 1 
+fi 
+
+cd $SIMDIR
+#============================================================
+
+#=============================================================
+# Do a small-copy (copy small files into new directory)
+if [ $SCOPY_FLAG -eq 1 ]
+then
+   list="
+    input.qlgyro
+    input.qlgyro.gen
+    input.profiles
+    input.profiles.gen
+    input.profiles.geo
+    out.qlgyro.run
+    out.gyro.t
+    out.gyro.freq
+    out.gyro.error
+    out.gyro.gbflux
+    out.gyro.gbflux_i
+    out.gyro.gbflux_n
+    out.gyro.gbflux_exc
+    out.gyro.geometry_arrays
+    out.gyro.kxkyspec
+    out.gyro.phase_space
+    out.gyro.profile
+    out.gyro.timing
+    out.gyro.units
+    out.gyro.zerobar"
+
+   # Funny syntax below removes trailing /
+   target=${SIMDIR%/}"-s"
+   mkdir $target
+   for i in $list
+   do
+      cp -av $i $target
+   done
+   exit 0
+fi
+#=============================================================
+
+#==========================================================
+# Check for "hard halt", otherwise initialize halt file:
+#
+if [ -f halt ] 
+then
+   if [ `cat halt` = "-1" ] 
+   then
+      exit 1
+   fi   
+fi
+echo 0 > halt
+#==========================================================
+
+#==========================================================
+# echo number of tasks, then parse INPUT
+#
+echo "[Parsing data in input.qlgyro]" > $RUNBASE
+
+python $QLGYRO_DIR/bin/qlgyro_parse.py >> $RUNBASE
+CODE=$(eval tail -n 1 $RUNBASE)
+
+if [ $CODE = "GYRO" ]
+then
+    python $GYRO_DIR/bin/gyro_parse.py >> $RUNBASE
+fi
+
+if [ $CODE = "CGYRO" ]
+then
+    python $CGYRO_DIR/bin/cgyro_parse.py >> $RUNBASE
+fi
+
+if [ $? -eq 1 ] 
+then
+   cat $RUNBASE
+   exit 1
+fi
+#==========================================================
+
+#===========================================================
+# Set flags for execute or test:
+
+# Execute:
+if [ $EXEC_FLAG -eq 1 ]
+then
+
+   #==========================================================
+   # Version stamp:  
+   echo `gacode_getversion` > $VERBASE
+   echo $GACODE_PLATFORM >> $VERBASE
+   date >> $VERBASE
+
+   gacode_printversion QLGYRO 
+   #==========================================================
+
+   echo "0" > "$SIMDIR/gyrotest_flag"
+fi
+
+# Test:
+if [ $TEST_FLAG -eq 1 ]
+then
+   NUMA=1
+   MPINUMA=1
+   echo "1" > "$SIMDIR/gyrotest_flag"
+fi
+#===========================================================
+
+#===========================================================
+# Manage start control
+# 
+case "$START" in
+  nosave) echo "-1 [nosave]" > restart.dat ;;
+  new)    echo  "0 [new]" > restart.dat ;;
+  cont)   echo  "1 [continue]" > restart.dat ;;
+  retry)  echo  "2 [retry]" > restart.dat ;;
+  init)   echo  "3 [init]" > restart.dat ;;
+  *) echo "ERROR: bad argument to -start." ; exit 1 ;;
+esac
+#===========================================================
+
+#===========================================================
+# RUN QLGYRO
+#
+if [ $INIT_FLAG -ne 1 ]
+then
+  $GACODE_ROOT/platform/exec/exec.$GACODE_PLATFORM \
+    $SIMDIR $NPROC $QLGYRO_DIR/src/qlgyro $NOMP $NUMA $MPINUMA
+fi
+
+if [ $TEST_FLAG -eq 1 ] ; then
+   python $GACODE_ROOT/shared/bin/osxlist.py $RUNBASE
+   cat out.expro.run
+fi
+#===========================================================
+
+exit 0
diff --git a/qlgyro/bin/qlgyro_parse.py b/qlgyro/bin/qlgyro_parse.py
new file mode 100755
index 000000000..75cbef2ab
--- /dev/null
+++ b/qlgyro/bin/qlgyro_parse.py
@@ -0,0 +1,36 @@
+
+from gacodeinput import *
+import sys
+
+x = SimpleInput()
+
+x.set_extension('.gen')
+
+# QLGYRO input parameters
+x.add('N_PARALLEL', '1')
+x.add('N_RUNS', '1')
+x.add('GAMMA_E', '0.0')
+x.add('CODE', '0')
+x.add('KYGRID_MODEL', '1')
+x.add('KY', '0.3')
+x.add('NKY', '12')
+x.add('XNU_MODEL', '3')
+x.add('AUTO_BOX_SIZE', '0')
+x.add('KX_MAX_BOX', '1000000.0')
+x.add('SAT_RULE', '1')
+x.add('N_PX0', '1')
+x.add('PX0GRID_MODEL', '1')
+
+# Perform the parsing
+x.read_input('input.qlgyro')
+
+x.printmsg()
+
+if x.data_dict['CODE'] == '0':
+    print('GYRO')
+else:
+    print('CGYRO')
+
+sys.exit(x.error)
+
+
diff --git a/qlgyro/bin/qlgyro_sim_kill b/qlgyro/bin/qlgyro_sim_kill
new file mode 100755
index 000000000..4609d71c7
--- /dev/null
+++ b/qlgyro/bin/qlgyro_sim_kill
@@ -0,0 +1,35 @@
+#!/bin/sh
+#
+# SCRIPT:
+#  qlgyro_sim_kill
+#
+# FUNCTION:
+#  Clean simulation kill
+
+# Check for valid directory
+if ! qlgyro_sim_warn $1
+then
+   exit 1 
+fi
+
+# Send appropriate kill signal
+
+cd $1 ; echo $2 > halt
+
+# Echo action
+
+case "${2}" in
+
+   -1 )
+
+    echo "[Sent persistant kill signal to $1]" ;;
+
+   0 )
+
+    echo "[Cleared kill signal in $1]" ;;
+
+   1 )
+
+    echo "[Sent non-persistent kill signal to $1]" ;;
+
+esac
diff --git a/qlgyro/src/Makefile b/qlgyro/src/Makefile
new file mode 100644
index 000000000..5331fa384
--- /dev/null
+++ b/qlgyro/src/Makefile
@@ -0,0 +1,50 @@
+USE_HARVEST=
+
+include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
+
+ifeq ($(OPT),debug)
+   FFLAGS=${FDEBUG}
+else
+   FFLAGS=${FOPT}
+endif
+
+FC += ${FOMP} ${FACC}
+
+EXEC = qlgyro
+
+OBJECTS += qlgyro_globals.o \
+	   qlgyro_allocate_globals.o \
+	   qlgyro_cgyro_interface.o \
+	   qlgyro_catch_error.o \
+	   qlgyro_cgyro_cleanup.o \
+	   qlgyro_cgyro_map.o \
+	   qlgyro_comm_setup.o \
+	   qlgyro_comm_sync.o \
+	   qlgyro_ky_spectrum.o \
+	   qlgyro_inout.o \
+	   qlgyro_px0_spectrum.o \
+	   qlgyro_read_input.o \
+	   qlgyro_run_cgyro_balloon.o \
+	   qlgyro_run_cgyro_fluxtube.o \
+	   qlgyro_run.o \
+	   qlgyro_sat1.o \
+	   qlgyro_sat_mg.o \
+	   qlgyro_sum_fluxes.o \
+	   qlgyro_tglf_map.o \
+	   qlgyro_trap_component_error.o
+
+.SUFFIXES : .o .f90 .F90
+
+all: qlgyro_lib.a $(EXEC).o $(EXTRA_LIBS)
+	$(FC) $(FFLAGS) -o $(EXEC) $(EXEC).o qlgyro_lib.a $(EXTRA_LIBS) $(LMATH) $(NN_LIB) 
+
+qlgyro_lib.a: $(OBJECTS)
+	$(ARCH) qlgyro_lib.a $(OBJECTS)
+
+.f90.o .F90.o:
+	$(FC) $(FMATH) $(FFLAGS) $(NN_LIB) -c $<
+
+clean:
+	rm -f $(EXEC)
+	rm -f *.o ${GACODE_ROOT}/modules/qlgyro*.mod
+	rm -f qlgyro_lib.a
diff --git a/qlgyro/src/qlgyro.f90 b/qlgyro/src/qlgyro.f90
new file mode 100644
index 000000000..307419674
--- /dev/null
+++ b/qlgyro/src/qlgyro.f90
@@ -0,0 +1,132 @@
+!-----------------------------------------------------------------
+! qlgyro.f90
+!
+! PURPOSE:
+!  Main program wrapper for *standalone* QLGYRO usage.
+!-----------------------------------------------------------------
+
+program qlgyro
+
+  use mpi
+  use qlgyro_globals
+  use qlgyro_cgyro_interface
+
+  !-----------------------------------------------------------------
+  implicit none
+  !
+  integer :: supported, n_omp
+  integer, external :: omp_get_max_threads
+  !-----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Query OpenMP for threads
+  !
+  n_omp = omp_get_max_threads()
+  !-----------------------------------------------------------------
+  
+  !-----------------------------------------------------------------
+  ! Initialize MPI_COMM_WORLD communicator, including support for 
+  ! funneled threading (needed if OpenMP is enabled).
+  !
+  if (n_omp > 1) then
+     call MPI_INIT_THREAD(MPI_THREAD_FUNNELED,supported,ierr)
+     if (supported < MPI_THREAD_FUNNELED) then
+        call qlgyro_catch_error('ERROR: (GYRO) Multi-threaded MPI not supported.')
+     endif
+  else 
+     call MPI_INIT_THREAD(MPI_THREAD_SINGLE,supported,ierr)
+  endif
+  !-----------------------------------------------------------------
+  
+  !-----------------------------------------------------------------
+  ! Path is cwd:
+  !
+  path= './'
+  !-----------------------------------------------------------------
+  
+  !-----------------------------------------------------------------
+  ! Query MPI for dimensions
+  !
+  QLGYRO_COMM_WORLD = MPI_COMM_WORLD
+  !
+  ! Query rank and size
+  !
+  call MPI_COMM_RANK(QLGYRO_COMM_WORLD,i_proc_global,ierr)
+  call MPI_COMM_SIZE(QLGYRO_COMM_WORLD,n_proc_global,ierr)
+  n_inst = n_proc_global
+  !-----------------------------------------------------------------
+  
+  !-----------------------------------------------------------------
+  ! Standard standalone operation
+  transport_method = 0
+  !
+
+  call qlgyro_allocate_globals
+  
+  call qlgyro_read_input
+
+  call qlgyro_comm_setup
+
+  if (code .eq. 0) then
+     ! Set GYRO communicator to local communicator (per instance).
+     !GYRO_COMM_WORLD = qlgyro_comm
+  
+     !call gyro_init(path, GYRO_COMM_WORLD)
+
+     !call qlgyro_run_gyro
+     print*, "GYRO not supported in QLGYRO"
+     call exit
+
+  else
+
+     CGYRO_COMM_WORLD = qlgyro_comm
+     call cgyro_init(path, CGYRO_COMM_WORLD)
+
+     ! Map CGYRO variables to their interface values
+     call map_global2interface
+     call allocate_cgyro_interface
+
+     if (cgyro_n_toroidal_in .gt. 1) then
+        call qlgyro_run_cgyro_fluxtube
+     else
+        call qlgyro_run_cgyro_balloon
+     end if
+
+  end if
+  ! Synchronise all cores
+  call qlgyro_comm_sync
+  
+  ! Apply saturation rule
+  if (sat_rule .eq. 1) then
+     call qlgyro_sat1
+  else if (sat_rule .eq. -1) then
+     call qlgyro_sat_mg
+  else
+     open(unit=1,file=trim(runfile),position='append')
+     write(1,*) '-----------------------------------------'
+     write(1,*) 'Sat rule ', sat_rule, 'not a valid option'
+     write(1,*) '-----------------------------------------'
+     stop
+  end if
+  
+  ! Sum flux over ky spectrum
+  call qlgyro_sum_fluxes
+
+  if (i_proc_global .eq. 0) then
+     ! write ky spectrum to file out.tglf.ky_spectrum
+     call write_qlgyro_ky_spectrum
+     call write_qlgyro_QL_weight_spectrum
+     call write_qlgyro_eigenvalue_spectrum
+     call write_qlgyro_flux_spectrum
+     call write_qlgyro_field_spectrum
+     call write_qlgyro_gbflux
+     call write_qlgyro_units
+     call write_qlgyro_sat_geo_spectrum
+     call write_qlgyro_kxrms_spectrum
+  
+     print*, 'Completed QLGYRO run'
+     
+  end if
+  
+  call MPI_FINALIZE(ierr)
+end program qlgyro
diff --git a/qlgyro/src/qlgyro_allocate_globals.f90 b/qlgyro/src/qlgyro_allocate_globals.f90
new file mode 100644
index 000000000..4bfb88356
--- /dev/null
+++ b/qlgyro/src/qlgyro_allocate_globals.f90
@@ -0,0 +1,20 @@
+subroutine qlgyro_allocate_globals
+
+  use qlgyro_globals
+
+  implicit none
+
+  ! Collision frequencies
+  if (.not. allocated(nui)) allocate(nui(n_ion_max))
+  if (.not. allocated(ti)) allocate(ti(n_ion_max))
+  if (.not. allocated(dlntidr)) allocate(dlntidr(n_ion_max))
+  if (.not. allocated(ni)) allocate(ni(n_ion_max))
+  if (.not. allocated(dlnnidr)) allocate(dlnnidr(n_ion_max))
+
+  if (.not. allocated(a_fourier_geo)) allocate(a_fourier_geo(8,0:32))
+  
+  pi = 4.0*atan(1.0)
+  !
+  mp  = 1
+
+end subroutine qlgyro_allocate_globals
diff --git a/qlgyro/src/qlgyro_catch_error.f90 b/qlgyro/src/qlgyro_catch_error.f90
new file mode 100644
index 000000000..f0e29ea34
--- /dev/null
+++ b/qlgyro/src/qlgyro_catch_error.f90
@@ -0,0 +1,29 @@
+!-----------------------------------------------------------
+! qlgyro_catch_error.f90
+!
+! PURPOSE:
+!  Routine to print error message, finalize MPI, and
+!  stop program execution gracefully. 
+!-----------------------------------------------------------
+
+subroutine qlgyro_catch_error(message)
+
+  use qlgyro_globals
+
+  implicit none
+
+  character (len=*), intent(in) :: message
+
+  if (i_proc_global == 0) then
+     open(unit=1,file=trim(runfile),status='old',position='append')
+     write(1,10) message
+     close(1)
+     print '(a)','** TGYRO HALTED ON ERROR ** (see out.tgyro.run)'
+  endif
+
+  call MPI_finalize(ierr)
+  stop
+
+10 format(a)
+
+end subroutine qlgyro_catch_error
diff --git a/qlgyro/src/qlgyro_cgyro_cleanup.F90 b/qlgyro/src/qlgyro_cgyro_cleanup.F90
new file mode 100644
index 000000000..553abc9b0
--- /dev/null
+++ b/qlgyro/src/qlgyro_cgyro_cleanup.F90
@@ -0,0 +1,530 @@
+!-----------------------------------------------------------
+! qlgyro_cgyro_cleanup.f90
+!
+! PURPOSE:
+!  Assign output to interface, Deallocate and clean up.
+!-----------------------------------------------------------
+
+subroutine qlgyro_cgyro_cleanup
+
+  use mpi
+  use parallel_lib
+  use timer_lib
+  use cgyro_globals
+  use qlgyro_cgyro_interface
+  use qlgyro_globals
+
+  implicit none
+
+  integer :: l, i_field, ir, it, pos, start, end
+  complex :: a_norm
+  complex :: ftemp(cgyro_n_theta_in, cgyro_n_radial_in)
+
+  ! No need for cleanup in test mode
+  if (test_flag == 1) return
+
+  ! Manage exit message
+  cgyro_error_status_out = error_status
+  cgyro_signal_out = signal
+  
+  if (signal == 1) then
+     cgyro_error_message_out = 'Linear converged'
+  else
+     cgyro_error_message_out = 'Linear terminated at max time'
+  endif
+
+  ! Write eigenvalues to interface
+  cgyro_omega_out = freq
+  cgyro_omega_error_out = freq_err
+
+  bgs2 = b_gs2
+
+  ! Convert to right units now
+  cgyro_k_perp_out = k_perp * rho / bgs2
+  
+  do ir=1, cgyro_n_radial_in
+     start = (ir - 1)* cgyro_n_theta_in + 1
+     end =  ir * cgyro_n_theta_in
+     cgyro_jacobian_out(start:end) = g_theta / bmag
+  end do
+
+  ! Fluxes - reorder output for QLGYRO
+  ! Re-normalise 
+  do i_tor=1,cgyro_n_toroidal_in
+     do l=1,3
+        cgyro_gbflux_out(l, :, :, i_tor) = real(gflux(0, :, l, :, i_tor))
+     end do
+  end do
+
+  ! Wavefunction
+  do i_tor=1,cgyro_n_toroidal_in
+     do i_field=1,cgyro_n_field_in
+        do ir=1,cgyro_n_radial_in
+           do it=1,cgyro_n_theta_in
+              ftemp(it,ir) = field(i_field,ic_c(ir,it),i_tor)
+           enddo
+        enddo
+
+        if (i_field == 1) then
+           it = maxloc(abs(ftemp(:,cgyro_n_radial_in/2+1)),dim=1)
+           a_norm = ftemp(it,cgyro_n_radial_in/2+1)
+        endif
+        call extended_ang(ftemp)
+     
+        ftemp = ftemp / a_norm
+        
+        cgyro_wavefunction_out(i_tor, i_field, :) = reshape(ftemp, (/cgyro_n_radial_in * cgyro_n_theta_in/))
+  end do
+enddo
+
+  if (auto_box_size .eq. 0) then
+     ! Get ballooning theta from out.cgyro.grids
+     open(unit=io, file=trim(runpath)//'out.cgyro.grids', status='old')
+     
+     ! Skip to thetab line in file
+     pos = (11 + cgyro_n_radial_in + cgyro_n_theta_in + cgyro_n_energy_in + cgyro_n_xi_in)
+     do l=1,pos
+        read(io, *)
+     end do
+    
+     read(io, '(1pe13.6)') cgyro_thetab_out
+     close(io)
+  else
+     cgyro_thetab_out = 0.0
+  end if
+  ! Free up commuicators
+  call MPI_COMM_FREE(NEW_COMM_1,i_err)
+  call MPI_COMM_FREE(NEW_COMM_2,i_err)
+
+  ! If in TGYRO remove tag
+  if (tag_removal .eq. 1) then
+     if (adjoint .eq. 0) then
+        open(unit=io, iostat=i_err, file=trim(runpath)//runfile_restart_tag, status='old')
+        if (i_err == 0) close(io, status='delete')
+     end if
+  end if
+  
+  ! Reset timer info
+  timer_cpu_maxindx = 0
+  timer_cpu_tag = ''
+  timer_cpu=0.0
+  timer_cpu_in=0.0
+
+  ! Deallocate arrays
+  !call cgyro_deallocate_arrays
+  
+end subroutine qlgyro_cgyro_cleanup
+
+
+subroutine qlgyro_cgyro_deallocate_arrays
+
+  use cgyro_globals
+  use parallel_lib
+  implicit none
+
+#if defined(_OPENACC) || defined(OMPGPU)
+#define CGYRO_GPU_FFT
+#endif
+
+#if defined(OMPGPU)
+
+#define ccl_del_device(x) \
+!$omp target exit data map(release:x)
+#define ccl_del_bigdevice(x) \
+!$omp target exit data map(release:x) if (gpu_bigmem_flag == 1)
+
+#elif defined(_OPENACC)
+
+#define ccl_del_device(x) \
+!$acc exit data delete(x)
+#define ccl_del_bigdevice(x) \
+!$acc exit data delete(x) if (gpu_bigmem_flag == 1)
+
+#else
+
+  ! nothing to do
+#define ccl_del_device(x)
+#define ccl_del_bigdevice(x)
+
+#endif
+
+  if(allocated(energy))        deallocate(energy)
+  if(allocated(vel))        then
+     ccl_del_device(vel)
+     deallocate(vel)
+  endif
+  if(allocated(vel2))        then
+     ccl_del_device(vel2)
+     deallocate(vel2)
+  endif
+  if(allocated(w_e))           deallocate(w_e)
+  if(allocated(e_deriv1_mat))  deallocate(e_deriv1_mat)
+  if(allocated(e_deriv1_rot_mat))  deallocate(e_deriv1_rot_mat)
+  if(allocated(xi))            then
+     ccl_del_device(xi)
+     deallocate(xi)
+  endif
+  if(allocated(w_xi))          deallocate(w_xi)
+  if(allocated(w_exi))         deallocate(w_exi)
+  if(allocated(xi_lor_mat))    deallocate(xi_lor_mat)
+  if(allocated(xi_deriv_mat))  deallocate(xi_deriv_mat)
+  
+  if(allocated(theta))          deallocate(theta)
+  if(allocated(thetab))         deallocate(thetab)
+  if(allocated(w_theta))        deallocate(w_theta)
+  if(allocated(g_theta))        deallocate(g_theta)
+  if(allocated(g_theta_geo))    deallocate(g_theta_geo)
+  if(allocated(bmag))           deallocate(bmag)
+  if(allocated(btor))           deallocate(btor)
+  if(allocated(bpol))           deallocate(bpol)
+  if(allocated(k_perp))         deallocate(k_perp)
+  if(allocated(k_x))            deallocate(k_x)
+  if(allocated(bigr))           deallocate(bigr)
+  if(allocated(bigr_r))         deallocate(bigr_r)
+  if(allocated(captheta))       deallocate(captheta)
+  if(allocated(itp))            deallocate(itp)
+  if(allocated(omega_stream))   then
+     ccl_del_device(omega_stream)
+     deallocate(omega_stream)
+  endif
+  if(allocated(omega_trap))          deallocate(omega_trap)
+  if(allocated(omega_rdrift))        deallocate(omega_rdrift)
+  if(allocated(omega_adrift))        deallocate(omega_adrift)
+  if(allocated(omega_aprdrift))      deallocate(omega_aprdrift)
+  if(allocated(omega_cdrift))        deallocate(omega_cdrift)
+  if(allocated(omega_cdrift_r))      deallocate(omega_cdrift_r)
+  if(allocated(omega_gammap))        deallocate(omega_gammap)
+  if(allocated(lambda_rot))          deallocate(lambda_rot)
+  if(allocated(dlambda_rot))         deallocate(dlambda_rot)
+  if(allocated(dens_rot))            deallocate(dens_rot)
+  if(allocated(dens2_rot))           deallocate(dens2_rot)
+  if(allocated(dens_ele_rot))        deallocate(dens_ele_rot)
+  if(allocated(dens_avg_rot))        deallocate(dens_avg_rot)
+  if(allocated(dlnndr_avg_rot))      deallocate(dlnndr_avg_rot)
+  if(allocated(omega_rot_trap))      deallocate(omega_rot_trap)
+  if(allocated(omega_rot_u))         deallocate(omega_rot_u)
+  if(allocated(omega_rot_drift))     deallocate(omega_rot_drift)
+  if(allocated(omega_rot_drift_r))   deallocate(omega_rot_drift_r)
+  if(allocated(omega_rot_edrift))    deallocate(omega_rot_edrift)
+  if(allocated(omega_rot_edrift_r))  deallocate(omega_rot_edrift_r)
+  if(allocated(omega_rot_star))      deallocate(omega_rot_star)
+  if(allocated(gtime))               deallocate(gtime)
+  if(allocated(freq))                deallocate(freq)
+  if(allocated(freq_err))            deallocate(freq_err)
+  if(allocated(fcoef))  then
+     ccl_del_device(fcoef)     
+     deallocate(fcoef)
+  endif
+  if(allocated(gcoef))  then
+     ccl_del_device(gcoef)     
+     deallocate(gcoef)
+  endif
+  if(allocated(field))  then
+     ccl_del_device(field)     
+     deallocate(field)
+  endif
+  if(allocated(field_loc))  then
+     ccl_del_device(field_loc)     
+     deallocate(field_loc)
+  endif
+  if(allocated(field_dot))           deallocate(field_dot)
+  if(allocated(field_old))           deallocate(field_old)
+  if(allocated(field_old2))          deallocate(field_old2)
+  if(allocated(field_old3))          deallocate(field_old3)
+  if(allocated(moment))              deallocate(moment)
+  if(allocated(moment_loc))          deallocate(moment_loc)
+  if(allocated(cflux))               deallocate(cflux)
+  if(allocated(cflux_loc))           deallocate(cflux_loc)
+  if(allocated(gflux))               deallocate(gflux)
+  if(allocated(gflux_loc))           deallocate(gflux_loc)
+  if(allocated(cflux_tave))          deallocate(cflux_tave)
+  if(allocated(gflux_tave))          deallocate(gflux_tave)
+  if(allocated(recv_status))         deallocate(recv_status)
+  if(allocated(icd_c))  then
+     ccl_del_device(icd_c)     
+     deallocate(icd_c)
+  endif
+  if(allocated(dtheta)) then
+     ccl_del_device(dtheta)     
+     deallocate(dtheta)
+  endif
+  if(allocated(dtheta_up))  then
+     ccl_del_device(dtheta_up)     
+     deallocate(dtheta_up)
+  endif
+  if(allocated(source)) then
+      ccl_del_device(source)      
+     deallocate(source)
+  endif
+  if(allocated(h0_old)) then
+     ccl_del_device(h0_old)      
+     deallocate(h0_old)
+  endif
+  if(allocated(rhs)) then
+     ccl_del_device(rhs)       
+     deallocate(rhs)
+  endif
+  if(allocated(h_x)) then
+     ccl_del_device(h_x)       
+     deallocate(h_x)
+  endif
+  if(allocated(g_x)) then
+     ccl_del_device(g_x)       
+     deallocate(g_x)
+  endif
+  if(allocated(h0_x)) then
+     ccl_del_device(h0_x)        
+     deallocate(h0_x)
+  endif
+  if(allocated(cap_h_c)) then
+     ccl_del_device(cap_h_c)       
+     deallocate(cap_h_c)
+  endif
+  if(allocated(cap_h_ct))  then
+     ccl_del_device(cap_h_ct)       
+     deallocate(cap_h_ct)
+  endif
+  if(allocated(cap_h_c_dot)) then
+     ccl_del_device(cap_h_c_dot)
+     deallocate(cap_h_c_dot)
+  endif
+  if(allocated(cap_h_c_old)) then
+     ccl_del_device(cap_h_c_old)
+     deallocate(cap_h_c_old)
+  endif
+  if(allocated(cap_h_c_old2)) then
+     ccl_del_device(cap_h_c_old2)
+     deallocate(cap_h_c_old2)
+  endif
+  if(allocated(omega_cap_h)) then
+     ccl_del_device(omega_cap_h)        
+     deallocate(omega_cap_h)
+  endif
+  if(allocated(omega_h)) then
+     ccl_del_device(omega_h)        
+     deallocate(omega_h)
+  endif
+  if(allocated(omega_s)) then
+     ccl_del_device(omega_s)        
+     deallocate(omega_s)
+  endif
+  if(allocated(omega_ss)) then
+     ccl_del_device(omega_ss)        
+     deallocate(omega_ss)
+  endif
+  if(allocated(jvec_c))  then
+     ccl_del_device(jvec_c)     
+     deallocate(jvec_c)
+  endif
+  if(allocated(jvec_c_nl))  then
+     ccl_del_device(jvec_c_nl)
+     deallocate(jvec_c_nl)
+  endif
+  if(allocated(jvec_v))              deallocate(jvec_v)
+  if(allocated(dvjvec_c)) then
+     ccl_del_device(dvjvec_c)     
+     deallocate(dvjvec_c)
+  endif
+  if(allocated(dvjvec_v)) then
+     ccl_del_device(dvjvec_v)     
+     deallocate(dvjvec_v)
+  endif
+  if(allocated(jxvec_c))  then
+     deallocate(jxvec_c)
+  endif
+  if(allocated(upfac1))   then
+     ccl_del_device(upfac1)
+     deallocate(upfac1)
+  endif
+  if(allocated(upfac2))   then
+     ccl_del_device(upfac2)
+     deallocate(upfac2)
+  endif
+  if(allocated(cap_h_v))  then
+     ccl_del_device(cap_h_v)     
+     deallocate(cap_h_v)
+  endif
+  if(allocated(upwind_res_loc))   then
+     ccl_del_device(upwind_res_loc)
+     deallocate(upwind_res_loc)
+  endif
+  if(allocated(upwind_res))   then
+     ccl_del_device(upwind_res)
+     deallocate(upwind_res)
+  endif
+  if(allocated(upwind32_res_loc))   then
+     ccl_del_device(upwind32_res_loc)
+     deallocate(upwind32_res_loc)
+  endif
+  if(allocated(upwind32_res))   then
+     ccl_del_device(upwind32_res)
+     deallocate(upwind32_res)
+  endif
+  if(allocated(fA_nl))   then
+     ccl_del_device(fA_nl)
+     deallocate(fA_nl)
+  endif
+  if(allocated(fB_nl))   then
+     ccl_del_device(fB_nl)
+     deallocate(fB_nl)
+  endif
+  if(allocated(g_nl))   then
+     ccl_del_device(g_nl)
+     deallocate(g_nl)
+  endif
+  if(allocated(fpackA))   then
+     ccl_del_device(fpackA)
+     deallocate(fpackA)
+  endif
+  if(allocated(fpackB))   then
+     ccl_del_device(fpackB)
+     deallocate(fpackB)
+  endif
+  if(allocated(gpack))   then
+     ccl_del_device(gpack)
+     deallocate(gpack)
+  endif
+  if (allocated(cmat)) then
+     ccl_del_bigdevice(cmat)
+     deallocate(cmat)
+  endif
+  if (allocated(cmat_fp32)) then
+     ccl_del_bigdevice(cmat_fp32)
+     deallocate(cmat_fp32)
+  endif
+  if (allocated(cmat_stripes)) then
+     ccl_del_bigdevice(cmat_stripes)
+     deallocate(cmat_stripes)
+  endif
+    if (allocated(cmat_simple)) then
+     ccl_del_device(cmat_simple)     
+     deallocate(cmat_simple)
+  endif
+
+#ifndef CGYRO_GPU_FFT
+  if(allocated(fx))                deallocate(fx)
+  if(allocated(gx))                deallocate(gx)
+  if(allocated(fy))                deallocate(fy)
+  if(allocated(gy))                deallocate(gy)
+  if(allocated(vxmany))            deallocate(vxmany)
+  if(allocated(vymany))            deallocate(vymany)
+  if(allocated(uxmany))            deallocate(uxmany)
+  if(allocated(uymany))            deallocate(uymany)
+  if(allocated(uv))                deallocate(uv)
+#endif  
+
+#ifdef CGYRO_GPU_FFT
+  if(allocated(fxmany))    then
+     ccl_del_device(fxmany)     
+     deallocate(fxmany)
+  endif
+  if(allocated(gxmany))    then
+     ccl_del_device(gxmany)     
+     deallocate(gxmany)
+  endif
+  if(allocated(fymany))    then
+     ccl_del_device(fymany)     
+     deallocate(fymany)
+  endif
+  if(allocated(gymany))    then
+     ccl_del_device(gymany)     
+     deallocate(gymany)
+  endif
+  if(allocated(uxmany))    then
+      ccl_del_device(uxmany)    
+     deallocate(uxmany)
+  endif
+  if(allocated(uymany))    then
+     ccl_del_device(uymany)     
+     deallocate(uymany)
+  endif
+  if(allocated(vxmany))     then
+     ccl_del_device(vxmany)     
+     deallocate(vxmany)
+  endif
+  if(allocated(vymany))     then
+     ccl_del_device(vymany)     
+     deallocate(vymany)
+  endif
+  if(allocated(uvmany))     then
+     ccl_del_device(uvmany)     
+     deallocate(uvmany)
+  endif
+#endif    
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!
+  ! From cgyro_make_profiles
+  !!!!!!!!!!!!!!!!!!!!!!!!!!
+  
+  if(allocated(px))  then
+     ccl_del_device(px)      
+     deallocate(px)
+  endif
+
+  if(allocated(geo_yin))          deallocate(geo_yin)
+  
+     ccl_del_device(z)
+
+     ccl_del_device(temp) 
+  
+  
+  !!!!!!!!!!!!!!!!!!!!!!!!!!
+  ! From cgyro_init_arrays
+  !!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  if(allocated(vfac))             deallocate(vfac)
+  if(allocated(sum_den_h))        deallocate(sum_den_h)
+  if(allocated(cderiv))           deallocate(cderiv)
+  if(allocated(uderiv))           deallocate(uderiv)
+  if(allocated(c_wave)) then
+     ccl_del_device(c_wave)     
+     deallocate(c_wave)
+  endif
+  if(allocated(hzf))              deallocate(hzf)
+  if(allocated(xzf))              deallocate(xzf)
+
+  !!!!!!!!!!!!!!!!!!!!!!!!!!
+  ! From cgyro_mpi_grid
+  !!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  if(allocated(ie_v)) then
+     ccl_del_device(ie_v)     
+     deallocate(ie_v)
+  endif
+
+  if(allocated(ix_v)) then
+     ccl_del_device(ix_v)     
+     deallocate(ix_v)
+  endif
+
+  if(allocated(is_v)) then
+     ccl_del_device(is_v)     
+     deallocate(is_v)
+  endif
+
+  if(allocated(iv_v)) then
+     ccl_del_device(iv_v)     
+     deallocate(iv_v)
+  endif
+
+    if(allocated(ir_c)) then
+     ccl_del_device(ir_c)     
+     deallocate(ir_c)
+  endif
+
+  if(allocated(it_c)) then
+     ccl_del_device(it_c)     
+     deallocate(it_c)
+  endif
+
+  if(allocated(ic_c)) then
+     ccl_del_device(ic_c)     
+     deallocate(ic_c)
+  endif
+
+  if(allocated(ica_c))            deallocate(ica_c)
+  if(allocated(icb_c))            deallocate(icb_c)
+  
+
+end subroutine qlgyro_cgyro_deallocate_arrays
+
diff --git a/qlgyro/src/qlgyro_cgyro_interface.f90 b/qlgyro/src/qlgyro_cgyro_interface.f90
new file mode 100644
index 000000000..554d727ca
--- /dev/null
+++ b/qlgyro/src/qlgyro_cgyro_interface.f90
@@ -0,0 +1,767 @@
+!-------------------------------------------------------------------------
+! cgyro_interface.f90
+!
+! PURPOSE:
+!  Provides interface description for CGYRO.
+!
+! CALLING SEQUENCE:
+!  call cgyro_init(...)
+!  set cgyro_*_in variables
+!  call cgyro_kernel(...)
+!  get cgyro_*_out variables
+!-------------------------------------------------------------------------
+
+module qlgyro_cgyro_interface
+
+  implicit none
+
+  ! Input parameters (set to default values from cgyro/bin/cgyro_parse.py)
+  integer :: cgyro_n_energy_in = 8
+  integer :: cgyro_n_xi_in = 16
+  integer :: cgyro_n_theta_in = 24
+  integer :: cgyro_n_radial_in = 4
+  integer :: cgyro_n_toroidal_in = 1
+  integer :: cgyro_n_field_in = 1
+  real :: cgyro_e_max_in = 8.0
+  real :: cgyro_alpha_poly_in = 0.0
+  integer :: cgyro_e_fix_in = 2
+  integer :: cgyro_delta_t_method_in = 0
+  real :: cgyro_delta_t_in = 0.01
+  real :: cgyro_error_tol_in = 6e-5
+  real :: cgyro_max_time_in = 100.0
+  integer :: cgyro_print_step_in = 100
+  integer :: cgyro_restart_step_in = 10
+  real :: cgyro_freq_tol_in = 0.001
+  integer :: cgyro_restart_flag_in = 0
+  real :: cgyro_up_radial_in = 1.0
+  real :: cgyro_up_theta_in = 1.0
+  real :: cgyro_up_alpha_in = 0.0
+  integer :: cgyro_nup_radial_in = 3
+  integer :: cgyro_nup_theta_in = 3
+  integer :: cgyro_nup_alpha_in = 3
+  integer :: cgyro_n_wave_in = 2
+  integer :: cgyro_constant_stream_flag_in = 1
+  integer :: cgyro_explicit_trap_flag_in = 0
+  real :: cgyro_ky_in = 0.3
+  integer :: cgyro_box_size_in = 1
+  real :: cgyro_ipccw_in = -1.0
+  real :: cgyro_btccw_in = -1.0
+  integer :: cgyro_silent_flag_in = 0
+  integer :: cgyro_profile_model_in = 1
+  integer :: cgyro_equilibrium_model_in = 2
+  integer :: cgyro_collision_model_in = 4
+  integer :: cgyro_collision_mom_restore_in = 1
+  integer :: cgyro_collision_ene_restore_in = 1
+  integer :: cgyro_collision_ene_diffusion_in = 1
+  integer :: cgyro_collision_kperp_in = 1
+  integer :: cgyro_collision_field_model_in = 1
+  integer :: cgyro_collision_ion_model_in = 0
+  integer :: cgyro_collision_precision_mode_in = 0
+  real :: cgyro_z_eff_in = 1.0
+  integer :: cgyro_z_eff_method_in = 2
+  integer :: cgyro_zf_test_mode_in = 0
+  integer :: cgyro_nonlinear_flag_in = 0
+  integer :: cgyro_ae_flag_in = 0
+  real :: cgyro_temp_ae_in = 1.0
+  real :: cgyro_dens_ae_in = 1.0
+  real :: cgyro_mass_ae_in = 0.0002724486
+  real :: cgyro_dlntdr_ae_in = 1.0
+  real :: cgyro_dlnndr_ae_in = 1.0
+  real :: cgyro_lambda_star_in = 0.0
+  integer :: cgyro_h_print_flag_in = 0
+  integer :: cgyro_moment_print_flag_in = 0
+  integer :: cgyro_gflux_print_flag_in = 0
+  integer :: cgyro_field_print_flag_in = 0
+  real :: cgyro_amp0_in = 0
+  real :: cgyro_amp_in = 0.1
+  real :: cgyro_gamma_e_in = 0.0
+  real :: cgyro_gamma_p_in = 0.0
+  real :: cgyro_mach_in = 0.0
+  integer :: cgyro_rotation_model_in = 1
+  integer :: cgyro_toroidals_per_proc_in = 1
+  integer :: cgyro_mpi_rank_order_in = 2
+  integer :: cgyro_velocity_order_in = 1
+  integer :: cgyro_hiprec_flag_in = 0
+  integer :: cgyro_udsymmetry_flag_in = 0
+  integer :: cgyro_shear_method_in = 2
+  integer :: cgyro_n_global_in = 4
+  real :: cgyro_nu_global_in = 15.0
+  integer :: cgyro_psym_flag_in = 0
+  integer :: cgyro_profile_shear_flag_in = 0
+  integer :: cgyro_theta_plot_in = 1
+  integer :: cgyro_gpu_bigmem_flag_in = 1
+  integer :: cgyro_upwind_single_flag_in = 0
+  real :: cgyro_px0_in = 0.0
+  integer :: cgyro_stream_term_in = 0
+  real :: cgyro_stream_factor_in = 1.0
+  integer :: cgyro_exch_flag_in = 0
+  real :: cgyro_res_weight_power_in = 1.0
+
+  real :: cgyro_rmin_in = 0.5
+  real :: cgyro_rmaj_in = 3.0
+  real :: cgyro_q_in = 2.0
+  real :: cgyro_s_in = 1.0
+  real :: cgyro_shift_in = 0.0
+  real :: cgyro_kappa_in = 1.0
+  real :: cgyro_s_kappa_in = 0.0
+  real :: cgyro_delta_in = 0.0  
+  real :: cgyro_s_delta_in = 0.0
+  real :: cgyro_zeta_in = 0.0
+  real :: cgyro_s_zeta_in = 0.0
+  real :: cgyro_zmag_in = 0.0  
+  real :: cgyro_dzmag_in = 0.0
+  integer, parameter :: n_shape=6
+  real :: cgyro_shape_sin3_in = 0.0
+  real :: cgyro_shape_s_sin3_in = 0.0
+  real :: cgyro_shape_sin4_in = 0.0
+  real :: cgyro_shape_s_sin4_in = 0.0
+  real :: cgyro_shape_sin5_in = 0.0
+  real :: cgyro_shape_s_sin5_in = 0.0
+  real :: cgyro_shape_sin6_in = 0.0
+  real :: cgyro_shape_s_sin6_in = 0.0
+  real :: cgyro_shape_cos0_in = 0.0
+  real :: cgyro_shape_s_cos0_in = 0.0
+  real :: cgyro_shape_cos1_in = 0.0
+  real :: cgyro_shape_s_cos1_in = 0.0
+  real :: cgyro_shape_cos2_in = 0.0
+  real :: cgyro_shape_s_cos2_in = 0.0
+  real :: cgyro_shape_cos3_in = 0.0
+  real :: cgyro_shape_s_cos3_in = 0.0
+  real :: cgyro_shape_cos4_in = 0.0
+  real :: cgyro_shape_s_cos4_in = 0.0
+  real :: cgyro_shape_cos5_in = 0.0
+  real :: cgyro_shape_s_cos5_in = 0.0
+  real :: cgyro_shape_cos6_in = 0.0
+  real :: cgyro_shape_s_cos6_in = 0.0
+  real :: cgyro_betae_unit_in = 0.0
+  integer :: cgyro_n_species_in = 1
+
+  real :: cgyro_nu_ee_in = 0.1
+  
+  real, dimension(11) :: cgyro_z_in = 1.0
+  real, dimension(11) :: cgyro_mass_in = 0.0
+  real, dimension(11) :: cgyro_dens_in = (/1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0/)
+  real, dimension(11) :: cgyro_temp_in = 1.0
+  real, dimension(11) :: cgyro_dlnndr_in = 1.0
+  real, dimension(11) :: cgyro_dlntdr_in = 1.0
+  real, dimension(11) :: cgyro_sdlnndr_in = 0.0
+  real, dimension(11) :: cgyro_sdlntdr_in = 0.0
+
+  integer :: cgyro_subroutine_flag_in = 1 
+  integer :: cgyro_quasineutral_flag_in = 1 
+  real :: cgyro_lambda_star_scale_in = 1.0
+  real :: cgyro_gamma_e_scale_in = 1.0
+  real :: cgyro_gamma_p_scale_in = 1.0
+  real :: cgyro_mach_scale_in = 1.0
+  real :: cgyro_beta_star_scale_in = 1.0
+  real :: cgyro_betae_unit_scale_in = 1.0
+  real :: cgyro_nu_ee_scale_in = 1.0
+  
+  real, dimension(11) :: cgyro_dlnndr_scale_in = 1.0
+  real, dimension(11) :: cgyro_dlntdr_scale_in = 1.0
+
+  ! Normalisation values
+  real :: cgyro_b_unit_in=1
+  real :: cgyro_b_gs2_in=1.0
+  real :: cgyro_a_meters_in=1
+  real :: cgyro_temp_norm_in=1.0
+  real :: cgyro_dens_norm_in=1.0
+  real :: cgyro_rho_star_norm_in=8.3333333e-4
+  real :: cgyro_vth_norm_in=2.1850387e5
+  
+  ! Output parameters
+  real, dimension(:), allocatable :: cgyro_elec_pflux_out 
+  real, dimension(:), allocatable :: cgyro_elec_mflux_out 
+  real, dimension(:), allocatable :: cgyro_elec_eflux_out
+  real, dimension(:), allocatable :: cgyro_elec_expwd_out 
+
+  real, dimension(:,:), allocatable :: cgyro_ion_pflux_out
+  real, dimension(:,:), allocatable :: cgyro_ion_mflux_out
+  real, dimension(:,:), allocatable :: cgyro_ion_eflux_out
+  real, dimension(:,:), allocatable :: cgyro_ion_expwd_out
+
+
+  complex, dimension(:, :, :), allocatable :: cgyro_wavefunction_out
+  real, dimension(:), allocatable :: cgyro_thetab_out
+  
+  real, dimension(:), allocatable :: cgyro_r_out
+
+  real, dimension(:, :, :, :), allocatable :: cgyro_gbflux_out
+  real, dimension(:, :), allocatable :: cgyro_k_perp_out
+  real, dimension(:), allocatable :: cgyro_jacobian_out
+
+  complex, dimension(:), allocatable :: cgyro_omega_out
+  complex, dimension(:), allocatable :: cgyro_omega_error_out
+
+  integer :: cgyro_signal_out
+  integer :: cgyro_error_status_out
+  character(len=80) :: cgyro_error_message_out
+
+  character(len=80) :: cgyro_path_in
+  real, dimension(2) :: cgyro_integration_error_in
+
+  logical :: cgyro_printout_in
+
+contains
+
+
+  ! Map GLOBAL variables to INTERFACE parameters
+  subroutine map_global2interface()
+
+    use cgyro_globals
+
+    implicit none
+    
+    cgyro_n_energy_in = n_energy
+    cgyro_n_xi_in = n_xi
+    cgyro_n_theta_in = n_theta
+    cgyro_n_radial_in = n_radial
+    cgyro_n_toroidal_in = n_toroidal
+    cgyro_n_field_in = n_field
+    cgyro_e_max_in = e_max
+    cgyro_alpha_poly_in = alpha_poly
+    cgyro_e_fix_in = e_fix
+    cgyro_delta_t_method_in = delta_t_method
+    cgyro_delta_t_in = delta_t
+    cgyro_error_tol_in = error_tol
+    cgyro_max_time_in = max_time
+    cgyro_print_step_in = print_step
+    cgyro_restart_step_in = restart_step
+    cgyro_freq_tol_in = freq_tol
+    cgyro_restart_flag_in = restart_flag
+    cgyro_up_radial_in = up_radial
+    cgyro_up_theta_in = up_theta
+    cgyro_up_alpha_in = up_alpha
+    cgyro_nup_radial_in = nup_radial
+    cgyro_nup_theta_in = nup_theta
+    cgyro_nup_alpha_in = nup_alpha
+    cgyro_n_wave_in = n_wave
+    cgyro_constant_stream_flag_in = constant_stream_flag
+    cgyro_explicit_trap_flag_in = explicit_trap_flag
+    cgyro_ky_in = ky
+    cgyro_box_size_in = box_size
+    cgyro_ipccw_in = ipccw
+    cgyro_btccw_in = btccw
+    cgyro_silent_flag_in = silent_flag
+    cgyro_profile_model_in = profile_model
+    cgyro_equilibrium_model_in = equilibrium_model
+    cgyro_collision_model_in = collision_model
+    cgyro_collision_mom_restore_in = collision_mom_restore
+    cgyro_collision_ene_restore_in = collision_ene_restore
+    cgyro_collision_ene_diffusion_in = collision_ene_diffusion
+    cgyro_collision_kperp_in = collision_kperp
+    cgyro_collision_field_model_in = collision_field_model
+    cgyro_collision_ion_model_in = collision_ion_model
+    cgyro_collision_precision_mode_in = collision_precision_mode
+    cgyro_z_eff_in = z_eff
+    cgyro_z_eff_method_in = z_eff_method
+    cgyro_zf_test_mode_in = zf_test_mode
+    cgyro_nonlinear_flag_in = nonlinear_flag
+    cgyro_ae_flag_in = ae_flag
+    cgyro_temp_ae_in = temp_ae
+    cgyro_dens_ae_in = dens_ae
+    cgyro_mass_ae_in = mass_ae
+    cgyro_dlntdr_ae_in = dlntdr_ae
+    cgyro_dlnndr_ae_in = dlnndr_ae
+    cgyro_lambda_star_in = lambda_star
+    cgyro_h_print_flag_in = h_print_flag
+    cgyro_moment_print_flag_in = moment_print_flag
+    cgyro_gflux_print_flag_in = gflux_print_flag
+    cgyro_field_print_flag_in = field_print_flag
+    cgyro_amp0_in = amp0
+    cgyro_amp_in = amp
+    cgyro_gamma_e_in = gamma_e
+    cgyro_gamma_p_in = gamma_p
+    cgyro_mach_in = mach
+    cgyro_rotation_model_in = rotation_model
+    cgyro_toroidals_per_proc_in = nt_loc
+    cgyro_mpi_rank_order_in = mpi_rank_order
+    cgyro_velocity_order_in = velocity_order
+    cgyro_hiprec_flag_in = hiprec_flag
+    cgyro_udsymmetry_flag_in = udsymmetry_flag
+    cgyro_shear_method_in = shear_method
+    cgyro_n_global_in = n_global
+    cgyro_nu_global_in = nu_global
+    cgyro_psym_flag_in = psym_flag
+    cgyro_profile_shear_flag_in = profile_shear_flag
+    cgyro_theta_plot_in = theta_plot
+    cgyro_gpu_bigmem_flag_in = gpu_bigmem_flag
+    cgyro_upwind_single_flag_in = upwind_single_flag
+    cgyro_px0_in = px0
+    cgyro_stream_term_in = stream_term
+    cgyro_stream_factor_in = stream_factor
+    cgyro_exch_flag_in = exch_flag
+    cgyro_res_weight_power_in = res_weight_power
+
+    cgyro_rmin_in = rmin
+    cgyro_rmaj_in = rmaj
+    cgyro_q_in = q
+    cgyro_s_in = s
+    cgyro_shift_in = shift
+    cgyro_kappa_in = kappa
+    cgyro_s_kappa_in = s_kappa
+    cgyro_delta_in = delta
+    cgyro_s_delta_in = s_delta
+    cgyro_zeta_in = zeta
+    cgyro_s_zeta_in = s_zeta
+    cgyro_zmag_in = zmag
+    cgyro_dzmag_in = dzmag
+    cgyro_shape_sin3_in = shape_sin(3)
+    cgyro_shape_s_sin3_in = shape_s_sin(3)
+    cgyro_shape_sin4_in = shape_sin(4)
+    cgyro_shape_s_sin4_in = shape_s_sin(4)
+    cgyro_shape_sin5_in = shape_sin(5)
+    cgyro_shape_s_sin5_in = shape_s_sin(5)
+    cgyro_shape_sin6_in = shape_sin(6)
+    cgyro_shape_s_sin6_in = shape_s_sin(6)
+    cgyro_shape_cos0_in = shape_cos(0)
+    cgyro_shape_s_cos0_in = shape_s_cos(0)
+    cgyro_shape_cos1_in = shape_cos(1)
+    cgyro_shape_s_cos1_in = shape_s_cos(1)
+    cgyro_shape_cos2_in = shape_cos(2)
+    cgyro_shape_s_cos2_in = shape_s_cos(2)
+    cgyro_shape_cos3_in = shape_cos(3)
+    cgyro_shape_s_cos3_in = shape_s_cos(3)
+    cgyro_shape_cos4_in = shape_cos(4)
+    cgyro_shape_s_cos4_in = shape_s_cos(4)
+    cgyro_shape_cos5_in = shape_cos(5)
+    cgyro_shape_s_cos5_in = shape_s_cos(5)
+    cgyro_shape_cos6_in = shape_cos(6)
+    cgyro_shape_s_cos6_in = shape_s_cos(6)
+    cgyro_betae_unit_in = betae_unit
+    cgyro_n_species_in = n_species
+    
+    cgyro_nu_ee_in = nu_ee
+    
+    cgyro_z_in = z
+    cgyro_mass_in = mass
+    cgyro_dens_in = dens
+    cgyro_temp_in = temp
+    cgyro_dlnndr_in = dlnndr
+    cgyro_dlntdr_in = dlntdr
+    cgyro_sdlnndr_in = sdlnndr
+    cgyro_sdlntdr_in = sdlntdr
+
+    cgyro_subroutine_flag_in = subroutine_flag
+    cgyro_quasineutral_flag_in = quasineutral_flag
+    cgyro_lambda_star_scale_in = lambda_star
+    cgyro_gamma_e_scale_in = gamma_e_scale
+    cgyro_gamma_p_scale_in = gamma_p_scale
+    cgyro_mach_scale_in = mach_scale
+    cgyro_beta_star_scale_in = beta_star_scale
+    cgyro_betae_unit_scale_in = betae_unit_scale
+    cgyro_nu_ee_scale_in = nu_ee_scale
+    
+    cgyro_dlnndr_scale_in = dlnndr_scale
+    cgyro_dlntdr_scale_in = dlntdr_scale
+
+    cgyro_path_in = path
+    cgyro_integration_error_in = integration_error
+
+    ! Normalisation Values
+    if (b_unit .ne. 0) cgyro_b_unit_in = b_unit
+    if (b_gs2 .ne. 0) cgyro_b_gs2_in = b_gs2
+    if (a_meters .ne. 0) cgyro_a_meters_in = a_meters
+    if (temp_norm .ne. 0) cgyro_temp_norm_in = temp_norm
+    if (dens_norm .ne. 0) cgyro_dens_norm_in = dens_norm
+    if (rho_star_norm .ne. 0) cgyro_rho_star_norm_in = rho_star_norm
+    if (vth_norm .ne. 0) cgyro_vth_norm_in = vth_norm
+    
+    ! Outputs
+    cgyro_error_status_out = error_status
+    cgyro_error_message_out = error_message
+
+    cgyro_printout_in = printout
+
+  end subroutine map_global2interface
+
+  subroutine allocate_cgyro_interface
+
+    use cgyro_globals
+
+    implicit none
+    
+    ! Output parameters
+        ! Allocate output arrays (deallocated in cgyro_cleanup)
+    if (.not.allocated(cgyro_elec_pflux_out)) allocate(cgyro_elec_pflux_out(n_radial))
+    if (.not.allocated(cgyro_elec_mflux_out)) allocate(cgyro_elec_mflux_out(n_radial))
+    if (.not.allocated(cgyro_elec_eflux_out)) allocate(cgyro_elec_eflux_out(n_radial))
+    if (.not.allocated(cgyro_elec_expwd_out)) allocate(cgyro_elec_expwd_out(n_radial))
+    if (.not.allocated(cgyro_ion_pflux_out)) allocate(cgyro_ion_pflux_out(n_radial,5))
+    if (.not.allocated(cgyro_ion_mflux_out)) allocate(cgyro_ion_mflux_out(n_radial,5))
+    if (.not.allocated(cgyro_ion_eflux_out)) allocate(cgyro_ion_eflux_out(n_radial,5))
+    if (.not.allocated(cgyro_ion_expwd_out)) allocate(cgyro_ion_expwd_out(n_radial,5))
+
+    if(.not.allocated(cgyro_gbflux_out)) allocate(cgyro_gbflux_out(3, n_species, n_field, n_toroidal))
+
+    if (.not.allocated(cgyro_wavefunction_out)) allocate(cgyro_wavefunction_out(n_toroidal, n_field, n_theta*n_radial))
+    if (.not.allocated(cgyro_thetab_out)) allocate(cgyro_thetab_out(n_theta*n_radial))
+    if (.not.allocated(cgyro_k_perp_out)) allocate(cgyro_k_perp_out(n_theta*n_radial, n_toroidal))
+    if (.not.allocated(cgyro_jacobian_out)) allocate(cgyro_jacobian_out(n_theta*n_radial))
+
+    if (.not.allocated(cgyro_omega_out)) allocate(cgyro_omega_out(n_toroidal))
+    if (.not.allocated(cgyro_omega_error_out)) allocate(cgyro_omega_error_out(n_toroidal))
+
+  end subroutine allocate_cgyro_interface
+
+  ! Map INTERFACE parameters to GLOBAL variables
+  subroutine map_interface2global()
+
+    use cgyro_globals
+
+    implicit none
+
+    n_energy = cgyro_n_energy_in
+    n_xi = cgyro_n_xi_in
+    n_theta = cgyro_n_theta_in
+    n_radial = cgyro_n_radial_in
+    n_toroidal = cgyro_n_toroidal_in
+    n_field = cgyro_n_field_in
+    e_max = cgyro_e_max_in
+    alpha_poly = cgyro_alpha_poly_in
+    e_fix = cgyro_e_fix_in
+    delta_t_method = cgyro_delta_t_method_in
+    delta_t = cgyro_delta_t_in
+    error_tol = cgyro_error_tol_in
+    max_time = cgyro_max_time_in
+    print_step = cgyro_print_step_in
+    restart_step = cgyro_restart_step_in
+    freq_tol = cgyro_freq_tol_in
+    restart_flag = cgyro_restart_flag_in
+    up_radial = cgyro_up_radial_in
+    up_theta = cgyro_up_theta_in
+    up_alpha = cgyro_up_alpha_in
+    nup_radial = cgyro_nup_radial_in
+    nup_theta = cgyro_nup_theta_in
+    nup_alpha = cgyro_nup_alpha_in
+    n_wave = cgyro_n_wave_in
+    constant_stream_flag = cgyro_constant_stream_flag_in
+    explicit_trap_flag = cgyro_explicit_trap_flag_in
+    ky = cgyro_ky_in
+    box_size = cgyro_box_size_in
+    ipccw = cgyro_ipccw_in
+    btccw = cgyro_btccw_in
+    silent_flag = cgyro_silent_flag_in
+    profile_model = cgyro_profile_model_in
+    equilibrium_model = cgyro_equilibrium_model_in
+    collision_model = cgyro_collision_model_in
+    collision_mom_restore = cgyro_collision_mom_restore_in
+    collision_ene_restore = cgyro_collision_ene_restore_in
+    collision_ene_diffusion = cgyro_collision_ene_diffusion_in
+    collision_kperp = cgyro_collision_kperp_in
+    collision_field_model = cgyro_collision_field_model_in
+    collision_ion_model = cgyro_collision_ion_model_in
+    collision_precision_mode = cgyro_collision_precision_mode_in
+    z_eff = cgyro_z_eff_in
+    z_eff_method = cgyro_z_eff_method_in
+    zf_test_mode = cgyro_zf_test_mode_in
+    nonlinear_flag = cgyro_nonlinear_flag_in
+    ae_flag = cgyro_ae_flag_in
+    temp_ae = cgyro_temp_ae_in
+    dens_ae = cgyro_dens_ae_in
+    mass_ae = cgyro_mass_ae_in
+    dlntdr_ae = cgyro_dlntdr_ae_in
+    dlnndr_ae = cgyro_dlnndr_ae_in
+    lambda_star = cgyro_lambda_star_in
+    h_print_flag = cgyro_h_print_flag_in
+    moment_print_flag = cgyro_moment_print_flag_in
+    gflux_print_flag = cgyro_gflux_print_flag_in
+    field_print_flag = cgyro_field_print_flag_in
+    amp0 = cgyro_amp0_in
+    amp = cgyro_amp_in
+    gamma_e = cgyro_gamma_e_in
+    gamma_p = cgyro_gamma_p_in
+    mach = cgyro_mach_in
+    rotation_model = cgyro_rotation_model_in
+    nt_loc = cgyro_toroidals_per_proc_in
+    mpi_rank_order = cgyro_mpi_rank_order_in
+    velocity_order = cgyro_velocity_order_in
+    hiprec_flag = cgyro_hiprec_flag_in
+    udsymmetry_flag = cgyro_udsymmetry_flag_in
+    shear_method = cgyro_shear_method_in
+    n_global = cgyro_n_global_in
+    nu_global = cgyro_nu_global_in
+    psym_flag = cgyro_psym_flag_in
+    profile_shear_flag = cgyro_profile_shear_flag_in
+    theta_plot = cgyro_theta_plot_in
+    gpu_bigmem_flag = cgyro_gpu_bigmem_flag_in
+    px0 = cgyro_px0_in
+    stream_term = cgyro_stream_term_in
+    stream_factor = cgyro_stream_factor_in
+    exch_flag = cgyro_exch_flag_in
+    res_weight_power = cgyro_res_weight_power_in
+
+    rmin = cgyro_rmin_in
+    rmaj = cgyro_rmaj_in
+    q = cgyro_q_in
+    s = cgyro_s_in
+    shift = cgyro_shift_in
+    kappa = cgyro_kappa_in
+    s_kappa = cgyro_s_kappa_in
+    delta = cgyro_delta_in
+    s_delta = cgyro_s_delta_in
+    zeta = cgyro_zeta_in
+    s_zeta = cgyro_s_zeta_in
+    zmag = cgyro_zmag_in
+    dzmag = cgyro_dzmag_in
+
+    shape_sin(3) = cgyro_shape_sin3_in
+    shape_s_sin(3) = cgyro_shape_s_sin3_in
+    shape_sin(4) = cgyro_shape_sin4_in
+    shape_s_sin(4) = cgyro_shape_s_sin4_in
+    shape_sin(5) = cgyro_shape_sin5_in
+    shape_s_sin(5) = cgyro_shape_s_sin5_in
+    shape_sin(6) = cgyro_shape_sin6_in
+    shape_s_sin(6) = cgyro_shape_s_sin6_in
+    shape_cos(0) = cgyro_shape_cos0_in
+    shape_s_cos(0) = cgyro_shape_s_cos0_in
+    shape_cos(1) = cgyro_shape_cos1_in
+    shape_s_cos(1) = cgyro_shape_s_cos1_in
+    shape_cos(2) = cgyro_shape_cos2_in
+    shape_s_cos(2) = cgyro_shape_s_cos2_in
+    shape_cos(3) = cgyro_shape_cos3_in
+    shape_s_cos(3) = cgyro_shape_s_cos3_in
+    shape_cos(4) = cgyro_shape_cos4_in
+    shape_s_cos(4) = cgyro_shape_s_cos4_in
+    shape_cos(5) = cgyro_shape_cos5_in
+    shape_s_cos(5) = cgyro_shape_s_cos5_in
+    shape_cos(6) = cgyro_shape_cos6_in
+    shape_s_cos(6) = cgyro_shape_s_cos6_in
+    betae_unit = cgyro_betae_unit_in
+    n_species = cgyro_n_species_in
+    
+    nu_ee = cgyro_nu_ee_in
+    
+    z = cgyro_z_in
+    mass = cgyro_mass_in
+    dens = cgyro_dens_in
+    temp = cgyro_temp_in
+    dlnndr = cgyro_dlnndr_in
+    dlntdr = cgyro_dlntdr_in
+    sdlnndr = cgyro_sdlnndr_in
+    sdlntdr = cgyro_sdlntdr_in
+    
+    subroutine_flag = cgyro_subroutine_flag_in
+
+    quasineutral_flag = cgyro_quasineutral_flag_in
+    lambda_star = cgyro_lambda_star_scale_in
+    gamma_e_scale = cgyro_gamma_e_scale_in
+    gamma_p_scale = cgyro_gamma_p_scale_in
+    mach_scale = cgyro_mach_scale_in
+    beta_star_scale = cgyro_beta_star_scale_in
+    betae_unit_scale = cgyro_betae_unit_scale_in
+    nu_ee_scale = cgyro_nu_ee_scale_in
+    
+    dlnndr_scale = cgyro_dlnndr_scale_in
+    dlntdr_scale = cgyro_dlntdr_scale_in
+
+    ! Normalisation Values
+    b_unit = cgyro_b_unit_in
+    b_gs2 = cgyro_b_gs2_in
+    a_meters = cgyro_a_meters_in
+    temp_norm = cgyro_temp_norm_in
+    dens_norm = cgyro_dens_norm_in
+    rho_star_norm = cgyro_rho_star_norm_in
+    vth_norm = cgyro_vth_norm_in
+
+    path = cgyro_path_in
+    integration_error = cgyro_integration_error_in
+    printout = cgyro_printout_in
+
+    signal = cgyro_signal_out
+
+  end subroutine map_interface2global
+
+
+  subroutine interfacelocaldump
+
+    use cgyro_globals
+
+    implicit none
+
+    if (i_proc > 0) return
+
+    open(unit=1, file=trim(path)//'out.cgyro.localdump', status='replace')
+    write(1,20) 'N_ENERGY', cgyro_n_energy_in
+    write(1,20) 'N_XI', cgyro_n_xi_in
+    write(1,20) 'N_THETA', cgyro_n_theta_in
+    write(1,20) 'N_RADIAL', cgyro_n_radial_in
+    write(1,20) 'N_TOROIDAL', cgyro_n_toroidal_in
+    write(1,20) 'N_FIELD', cgyro_n_field_in
+    write(1,30) 'E_MAX', cgyro_e_max_in
+    write(1,30) 'ALPHA_POLY', cgyro_alpha_poly_in
+    write(1,20) 'E_FIX', cgyro_e_fix_in
+    write(1,20) 'DELTA_T_METHOD', cgyro_delta_t_method_in
+    write(1,30) 'DELTA_T', cgyro_delta_t_in
+    write(1,30) 'ERROR_TOL',cgyro_error_tol_in
+    write(1,30) 'MAX_TIME', cgyro_max_time_in
+    write(1,20) 'PRINT_STEP',cgyro_print_step_in
+    write(1,20) 'RESTART_STEP',cgyro_restart_step_in
+    write(1,30) 'FREQ_TOL',cgyro_freq_tol_in
+    write(1,30) 'UP_RADIAL',cgyro_up_radial_in
+    write(1,30) 'UP_THETA',cgyro_up_theta_in
+    write(1,30) 'UP_ALPHA',cgyro_up_alpha_in
+    write(1,20) 'NUP_RADIAL',cgyro_nup_radial_in
+    write(1,20) 'NUP_THETA',cgyro_nup_theta_in
+    write(1,20) 'NUP_ALPHA',cgyro_nup_alpha_in
+    write(1,20) 'N_WAVE',cgyro_n_wave_in
+    write(1,20) 'CONSTANT_STREAM_FLAG',cgyro_constant_stream_flag_in
+    write(1,20) 'EXPLICIT_TRAP_FLAG',cgyro_explicit_trap_flag_in
+    write(1,30) 'KY',cgyro_ky_in
+    write(1,20) 'BOX_SIZE',cgyro_box_size_in
+    write(1,30) 'IPCCW',cgyro_ipccw_in
+    write(1,30) 'BTCCW',cgyro_btccw_in
+    write(1,20) 'SILENT_FLAG',cgyro_silent_flag_in
+    write(1,20) 'PROFILE_MODEL',cgyro_profile_model_in
+    write(1,20) 'EQUILIBRIUM_MODEL',cgyro_equilibrium_model_in
+    write(1,20) 'COLLISION_MODEL',cgyro_collision_model_in
+    write(1,20) 'COLLISION_MOM_RESTORE',cgyro_collision_mom_restore_in
+    write(1,20) 'COLLISION_ENE_RESTORE',cgyro_collision_ene_restore_in
+    write(1,20) 'COLLISION_ENE_DIFFUSION',cgyro_collision_ene_diffusion_in
+    write(1,20) 'COLLISION_KPERP',cgyro_collision_kperp_in
+    write(1,20) 'COLLISION_FIELD_MODEL',cgyro_collision_field_model_in
+    write(1,20) 'COLLISION_ION_MODEL',cgyro_collision_ion_model_in
+    write(1,20) 'COLLISION_PRECISION_MODE',cgyro_collision_precision_mode_in
+    write(1,30) 'Z_EFF',cgyro_z_eff_in
+    write(1,20) 'Z_EFF_METHOD',cgyro_z_eff_method_in
+    write(1,20) 'ZF_TEST_MODE',cgyro_zf_test_mode_in
+    write(1,20) 'NONLINEAR_FLAG',cgyro_nonlinear_flag_in
+    write(1,20) 'AE_FLAG',cgyro_ae_flag_in
+    write(1,30) 'TEMP_AE',cgyro_temp_ae_in
+    write(1,30) 'DENS_AE',cgyro_dens_ae_in
+    write(1,30) 'MASS_AE',cgyro_mass_ae_in
+    write(1,30) 'DLNTDR_AE',cgyro_dlntdr_ae_in
+    write(1,30) 'DLNNDR_AE',cgyro_dlnndr_ae_in
+    write(1,30) 'LAMBDA_STAR',cgyro_lambda_star_in
+    write(1,20) 'H_PRINT_FLAG',cgyro_h_print_flag_in
+    write(1,20) 'MOMENT_PRINT_FLAG',cgyro_moment_print_flag_in
+    write(1,20) 'GFLUX_PRINT_FLAG',cgyro_gflux_print_flag_in
+    write(1,20) 'FIELD_PRINT_FLAG',cgyro_field_print_flag_in
+    write(1,30) 'AMP0',cgyro_amp0_in
+    write(1,30) 'AMP',cgyro_amp_in
+    write(1,30) 'GAMMA_E',cgyro_gamma_e_in
+    write(1,30) 'GAMMA_P',cgyro_gamma_p_in
+    write(1,30) 'MACH',cgyro_mach_in
+    write(1,20) 'ROTATION_MODEL',cgyro_rotation_model_in
+    write(1,20) 'TOROIDALS_PER_PROC',cgyro_toroidals_per_proc_in
+    write(1,20) 'MPI_RANK_ORDER',cgyro_mpi_rank_order_in
+    write(1,20) 'VELOCITY_ORDER',cgyro_velocity_order_in
+    write(1,20) 'HIPREC_FLAG',cgyro_hiprec_flag_in
+    write(1,20) 'UDSYMMETRY_FLAG',cgyro_udsymmetry_flag_in
+    write(1,20) 'SHEAR_METHOD',cgyro_shear_method_in
+    write(1,20) 'N_GLOBAL',cgyro_n_global_in
+    write(1,30) 'NU_GLOBAL',cgyro_nu_global_in
+    write(1,20) 'PSYM_FLAG',cgyro_psym_flag_in
+    write(1,20) 'PROFILE_SHEAR_FLAG',cgyro_profile_shear_flag_in
+    write(1,20) 'THETA_PLOT', cgyro_theta_plot_in
+    write(1,30) 'PX0',cgyro_px0_in
+    write(1,20) 'STREAM_TERM',cgyro_stream_term_in
+    write(1,30) 'STREAM_FACTOR',cgyro_stream_factor_in
+    write(1,20) 'EXCH_FLAG',cgyro_exch_flag_in
+    write(1,30) 'RES_WEIGHT_POWER',cgyro_res_weight_power_in
+
+    write(1,30) 'RMIN',cgyro_rmin_in
+    write(1,30) 'RMAJ',cgyro_rmaj_in
+    write(1,30) 'Q',cgyro_q_in
+    write(1,30) 'S',cgyro_s_in
+    write(1,30) 'SHIFT',cgyro_shift_in
+    write(1,30) 'KAPPA',cgyro_kappa_in
+    write(1,30) 'S_KAPPA',cgyro_s_kappa_in
+    write(1,30) 'DELTA',cgyro_delta_in
+    write(1,30) 'S_DELTA',cgyro_s_delta_in
+    write(1,30) 'ZETA',cgyro_zeta_in
+    write(1,30) 'S_ZETA',cgyro_s_zeta_in
+    write(1,30) 'ZMAG',cgyro_zmag_in
+    write(1,30) 'DZMAG',cgyro_dzmag_in
+    write(1,30) 'SHAPE_SIN3',cgyro_shape_sin3_in
+    write(1,30) 'SHAPE_S_SIN3',cgyro_shape_s_sin3_in
+    write(1,30) 'SHAPE_COS0',cgyro_shape_cos0_in
+    write(1,30) 'SHAPE_S_COS0',cgyro_shape_s_cos0_in
+    write(1,30) 'SHAPE_COS1',cgyro_shape_cos1_in
+    write(1,30) 'SHAPE_S_COS1',cgyro_shape_s_cos1_in
+    write(1,30) 'SHAPE_COS2',cgyro_shape_cos2_in
+    write(1,30) 'SHAPE_S_COS2',cgyro_shape_s_cos2_in
+    write(1,30) 'SHAPE_COS3',cgyro_shape_cos3_in
+    write(1,30) 'SHAPE_S_COS3',cgyro_shape_s_cos3_in
+    write(1,30) 'BETAE_UNIT',cgyro_betae_unit_in
+    write(1,20) 'SUBROUTINE_FLAG',cgyro_subroutine_flag_in
+
+    write(1,20) 'N_SPECIES',cgyro_n_species_in
+    write(1,30) 'NU_EE',cgyro_nu_ee_in
+    write(1,30) 'Z_1',cgyro_z_in(1)
+    write(1,30) 'MASS_1',cgyro_mass_in(1)
+    write(1,30) 'DENS_1',cgyro_dens_in(1)
+    write(1,30) 'TEMP_1',cgyro_temp_in(1)
+    write(1,30) 'DLNNDR_1',cgyro_dlnndr_in(1)
+    write(1,30) 'DLNTDR_1',cgyro_dlntdr_in(1)
+    write(1,30) 'SDLNNDR_1',cgyro_sdlnndr_in(1)
+    write(1,30) 'SDLNTDR_1',cgyro_sdlntdr_in(1)
+    write(1,30) 'Z_2',cgyro_z_in(2)
+    write(1,30) 'MASS_2',cgyro_mass_in(2)
+    write(1,30) 'DENS_2',cgyro_dens_in(2)
+    write(1,30) 'TEMP_2',cgyro_temp_in(2)
+    write(1,30) 'DLNNDR_2',cgyro_dlnndr_in(2)
+    write(1,30) 'DLNTDR_2',cgyro_dlntdr_in(2)
+    write(1,30) 'SDLNNDR_2',cgyro_sdlnndr_in(2)
+    write(1,30) 'SDLNTDR_2',cgyro_sdlntdr_in(2)
+    write(1,30) 'Z_3',cgyro_z_in(3)
+    write(1,30) 'MASS_3',cgyro_mass_in(3)
+    write(1,30) 'DENS_3',cgyro_dens_in(3)
+    write(1,30) 'TEMP_3',cgyro_temp_in(3)
+    write(1,30) 'DLNNDR_3',cgyro_dlnndr_in(3)
+    write(1,30) 'DLNTDR_3',cgyro_dlntdr_in(3)
+    write(1,30) 'SDLNNDR_3',cgyro_sdlnndr_in(3)
+    write(1,30) 'SDLNTDR_3',cgyro_sdlntdr_in(3)
+    write(1,30) 'Z_4',cgyro_z_in(4)
+    write(1,30) 'MASS_4',cgyro_mass_in(4)
+    write(1,30) 'DENS_4',cgyro_dens_in(4)
+    write(1,30) 'TEMP_4',cgyro_temp_in(4)
+    write(1,30) 'DLNNDR_4',cgyro_dlnndr_in(4)
+    write(1,30) 'DLNTDR_4',cgyro_dlntdr_in(4)
+    write(1,30) 'SDLNNDR_4',cgyro_sdlnndr_in(4)
+    write(1,30) 'SDLNTDR_4',cgyro_sdlntdr_in(4)
+    write(1,30) 'Z_5',cgyro_z_in(5)
+    write(1,30) 'MASS_5',cgyro_mass_in(5)
+    write(1,30) 'DENS_5',cgyro_dens_in(5)
+    write(1,30) 'TEMP_5',cgyro_temp_in(5)
+    write(1,30) 'DLNNDR_5',cgyro_dlnndr_in(5)
+    write(1,30) 'DLNTDR_5',cgyro_dlntdr_in(5)
+    write(1,30) 'SDLNNDR_5',cgyro_sdlnndr_in(5)
+    write(1,30) 'SDLNTDR_5',cgyro_sdlntdr_in(5)
+    write(1,30) 'Z_6',cgyro_z_in(6)
+    write(1,30) 'MASS_6',cgyro_mass_in(6)
+    write(1,30) 'DENS_6',cgyro_dens_in(6)
+    write(1,30) 'TEMP_6',cgyro_temp_in(6)
+    write(1,30) 'DLNNDR_6',cgyro_dlnndr_in(6)
+    write(1,30) 'DLNTDR_6',cgyro_dlntdr_in(6)
+    write(1,30) 'SDLNNDR_6',cgyro_sdlnndr_in(6)
+    write(1,30) 'SDLNTDR_6',cgyro_sdlntdr_in(6)
+    
+    write(1,20) 'QUASINEUTRAL_FLAG',cgyro_quasineutral_flag_in
+    write(1,30) 'LAMBDA_STAR_SCALE',cgyro_lambda_star_scale_in
+    write(1,30) 'GAMMA_E_SCALE',cgyro_gamma_e_scale_in
+    write(1,30) 'GAMMA_P_SCALE',cgyro_gamma_p_scale_in
+    write(1,30) 'MACH_SCALE',cgyro_mach_scale_in
+    write(1,30) 'BETA_STAR_SCALE',cgyro_beta_star_scale_in
+    write(1,30) 'BETAE_UNIT_SCALE',cgyro_betae_unit_scale_in
+    write(1,30) 'NU_EE_SCALE',cgyro_nu_ee_scale_in
+    write(1,30) 'DLNNDR_1_SCALE',cgyro_dlnndr_in(1)
+    write(1,30) 'DLNTDR_1_SCALE',cgyro_dlntdr_in(1)
+    write(1,30) 'DLNNDR_2_SCALE',cgyro_dlnndr_in(2)
+    write(1,30) 'DLNTDR_2_SCALE',cgyro_dlntdr_in(2)
+    write(1,30) 'DLNNDR_3_SCALE',cgyro_dlnndr_in(3)
+    write(1,30) 'DLNTDR_3_SCALE',cgyro_dlntdr_in(3)
+    write(1,30) 'DLNNDR_4_SCALE',cgyro_dlnndr_in(4)
+    write(1,30) 'DLNTDR_4_SCALE',cgyro_dlntdr_in(4)
+    write(1,30) 'DLNNDR_5_SCALE',cgyro_dlnndr_in(5)
+    write(1,30) 'DLNTDR_5_SCALE',cgyro_dlntdr_in(5)
+    write(1,30) 'DLNNDR_6_SCALE',cgyro_dlnndr_in(6)
+    write(1,30) 'DLNTDR_6_SCALE',cgyro_dlntdr_in(6)
+    close(1)
+    
+20  format(a,'=',i3)
+30  format(a,'=',1pe12.5)
+    
+  end subroutine interfacelocaldump
+    
+end module qlgyro_cgyro_interface
diff --git a/qlgyro/src/qlgyro_cgyro_map.f90 b/qlgyro/src/qlgyro_cgyro_map.f90
new file mode 100644
index 000000000..9820aa722
--- /dev/null
+++ b/qlgyro/src/qlgyro_cgyro_map.f90
@@ -0,0 +1,251 @@
+subroutine qlgyro_cgyro_map
+
+  use qlgyro_globals
+  use qlgyro_cgyro_interface
+
+  implicit none
+
+  integer :: i
+
+  n_species = cgyro_n_species_in
+  n_ion = n_species - 1
+
+  if (n_ion .eq. 0) n_ion = 1
+
+  do i=1, n_species
+     if (cgyro_z_in(i) .lt. 0) then
+        elec_ind = i
+        if (i .eq. 1) then
+           ion_start = 2
+           ion_end = n_species
+        else
+           ion_start = 1
+           ion_end = n_species-1
+        end if
+     endif
+  end do
+  
+  q = abs(cgyro_q_in)
+  s = cgyro_s_in
+  delta = cgyro_delta_in
+  s_delta = cgyro_s_delta_in
+  kappa = cgyro_kappa_in
+  s_kappa = cgyro_s_kappa_in
+  shift = cgyro_shift_in
+  r_maj = cgyro_rmaj_in
+  r_min = cgyro_rmin_in
+  betae_unit = cgyro_betae_unit_in
+
+  if (cgyro_ae_flag_in .eq. 0) then
+     me = cgyro_mass_in(elec_ind)
+     ne = cgyro_dens_in(elec_ind)
+     te = cgyro_temp_in(elec_ind)
+     dlnnedr = cgyro_dlnndr_in(elec_ind)
+     dlntedr = cgyro_dlntdr_in(elec_ind)
+  else
+     me = cgyro_mass_ae_in
+     ne = cgyro_dens_ae_in
+     te = cgyro_temp_ae_in
+     dlnnedr = cgyro_dlnndr_ae_in
+     dlntedr = cgyro_dlntdr_ae_in
+  end if
+  ! Note that CGYRO normalizing mass is mD = 2*mp.
+
+  zi_vec(1:n_ion) = cgyro_z_in(ion_start:ion_end)
+  ni(1:n_ion) = cgyro_dens_in(ion_start:ion_end)
+  ti(1:n_ion) = cgyro_temp_in(ion_start:ion_end)
+  mi(1:n_ion) = cgyro_mass_in(ion_start:ion_end)
+  dlnnidr(1:n_ion) = cgyro_dlnndr_in(ion_start:ion_end)
+  dlntidr(1:n_ion) = cgyro_dlntdr_in(ion_start:ion_end)
+
+  nue = cgyro_nu_ee_in
+
+  lambda_star = cgyro_lambda_star_in
+  
+  z_eff  = cgyro_z_eff_in
+  zmag   = cgyro_zmag_in
+  dzmag  = cgyro_dzmag_in
+  zeta   = cgyro_zeta_in
+  s_zeta = cgyro_s_zeta_in
+  shape_sin3 = cgyro_shape_sin3_in
+  shape_ssin3 = cgyro_shape_s_sin3_in
+  shape_cos0 = cgyro_shape_cos0_in
+  shape_scos0 = cgyro_shape_s_cos0_in
+  shape_cos1 = cgyro_shape_cos1_in
+  shape_scos1 = cgyro_shape_s_cos1_in
+  shape_cos2 = cgyro_shape_cos2_in
+  shape_scos2 = cgyro_shape_s_cos2_in
+  shape_cos3 = cgyro_shape_cos3_in
+  shape_scos3 = cgyro_shape_s_cos3_in
+
+  ! General geometry Fourier coefficients
+
+  qlgyro_num_equil_flag = cgyro_equilibrium_model_in
+
+  !rho_s = c_s* 
+
+  if (qlgyro_rotation_flag == 1) then
+
+     gamma_e = -cgyro_gamma_e_in
+     gamma_p = -cgyro_gamma_p_in
+     w0 = cgyro_mach_in
+
+  else
+
+     gamma_e = 0.0
+     gamma_p = 0.0
+     w0 = 0.0
+
+  endif
+
+  signb = -int(cgyro_btccw_in)
+  signq = int(cgyro_btccw_in*cgyro_ipccw_in)
+
+  bunit = cgyro_b_unit_in
+  bgs2 = cgyro_b_gs2_in
+  a_meters = cgyro_a_meters_in
+  temp_norm = cgyro_temp_norm_in
+  dens_norm = cgyro_dens_norm_in
+  rho_star_norm = cgyro_rho_star_norm_in
+  csda_norm = cgyro_vth_norm_in
+
+end subroutine qlgyro_cgyro_map
+
+
+!------------------------------------------------------------
+! cgyro_qlgyro_map.f90
+!
+! PURPOSE:
+!  Mapping from QLGYRO internal variables to CGYRO interface.
+!------------------------------------------------------------
+
+subroutine cgyro_qlgyro_map
+
+  use qlgyro_globals
+  use qlgyro_cgyro_interface
+
+  implicit none
+
+  integer :: i0
+  real :: gamma_eb0
+
+  !----------------------------------------------------------------
+  ! Signs of toroidal magnetic field and current
+  cgyro_btccw_in = -1.0*signb
+  cgyro_btccw_in = -1.0*signb*signq
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Number of species (max=11)
+  cgyro_n_species_in = n_species
+
+  if (cgyro_n_species_in > 11) then
+     call qlgyro_catch_error('ERROR: (qlgyro_cgyro_map) Too many ions in CGYRO.')
+  endif
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Species loop:
+  !
+  ! Charges: e,i,z
+  cgyro_z_in(elec_ind) = -1.0
+  !
+  ! Mass ratios: me/md,m(1)/md,m(2)/md, ...
+  cgyro_mass_in(elec_ind) = me
+  !
+  ! Density ratios: ne/ne,ni(1)/ne,ni(2)/ne, ...
+  cgyro_dens_in(elec_ind) = ne
+  !
+  ! Density gradients (e,i,z)
+  cgyro_dlnndr_in(elec_ind) = dlnnedr
+  !
+  ! Temperature gradients (e,i,z)
+  cgyro_dlntdr_in(elec_ind) = dlntedr
+  !
+  ! Temperature ratios: Te/Te,Ti(1)/Te,Ti(2)/Te
+  cgyro_temp_in(elec_ind) = te
+
+  cgyro_z_in(ion_start:ion_end) = zi_vec(1:n_ion)
+  cgyro_dens_in(ion_start:ion_end) = ni(1:n_ion)
+  cgyro_temp_in(ion_start:ion_end) = ti(1:n_ion)
+  cgyro_mass_in(ion_start:ion_end) = mi(1:n_ion)
+  cgyro_dlnndr_in(ion_start:ion_end) = dlnnidr(1:n_ion)
+  cgyro_dlntdr_in(ion_start:ion_end) = dlntidr(1:n_ion)
+
+  !----------------------------------------------------------------
+  !   debye length/rhos   te in ev, rho_s in cm ne in 10^13/cm^3
+  cgyro_lambda_star_in = lambda_star
+
+  ! Model (Miller) shape
+  cgyro_equilibrium_model_in = 2
+
+  cgyro_rmin_in    = r_min
+  cgyro_rmaj_in    = r_maj
+  cgyro_zmag_in    = zmag
+  cgyro_shift_in = shift
+  cgyro_dzmag_in = dzmag
+  cgyro_kappa_in   = kappa
+  cgyro_s_kappa_in = s_kappa
+  cgyro_delta_in   = delta
+  cgyro_s_delta_in = s_delta
+  cgyro_zeta_in    = zeta
+  cgyro_s_zeta_in  = s_zeta
+  cgyro_q_in       = q
+  cgyro_s_in = s
+  cgyro_shape_sin3_in = shape_sin3
+  cgyro_shape_s_sin3_in = shape_ssin3
+  cgyro_shape_cos0_in = shape_cos0
+  cgyro_shape_s_cos0_in = shape_scos0
+  cgyro_shape_cos1_in = shape_cos1
+  cgyro_shape_s_cos1_in = shape_scos1
+  cgyro_shape_cos2_in = shape_cos2
+  cgyro_shape_s_cos2_in = shape_scos2
+  cgyro_shape_cos3_in = shape_cos3
+  cgyro_shape_s_cos3_in = shape_scos3
+
+  ! What should this be?
+  cgyro_beta_star_scale_in = 1.0
+
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Electron beta used for electromagnetic calculations
+  cgyro_betae_unit_in = betae_unit
+  !----------------------------------------------------------------
+  !----------------------------------------------------------------
+  ! Collisions:
+  !
+  ! Electron collision frequency
+  cgyro_nu_ee_in = nue
+  !
+  ! Zeff
+  cgyro_z_eff_in = z_eff
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Gamma_ExB (ExB shearing rate, units of a/cs)
+  if (qlgyro_rotation_flag == 1) then
+
+     cgyro_gamma_e_in  = -gamma_e
+     cgyro_gamma_p_in = -gamma_p
+     cgyro_mach_in = -w0
+  else
+
+     cgyro_gamma_e_in = 0.0
+     cgyro_gamma_p_in = 0.0
+     cgyro_mach_in = 0.0
+
+  endif
+
+  cgyro_delta_t_method_in = 1
+
+  cgyro_b_unit_in = bunit
+  cgyro_b_gs2_in = bgs2
+  cgyro_a_meters_in = a_meters
+  cgyro_temp_norm_in = temp_norm
+  cgyro_dens_norm_in = dens_norm
+  cgyro_rho_star_norm_in = rho_star_norm
+  cgyro_vth_norm_in = csda_norm
+
+
+end subroutine cgyro_qlgyro_map
diff --git a/qlgyro/src/qlgyro_comm_setup.f90 b/qlgyro/src/qlgyro_comm_setup.f90
new file mode 100644
index 000000000..01dff5102
--- /dev/null
+++ b/qlgyro/src/qlgyro_comm_setup.f90
@@ -0,0 +1,125 @@
+!-----------------------------------------------------------------
+! qlgyro_comm_setup.f90
+!
+! PURPOSE:
+!  Broadcast path and other information specific to each 
+!  code instance.  Also, split QLGYRO_COMM_WORLD into 
+!  required communicators:
+!
+!   - qlgyro_comm
+!   - qlgyro_adj
+!   - qlgyro_rad (for parallel block method)
+!-----------------------------------------------------------------
+
+subroutine qlgyro_comm_setup
+
+  use mpi
+  use qlgyro_globals
+
+  implicit none
+
+  integer :: i
+  integer :: j
+  integer :: i_color
+  integer :: ip
+  integer :: is
+
+  integer :: low
+  integer :: high
+  integer :: splitkey
+
+  integer, dimension(n_proc_global) :: colorvec
+  integer, dimension(n_proc_global) :: workervec
+  integer, dimension(n_proc_global) :: adjointvec
+  integer, dimension(n_proc_global) :: workeradjvec
+
+
+  ! Determine the number of cores for each ky 
+  !-----------------------------
+  ! Multi-job 
+  !-----------------------------
+  
+  ! 1 worker; each DIR line specifies exact number of cores to GYRO
+  
+  !n_worker = 1
+
+  ! Sort processors into communicators (color), workers
+  ! and adjoint (to color).
+  !  
+  ! -   color: a specific communicator
+  ! -  worker: color index at a given ky
+  ! - adjoint: adjoint group to color 
+  ! -   lproc: number of tasks per color
+  ! -   lpath: local simulation path (fix this for GYRO) 
+  
+  low     = 0
+  i_color = 0
+  color = int(i_proc_global/procs)
+  worker = 0
+  adjoint = mod(i_proc_global, procs)
+  workeradj = i_proc_global
+  
+  
+  call MPI_GATHER(color,1,MPI_INTEGER,&
+       colorvec,1,MPI_INTEGER,0,QLGYRO_COMM_WORLD,ierr)
+  call MPI_GATHER(worker,1,MPI_INTEGER,&
+       workervec,1,MPI_INTEGER,0,QLGYRO_COMM_WORLD,ierr)
+  call MPI_GATHER(adjoint,1,MPI_INTEGER,&
+       adjointvec,1,MPI_INTEGER,0,QLGYRO_COMM_WORLD,ierr)
+  call MPI_GATHER(workeradj,1,MPI_INTEGER,&
+       workeradjvec,1,MPI_INTEGER,0,QLGYRO_COMM_WORLD,ierr)
+
+  if (i_proc_global == 0) then
+     open(unit=1,file='out.qlgyro.taskmapping',status='replace')
+     write(1,'(t2,a,t10,a,t18,a,t26,a,t34,a)') &
+          'core','gcomm','worker','adjoint','workeradj'
+     do i=1,n_proc_global
+        write(1,'(5(i5,3x),a)') &
+             i-1,colorvec(i),workervec(i),adjointvec(i),workeradjvec(i)
+     enddo
+     close(1)
+  endif
+
+  ! Split QLGYRO_COMM_WORLD into n_inst*n_worker different communicators.
+
+  ! Choose key for task ordering
+  splitkey = i_proc_global
+
+  call MPI_COMM_SPLIT(QLGYRO_COMM_WORLD,&
+       color,&
+       splitkey,&
+       qlgyro_comm,&
+       ierr)
+  if (ierr /= 0) then
+     call qlgyro_catch_error('ERROR: (QLGYRO) GYRO_COMM not created') 
+  endif
+
+  call MPI_COMM_SPLIT(QLGYRO_COMM_WORLD,&
+       adjoint,&
+       splitkey,&
+       qlgyro_adj,&
+       ierr)
+  if (ierr /= 0) then
+     call qlgyro_catch_error('ERROR: (QLGYRO) GYRO_ADJ not created') 
+  endif
+
+  call MPI_COMM_SPLIT(QLGYRO_COMM_WORLD,&
+       workeradj,&
+       splitkey,&
+       qlgyro_rad,&
+       ierr)
+  if (ierr /= 0) then
+     call qlgyro_catch_error('ERROR: (QLGYRO) GYRO_RAD not created') 
+  endif
+
+  call MPI_COMM_RANK(qlgyro_comm,qlgyro_comm_rank,ierr)
+  call MPI_COMM_RANK(qlgyro_adj,qlgyro_adj_rank,ierr)
+  call MPI_COMM_RANK(qlgyro_rad,qlgyro_rad_rank,ierr)
+
+  if (i_proc_global == 0) then
+     open(unit=1,file=trim(runfile),position='append')
+     write(1,'(t2,a)') 'INFO: (QLGYRO) MPI communicators split in QLGYRO'
+     close(1)
+  endif
+
+end subroutine qlgyro_comm_setup
diff --git a/qlgyro/src/qlgyro_comm_sync.f90 b/qlgyro/src/qlgyro_comm_sync.f90
new file mode 100644
index 000000000..dba332ff1
--- /dev/null
+++ b/qlgyro/src/qlgyro_comm_sync.f90
@@ -0,0 +1,75 @@
+  !--------------------------------------------------------
+  ! qlgyro_comm_sync.f90
+  !
+  ! PURPOSE
+  ! Synchronises (broadcast) outputs on all color groups
+  ! -------------------------------------------------------
+
+
+subroutine qlgyro_comm_sync
+
+  use mpi
+  use qlgyro_globals
+  use tglf_interface
+  
+  implicit none
+
+  integer :: i_kypx0, core, i_theta
+  integer, dimension(n_kypx0) :: ky_run
+  
+  ! Sync all proc
+  call MPI_BARRIER(QLGYRO_COMM_WORLD, ierr)
+  
+  ! Get core for each 
+  call read_qlgyro_status(ky_run, ky_color)
+  
+  do i_kypx0 = 1, n_kypx0
+
+     ! Core to bcast data
+     core = ky_color(i_kypx0) * procs
+     
+     call MPI_BCAST(qlgyro_eigenvalue_spectrum_out(1:2, i_ky(i_kypx0), i_px0(i_kypx0)) , &
+          2, &
+          MPI_DOUBLE, &
+          core, &
+          QLGYRO_COMM_WORLD, &
+          ierr)
+
+     call MPI_BCAST(qlgyro_flux_spectrum_out(1:5, 1:n_species, 1:3,  i_ky(i_kypx0), i_px0(i_kypx0)), &
+          (5* n_species* 3),  &
+          MPI_DOUBLE, &
+          core, &
+          QLGYRO_COMM_WORLD, &
+          ierr)
+
+     call MPI_BCAST(sat_geo_spectrum(i_ky(i_kypx0)), &
+          1,  &
+          MPI_DOUBLE, &
+          core, &
+          QLGYRO_COMM_WORLD, &
+          ierr)
+
+     call MPI_BCAST(qlgyro_field_spectrum_out(1:3, 1:n_thetab, i_ky(i_kypx0), i_px0(i_kypx0)), &
+          (6*n_thetab),  &
+          MPI_DOUBLE, &
+          core, &
+          QLGYRO_COMM_WORLD, &
+          ierr)
+
+     call MPI_BCAST(qlgyro_k_perp(1:n_thetab, i_ky(i_kypx0), i_px0(i_kypx0)), &
+          n_thetab,  &
+          MPI_DOUBLE, &
+          core, &
+          QLGYRO_COMM_WORLD, &
+          ierr)
+          
+     call MPI_BCAST(qlgyro_jacobian(1:n_thetab, i_ky(i_kypx0), i_px0(i_kypx0)), &
+          n_thetab,  &
+          MPI_DOUBLE, &
+          core, &
+          QLGYRO_COMM_WORLD, &
+          ierr)
+
+  end do
+
+end subroutine qlgyro_comm_sync
diff --git a/qlgyro/src/qlgyro_globals.f90 b/qlgyro/src/qlgyro_globals.f90
new file mode 100644
index 000000000..7a389a9a4
--- /dev/null
+++ b/qlgyro/src/qlgyro_globals.f90
@@ -0,0 +1,326 @@
+!-----------------------------------------------------
+! qlgyro_globals.f90
+!
+! PURPOSE:
+!  Fundamental module containing most of the shared 
+!  variables and arrays for qlgyro
+!
+! NOTES:
+!  Variables are split into three major categories:
+!  1. Shared 
+!  2. Specific to LOCAL method
+!  3. Specific to GLOBAL method 
+!-----------------------------------------------------
+
+module qlgyro_globals
+
+  !===============================================================
+  ! SHARED parameters for both transport methods:
+  !
+  ! MPI related integers
+  !
+  integer :: i_proc_global
+  integer :: n_proc_global
+  integer :: block
+  integer :: color
+  integer :: worker
+  integer :: adjoint
+  integer :: workeradj
+  integer :: worker_index
+  !
+  integer :: qlgyro_comm
+  integer :: qlgyro_comm_rank
+  integer :: qlgyro_adj
+  integer :: qlgyro_adj_rank
+  integer :: qlgyro_rad
+  integer :: qlgyro_rad_rank
+  integer :: GYRO_COMM_WORLD
+  integer :: CGYRO_COMM_WORLD
+  integer :: QLGYRO_COMM_WORLD
+  !
+  integer :: ierr
+  !
+  ! Containers for simulation path information
+  !
+  integer :: n_inst
+  integer :: n_worker
+  !
+  character(len=80) :: path
+  integer :: procs
+  real, dimension(:), allocatable :: inputrads
+
+  ! Code to run, 0 for GYRO, 1 for CGYRO
+  integer :: code
+  !
+  character(80) :: lpath, linput
+  integer :: lproc
+  character(len=5) :: lcode
+  !
+  ! Control variables
+  !
+  integer :: transport_method
+  integer :: tag_removal = 0
+  integer :: gyrotest_flag
+  integer :: gyro_restart_method
+  !
+  integer :: error_flag
+  character(len=80) :: error_msg
+  !
+  ! Ky run status string
+  integer :: statstr
+  !
+  ! Automatically set box size
+  integer :: auto_box_size = 0
+  real :: kx_max_box = 1e10
+  
+  !===============================================================
+
+  !===============================================================
+  ! Variables for LOCAL transport mode
+  !
+  integer :: shot
+  integer, parameter :: n_ion_max = 9
+  integer, parameter :: n_evolve_max = 5
+  character(len=14) :: runfile='out.qlgyro.run'
+  character(len=1), dimension(n_ion_max) :: &
+       ion_tag=(/'1','2','3','4','5','6','7','8','9'/)
+  !
+  ! Component fluxes
+  !
+  ! neo    -> neoclassical
+  ! tur    -> turbulent
+  ! tot    -> total
+  ! target -> target (source) 
+
+  ! - particle fluxes
+  real  :: pflux_e_tur
+  real  :: pflux_i_tur
+  
+  ! - momentum fluxes
+  real  :: mflux_e_tur
+  real  :: mflux_i_tur
+
+  ! - energy fluxes
+  real  :: eflux_e_tur
+  real  :: eflux_i_tur
+
+  ! - exchange power densities
+  real :: expwd_e_tur
+  real :: expwd_i_tur
+
+  
+  ! Moving gyroBohm diffusivity
+  real :: chi_gb
+
+  ! Moving gyroBohm fluxes
+  real :: gamma_gb
+  real :: pi_gb
+  real :: q_gb
+  real :: s_gb
+
+  ! Collision frequencies
+  real :: nue
+  real, dimension(:), allocatable :: nui
+  real :: nui_HH
+  real :: nue_HH
+  real :: nue_star
+
+  real :: z_eff
+
+  ! Formulary exchange rate
+  real :: nu_exch
+
+  ! Alpha heating coefficients
+  real :: frac_ae
+  real :: frac_ai
+  real :: e_cross
+
+  ! Electron and ion temperatures
+  real :: te
+  real :: dlntedr
+  real, dimension(:), allocatable :: ti
+  real, dimension(:), allocatable :: dlntidr
+
+  ! Electron and ion densities
+  real :: ne
+  real :: dlnnedr
+  real, dimension(:), allocatable :: ni
+  real, dimension(:), allocatable :: dlnnidr
+
+  real, dimension(n_ion_max) :: mi
+  real, dimension(n_ion_max) :: zi_vec
+  real, dimension(n_ion_max) :: mi_vec
+  integer, dimension(n_ion_max) :: therm_flag
+
+  
+  ! Rotation parameters
+  real :: w0
+  Real :: w0p
+  real :: gamma_e
+  real :: gamma_p
+  real :: u00
+  real :: w0_norm
+  integer :: qlgyro_rotation_flag=1
+
+  real :: pr
+  real :: ptot
+  real :: pext
+  real :: dpext
+  real :: dlnpdr
+  real :: dlnptotdr
+  real :: beta_unit
+  real :: betae_unit
+  real :: c_s
+  real :: v_i
+  real :: rho_s
+  real :: rho_i
+
+  real :: a_min
+  real :: r_min
+  real :: r_maj
+  real :: q
+  real :: s
+  real :: kappa
+  real :: delta
+  real :: s_kappa
+  real :: s_delta
+  real :: shift
+  real :: zmag
+  real :: dzmag
+  real :: zeta
+  real :: s_zeta
+  real :: shape_sin3
+  real :: shape_ssin3
+  real :: shape_cos0
+  real :: shape_scos0
+  real :: shape_cos1
+  real :: shape_scos1
+  real :: shape_cos2
+  real :: shape_scos2
+  real :: shape_cos3
+  real :: shape_scos3
+
+  real :: bunit
+  real :: bgs2
+  real :: volp
+  real :: vol
+  real :: ave_grad_r
+  real :: er
+  real :: f_rot
+
+
+  ! Physical constants
+  real :: pi
+  real :: e_alpha
+  real :: e
+  real :: bk
+  real :: me
+  real :: mp
+  real :: malpha
+  real :: c
+  real :: aspect_rat
+  real :: mu_0
+  
+  real :: gamma_exb
+  real :: gamma_p0
+
+  !---------------------------------------------------------
+  ! Equilibrium normalisations
+  !
+  real :: a_meters
+  !
+
+  real :: rho_star_norm
+  real :: csda_norm
+  real :: temp_norm
+  real :: dens_norm
+  real :: lambda_star
+  ! Proton mass in kg:
+  !
+  real, parameter :: kg_proton = 1.6726e-27
+
+  !
+  real :: b_ref
+  !
+  ! Geometry
+  !
+  integer :: n_fourier_geo
+  real, dimension(:,:), allocatable :: a_fourier_geo
+  !
+  ! Orientation
+  !
+  integer :: signb
+  integer :: signq
+  !
+  integer :: qlgyro_num_equil_flag=1
+
+  integer :: nspec_max=6
+
+  ! Grad r correction term
+  real, dimension(:), allocatable :: sat_geo_spectrum
+  real, dimension(:), allocatable :: kxrms_spectrum
+
+  real, dimension(:, :, :), allocatable :: qlgyro_eigenvalue_spectrum_out
+  real, dimension(:, :, :, :, :), allocatable :: qlgyro_flux_spectrum_out
+  complex, dimension(:, :, :, :), allocatable :: qlgyro_field_spectrum_out
+  real, dimension(:), allocatable :: qlgyro_theta_ballooning
+
+  real, dimension(:, :, :), allocatable :: qlgyro_k_perp, qlgyro_jacobian
+  
+  integer :: sat_rule
+  !
+  !
+  ! Iteration variables (global)
+  !
+  integer :: n_evolve
+  integer :: p_max
+  integer :: i_ion
+  integer :: n_ion=1
+  integer :: n_ky
+  integer :: n_px0
+  integer :: n_kypx0
+  integer :: n_modes=1
+  integer :: n_field=1
+  integer :: n_theta
+  integer :: n_species
+  integer :: n_thetab
+  integer :: i_tor
+
+  ! No. of parallel runs
+  integer :: n_parallel=1
+
+  ! No. of GYRO runs to attempt to converge
+  integer :: n_runs=1
+
+  ! Color. of cores running each ky value
+  integer, dimension(:), allocatable :: ky_color
+  real, dimension(:), allocatable :: px0_spectrum
+  integer, dimension(:), allocatable :: i_ky, i_px0
+  integer :: kygrid_model=1
+  integer :: px0grid_model=1
+  real :: ky_in
+  integer :: xnu_model
+  
+  integer :: flux_method
+  integer, dimension(:), allocatable :: flux_method_vec
+  integer :: i_tran=1
+  character(13) :: iter_path="./           "
+  integer :: i_bc
+  integer :: flux_counter
+  integer :: i_ash
+  integer :: evolve_indx(5)
+
+  integer :: elec_ind, ion_start, ion_end, loc_n_ion
+  !
+  integer :: use_trap
+  !---------------------------------------------------------
+  integer :: debug_flag=0
+  
+  ! runpath for eachh KY
+  character(len=80) :: runpath
+  
+  ! TGLF specific parameters
+  real :: qlgyro_tglf_nn_max_error=1.0e-3
+  integer :: qlgyro_tglf_revision=2
+  integer ::qlgyro_tglf_dump_flag=0
+end module qlgyro_globals
diff --git a/qlgyro/src/qlgyro_gyro_cleanup.f90 b/qlgyro/src/qlgyro_gyro_cleanup.f90
new file mode 100644
index 000000000..828ed4966
--- /dev/null
+++ b/qlgyro/src/qlgyro_gyro_cleanup.f90
@@ -0,0 +1,96 @@
+!-----------------------------------------------------------
+! gyro_cleanup.f90
+!
+! PURPOSE:
+!  Assign output to interface, Deallocate and clean up.
+!-----------------------------------------------------------
+
+subroutine qlgyro_gyro_cleanup
+
+  use mpi
+  use qlgyro_globals
+  use gyro_globals
+  use gyro_interface
+
+  implicit none
+
+  integer :: l, i_field, n_ball, io, pos, n_flux
+  complex :: omega_data(2)
+  complex :: ftemp(gyro_theta_plot_in*gyro_radial_grid_in)
+  real(4) :: flux_temp(n_kinetic, gyro_n_field_in, p_moment, n_x), flux_loc_temp(n_kinetic, gyro_n_field_in, p_moment)
+  character(len=24), dimension(3) :: field_files
+
+  io = 21
+  
+  ! Write eigenvalues to interface from final line in out.gyro.freq file
+  open(unit=io, file=trim(runpath)//'/out.gyro.freq', position="append")
+  backspace(unit=io)
+  read(io, 20) omega_data
+  close(io)
+  
+20 format(4(es11.4,1x))
+
+  gyro_omega_out = omega_data(1)
+  gyro_omega_error_out = omega_data(2)
+
+  ! Fluxes - reorder output for QLGYRO
+  if(.not.allocated(gyro_gbflux_out)) allocate(gyro_gbflux_out(4, n_species, gyro_n_field_in))
+
+  n_flux = n_kinetic * gyro_n_field_in * 4 * n_x
+
+  ! Read out.gyro.gbflux_i file and skip to the final time step
+  pos = (data_step * n_flux* BYTE) +1
+  
+  open(unit=io,file=trim(runpath)//'/bin.gyro.gbflux_i',status='old',access='stream', form='unformatted')
+  read(io, pos=pos) flux_temp
+  close(io)
+
+  ! Calculate average in radial positions of interest
+  flux_loc_temp = 0.0
+  do l=1+n_explicit_damp,n_x-n_explicit_damp
+     flux_loc_temp(:,:,:) = flux_loc_temp(:,:,:)+flux_temp(:,:,:,l)
+  enddo ! l
+  
+  flux_loc_temp(:,:,:) = flux_loc_temp(:,:,:)/(n_x-2*n_explicit_damp)
+
+  ! Re order output for QL-GYRO
+  do l=1,p_moment
+     gyro_gbflux_out(l, :, :) = real(flux_loc_temp(:, :, l))
+  end do
+
+  
+  ! Wavefunction read from file
+  field_files = (/'/out.gyro.balloon_phi  ', '/out.gyro.balloon_a    ', '/out.gyro.balloon_aperp'/)
+
+  n_ball =  gyro_theta_plot_in*gyro_radial_grid_in
+  
+  if(.not.allocated(gyro_wavefunction_out)) allocate(gyro_wavefunction_out(gyro_n_field_in, n_ball))
+  if(.not.allocated(gyro_thetab_out)) allocate(gyro_thetab_out(n_ball))
+  
+  do i_field=1,gyro_n_field_in
+
+     ! Start at end and work back to final timestep
+     open(unit=io,file=trim(runpath)//trim(field_files(i_field)), status='old', position='append')
+
+     do l=1, n_ball
+        backspace(io)
+     end do
+     
+     do l=1, n_ball
+        read(io, fmtstr2) ftemp(l)
+     end do
+     close(io)
+     
+     gyro_wavefunction_out(i_field, :) = ftemp
+
+  end do
+
+  ! Theta ballooning grid
+  do l=1, n_ball
+     gyro_thetab_out(l) = -(1.0+gyro_radial_grid_in)+(2.0*gyro_radial_grid_in*(l-1.0)/n_ball)
+  end do
+  
+  gyro_thetab_out = gyro_thetab_out * pi
+
+end subroutine qlgyro_gyro_cleanup
+
diff --git a/qlgyro/src/qlgyro_gyro_map.f90 b/qlgyro/src/qlgyro_gyro_map.f90
new file mode 100644
index 000000000..1069c6f9d
--- /dev/null
+++ b/qlgyro/src/qlgyro_gyro_map.f90
@@ -0,0 +1,148 @@
+subroutine qlgyro_gyro_map
+
+  use qlgyro_globals
+  use gyro_interface
+
+  implicit none
+
+  if (n_ion > 5) then
+     call qlgyro_catch_error('ERROR: (QLGYRO) n_ion > 5 not supported in GYRO interface.')
+  endif
+
+  a_min = 1
+  c_s = 1
+  ne = 1.0
+  te = 1.0
+
+  !Find no. of ions
+  if (gyro_ni_over_ne_2_in == 0) then
+     n_ion = 1
+  else if (gyro_ni_over_ne_3_in == 0) then
+     n_ion = 2
+  else if (gyro_ni_over_ne_4_in == 0) then
+     n_ion = 3
+  else if (gyro_ni_over_ne_5_in == 0) then
+     n_ion = 4
+  else
+     n_ion = 5
+  end if
+
+  n_species = n_ion+1
+  
+  q = abs(gyro_safety_factor_in)
+  s = gyro_shear_in
+  delta = gyro_delta_in
+  s_delta = gyro_s_delta_in
+  kappa = gyro_kappa_in
+  s_kappa = gyro_s_kappa_in
+  shift = gyro_shift_in
+  r_maj = gyro_aspect_ratio_in * a_min
+  r_min = gyro_radius_in * a_min
+  betae_unit = gyro_betae_unit_in
+
+  ! Note that GYRO normalizing mass is mD = 2*mp.
+
+  zi_vec(1)  = gyro_z_in
+  ni(1) = gyro_ni_over_ne_in * ne
+  ti(1) = gyro_ti_over_te_in * te
+  mi(1) = 2*mp/gyro_mu_1_in**2
+  dlnnidr(1) = gyro_dlnndr_in / a_min
+  dlntidr(1) = gyro_dlntdr_in / a_min
+  
+  if (n_ion > 1) then
+     zi_vec(2)  = gyro_z_2_in
+     ni(2) = gyro_ni_over_ne_2_in * ne
+     ti(2) = gyro_ti_over_te_2_in * te
+     mi(2) = 2*mp/gyro_mu_2_in**2
+     dlnnidr(2) = gyro_dlnndr_2_in / a_min
+     dlntidr(2) = gyro_dlntdr_2_in / a_min
+  endif
+
+  if (n_ion > 2) then
+     zi_vec(3)  = gyro_z_3_in
+     ni(3) = gyro_ni_over_ne_3_in * ne
+     ti(3) = gyro_ti_over_te_3_in * te
+     mi(3) = 2*mp/gyro_mu_3_in**2
+     dlnnidr(3) = gyro_dlnndr_3_in / a_min
+     dlntidr(3) = gyro_dlntdr_3_in / a_min
+  endif
+
+  if (n_ion > 3) then
+     zi_vec(4)  = gyro_z_4_in
+     ni(4) = gyro_ni_over_ne_4_in * ne
+     ti(4) = gyro_ti_over_te_4_in * te
+     mi(4) = 2*mp/gyro_mu_4_in**2
+     dlnnidr(4) = gyro_dlnndr_4_in / a_min
+     dlntidr(4) = gyro_dlntdr_4_in / a_min
+  endif
+
+  if (n_ion > 4) then
+     zi_vec(5)  = gyro_z_5_in
+     ni(5) = gyro_ni_over_ne_5_in * ne
+     ti(5) = gyro_ti_over_te_5_in * te
+     mi(5) = 2*mp/gyro_mu_5_in**2
+     dlnnidr(5) = gyro_dlnndr_5_in / a_min
+     dlntidr(5) = gyro_dlntdr_5_in / a_min
+  endif
+
+  me =  mi(1)/ gyro_mu_electron_in**2
+  nue = gyro_nu_ei_in * c_s/a_min
+  dlnnedr = gyro_dlnndr_electron_in / a_min
+  dlntedr = gyro_dlntdr_electron_in / a_min
+
+  z_eff  = gyro_z_eff_in
+  zmag   = gyro_zmag_in
+  dzmag  = gyro_dzmag_in
+  zeta   = gyro_zeta_in
+  s_zeta = gyro_s_zeta_in
+
+  ! General geometry Fourier coefficients
+
+  qlgyro_num_equil_flag = gyro_num_equil_flag_in
+
+  n_fourier_geo = gyro_n_fourier_geo_in
+  a_fourier_geo(:,:) = gyro_a_fourier_geo_in(:,:)
+
+  !rho_s = c_s* 
+
+  if (qlgyro_rotation_flag == 1) then
+
+     ! COORDINATES: The signs of all rotation-related quantities below are 
+     ! inherited (unchanged) from input.profiles.  In general GYRO expects 
+     ! these to be correctly signed/oriented.
+     ! NEED TO DOUBLE CHECK ALL OF THIS
+
+     !gamma_eb0 = gyro_gamma_e_in * c_s / a_min
+     !gamma_p0  = gyro_gamma_p_in * c_s / a_min
+
+     ! Not normalisedd correcttly as a_min set to 1
+     !w0        = gyro_mach_in*c_s/r_maj
+
+     ! Set flow terms in input.qlgyro
+
+     !gamma_eb0 = 0.0
+     gamma_p0 = 0.0
+     w0 = 0.0
+     
+
+  else
+
+     !gamma_eb0 = 0.0
+     gamma_p0 = 0.0
+     w0 = 0.0
+
+  endif
+
+  signb = -int(gyro_btccw_in)
+  signq = int(gyro_btccw_in*gyro_ipccw_in)
+
+  bunit = gyro_b_unit_norm_in
+  a_meters = gyro_a_meters_in
+  temp_norm = gyro_tem_norm_in
+  dens_norm = gyro_den_norm_in
+  rho_star_norm = gyro_rhos_norm_in
+  csda_norm = gyro_csda_norm_in
+
+end subroutine qlgyro_gyro_map
+
+
diff --git a/qlgyro/src/qlgyro_inout.f90 b/qlgyro/src/qlgyro_inout.f90
new file mode 100644
index 000000000..7bbb0f60e
--- /dev/null
+++ b/qlgyro/src/qlgyro_inout.f90
@@ -0,0 +1,771 @@
+!
+SUBROUTINE write_qlgyro_flux_spectrum
+  !
+  use qlgyro_globals
+  use tglf_interface
+  !   
+  IMPLICIT NONE
+  CHARACTER(24) :: fluxfile="out.qlgyro.flux_spectrum"
+  INTEGER :: i,j,is,imax,jmax
+  real :: ky
+  REAL :: dky
+  REAL :: dky0,dky1,ky0,ky1
+  REAL :: pflux0(n_species,3),eflux0(n_species,3)
+  REAL :: stress_par0(n_species,3),stress_tor0(n_species,3)
+  REAL :: exch0(n_species,3)
+  REAL :: pflux1(n_species,3),eflux1(n_species,3)
+  REAL :: stress_par1(n_species,3),stress_tor1(n_species,3)
+  REAL :: exch1(n_species,3)
+  REAL :: pflux_out,eflux_out,mflux_tor_out,mflux_par_out,exch_out
+  CHARACTER (117) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+
+  !
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+  !
+  ! initialize fluxes
+  !
+!  write(*,*)"ns0,ns,nky,nmodes",ns0,ns,nky,nmodes_in
+!
+  do is=1,n_species
+     do j=1,3 
+        pflux0(is,j) = 0.0
+        eflux0(is,j) = 0.0
+        stress_par0(is,j) = 0.0
+        stress_tor0(is,j) = 0.0
+        exch0(is,j) = 0.0
+     enddo
+  enddo
+  ! set number of field
+  jmax = 1
+  if(tglf_use_bper_in)jmax=2
+  if(tglf_use_Bpar_in)jmax=3
+  ! loop over species and fields
+  do is=1,n_species
+     do j=1,jmax
+        write(33,*)"species = ",is,"field =",j
+        write(33,*)" ky,particle flux,energy flux,toroidal stress,parallel stress,exchange"
+
+        !
+        ! loop over ky spectrum
+        !
+        tglf_iflux_in=.TRUE. 
+        dky0=0.0
+        ky0=0.0 
+        do i=1,n_ky
+           ky = tglf_ky_spectrum_out(i)
+           dky = tglf_dky_spectrum_out(i)
+           ky1=ky
+           if(i.eq.1)then
+              dky1=ky1
+           else
+              dky = LOG(ky1/ky0)/(ky1-ky0)
+              dky1 = ky1*(1.0 - ky0*dky)
+              dky0 = ky0*(ky1*dky - 1.0)
+           endif
+           ! normalize the ky integral to make it independent of the 
+           ! choice of temperature and mass scales 
+           dky0 = dky0*SQRT(tglf_taus_in(1)*tglf_mass_in(2))
+           dky1 = dky1*SQRT(tglf_taus_in(1)*tglf_mass_in(2))
+           !
+           ! compute the fluxes in the same way as tglf_TM.f90 
+           !
+           pflux1(is,j) = 0.0
+           eflux1(is,j) = 0.0
+           stress_tor1(is,j) = 0.0
+           stress_par1(is,j) = 0.0
+           exch1(is,j) = 0.0
+           do imax = 1,n_modes
+              pflux1(is,j) = pflux1(is,j) + tglf_flux_spectrum_out(1,is,j,i,imax)
+              eflux1(is,j) = eflux1(is,j) + tglf_flux_spectrum_out(2,is,j,i,imax)
+              stress_tor1(is,j) = stress_tor1(is,j) + &
+                   tglf_flux_spectrum_out(3,is,j,i,imax)
+              !stress_par1(is,j) = stress_par1(is,j) + &
+              !     flux_spectrum_out(4,is,j,i,imax)
+              exch1(is,j) = exch1(is,j) + tglf_flux_spectrum_out(4,is,j,i,imax)
+           enddo !imax
+           pflux_out = dky0*pflux0(is,j) + dky1*pflux1(is,j)
+           eflux_out = dky0*eflux0(is,j) + dky1*eflux1(is,j)
+           mflux_tor_out = dky0*stress_tor0(is,j) + dky1*stress_tor1(is,j)
+           mflux_par_out = 0.0 !dky0*stress_par0(is,j) + dky1*stress_par1(is,j)
+           exch_out = dky0*exch0(is,j) + dky1*exch1(is,j)
+           write(33,*)ky,pflux_out,eflux_out,mflux_tor_out,mflux_par_out,exch_out
+           pflux0(is,j) = pflux1(is,j)
+           eflux0(is,j) = eflux1(is,j)
+           stress_par0(is,j) = stress_par1(is,j)
+           stress_tor0(is,j) = stress_tor1(is,j)
+           exch0(is,j) = exch1(is,j)
+           ky0 = ky1
+        enddo  ! i
+     enddo  ! j
+  enddo  ! is 
+  !
+  CLOSE(33)
+  !    
+END SUBROUTINE write_qlgyro_flux_spectrum
+!-----------------------------------------------------------------
+
+
+SUBROUTINE write_qlgyro_field_spectrum
+  !
+  USE qlgyro_globals
+  USE tglf_interface
+
+  IMPLICIT NONE
+  CHARACTER(29) :: fluxfile="out.qlgyro.field_spectrum"
+  INTEGER :: i
+  REAL :: phi,a_par,b_par
+  CHARACTER (122) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+!
+  write(33,*)"gyro-bohm normalized field fluctuation intensity spectra per mode"
+  write(33,*)"potential,A_par,B_par"
+  write(33,*)"index limits: nky"
+  
+  write(33,*)n_ky
+
+  if(tglf_use_bper_in)then
+     write(33,*)"a_par_yes"
+  else
+     write(33,*)"a_par_no"
+  endif
+  if(tglf_use_bpar_in) then
+     write(33,*)"b_par_yes"
+  else
+     write(33,*)"b_par_no"
+  endif
+
+  do i=1,n_ky
+    phi = 0.0
+    a_par=0.0
+    b_par=0.0
+    phi = phi + tglf_field_spectrum_out(2,i,1)
+    if(tglf_use_bper_in)a_par = a_par + tglf_field_spectrum_out(3,i,1)
+    if(tglf_use_bpar_in)b_par = b_par + tglf_field_spectrum_out(4,i,1)
+    write(33,*)phi,a_par,b_par
+  enddo
+!
+  CLOSE(33)
+!
+END SUBROUTINE write_qlgyro_field_spectrum
+
+SUBROUTINE write_qlgyro_ky_spectrum
+!
+  USE qlgyro_globals
+  use tglf_interface
+!
+  IMPLICIT NONE
+  CHARACTER(22) :: fluxfile="out.qlgyro.ky_spectrum"
+  INTEGER :: i
+  CHARACTER (115) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+!
+  write(33,*)"index limits: nky"
+  write(33,*)tglf_nky_in
+!
+  do i=1,tglf_nky_in
+    write(33,*)tglf_ky_spectrum_out(i)
+  enddo
+  CLOSE(33)
+!
+ END SUBROUTINE write_qlgyro_ky_spectrum
+
+
+SUBROUTINE write_qlgyro_eigenvalue_spectrum
+  !
+  USE qlgyro_globals
+  use tglf_interface
+  
+  IMPLICIT NONE
+  CHARACTER(30) :: fluxfile="out.qlgyro.eigenvalue_spectrum"
+  INTEGER :: i,n
+  CHARACTER (123) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+
+  !
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+!
+  write(33,*)"gyro-bohm normalized eigenvalue spectra"
+  write(33,*)"(gamma(n),freq(n),n=1,nmodes_in)"
+  do i=1,n_ky
+    write(33,*)(tglf_eigenvalue_spectrum_out(1,i,n),tglf_eigenvalue_spectrum_out(2,i,n),n=1,tglf_nmodes_in)
+  enddo
+!
+  CLOSE(33)
+!
+END SUBROUTINE write_qlgyro_eigenvalue_spectrum
+
+ SUBROUTINE write_qlgyro_QL_weight_spectrum
+   !
+
+   use qlgyro_globals
+   use tglf_interface
+  IMPLICIT NONE
+  CHARACTER(35) :: fluxfile="out.qlgyro.QL_weight_spectrum"
+  INTEGER :: i,j,k,is
+  REAL :: phinorm
+  REAL,PARAMETER :: small=1.0E-10
+  CHARACTER (128) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+!
+  write(33,*)"QL weights per mode:"
+  write(33,*)"type: 1=particle,2=energy,3=toroidal stress,4=parallel stress,5=exchange"
+  write(33,*)"index limits: nky,nmodes,ns,field,type"
+  write(33,*)n_ky,n_modes,n_species,3,5
+!
+      ! renormalize the fluxes and intensities to the phi-norm from the v-norm
+      do j=1,n_ky
+         do i=1,n_modes
+            phinorm=1.0
+            if(ABS(tglf_field_spectrum_out(2,j,i)).gt.small)phinorm=tglf_field_spectrum_out(2,j,i)
+            do is=1,n_species
+               do k=1,3
+                  write(33,*)tglf_flux_spectrum_out(1,is,k,j,i)/phinorm
+                  write(33,*)tglf_flux_spectrum_out(2,is,k,j,i)/phinorm
+                  write(33,*)tglf_flux_spectrum_out(3,is,k,j,i)/phinorm
+                  write(33,*)tglf_flux_spectrum_out(4,is,k,j,i)/phinorm
+                  write(33,*)tglf_flux_spectrum_out(5,is,k,j,i)/phinorm
+              enddo
+           enddo
+        enddo
+      enddo
+  CLOSE(33)
+!
+ END SUBROUTINE write_qlgyro_QL_weight_spectrum
+
+ subroutine write_qlgyro_gbflux
+
+   use qlgyro_globals
+   use tglf_interface
+   implicit none
+
+   CHARACTER (17) :: fluxfile="out.qlgyro.gbflux"
+   CHARACTER (110) :: full_fluxfile
+
+   full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+
+   open(unit=1,file=full_fluxfile,status='replace')
+   write(1,'(32(1pe11.4,1x))') tglf_elec_pflux_out,tglf_ion_pflux_out(1:n_ion),&
+        tglf_elec_eflux_out,tglf_ion_eflux_out(1:n_ion),&
+        tglf_elec_mflux_out,tglf_ion_mflux_out(1:n_ion),&
+        tglf_elec_expwd_out,tglf_ion_expwd_out(1:n_ion)
+   close(1)
+
+ end subroutine write_qlgyro_gbflux
+
+ subroutine write_qlgyro_units
+
+   use mpi
+   use qlgyro_globals
+   implicit none
+
+   integer :: io=21
+   character(16) :: datafile='out.qlgyro.units'
+   real :: kt
+   CHARACTER (109) :: full_datafile
+
+   full_datafile = trim(path)//trim(iter_path)//datafile
+
+   open(unit=io,file=full_datafile,status='replace')
+   
+   ! kT in MJ (note the conversion 1.6022e-22 MJ/keV)
+   kt = 1.6022e-22*temp_norm
+   
+   write(io,26) 2.0*kg_proton,'m_ref (kg)'
+   write(io,26) bunit,'b_unit (Tesla)'
+   write(io,26) a_meters,'a (m)'
+   write(io,26) csda_norm,'csD/a (1/s)'
+   write(io,26) csda_norm*a_meters,'csD (m/s)'
+   write(io,26) temp_norm,'Te (keV)'
+   write(io,26) dens_norm,'ne (10^19/m^3)'
+   write(io,26) rho_star_norm*a_meters,'rho_sD (m)'
+   write(io,26) csda_norm*(rho_star_norm*a_meters)**2,&
+        'chi_gBD (m^2/s)'
+
+   write(io,26) 1e19*dens_norm*(csda_norm*a_meters)*rho_star_norm**2/0.624e22,&
+        'Gamma_gBD (0.624e22/m^2/s) = (MW/keV/m^2)'
+   
+   write(io,26) 1e19*dens_norm*(csda_norm*a_meters)*kt*rho_star_norm**2,&
+        'Q_gBD (MJ/m^2/s) = (MW/m^2)'
+
+   write(io,26) 1e19*dens_norm*a_meters*kt*rho_star_norm**2*1e6,&
+        'Pi_gBD (J/m^2) = (Nm/m^2)'
+   
+   write(io,26) 1e19*dens_norm*csda_norm*kt*rho_star_norm**2,&
+        'S_gBD (MJ/m^3/s) = (MW/m^3)'
+   
+   close(io)
+
+26 format(t2,1pe15.8,2x,a) 
+
+ end subroutine write_qlgyro_units
+
+  SUBROUTINE write_qlgyro_sat_geo_spectrum
+!
+  USE qlgyro_globals
+ 
+  IMPLICIT NONE
+  CHARACTER(33) :: fluxfile="out.qlgyro.sat_geo_spectrum"
+  INTEGER :: i
+  CHARACTER (126) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+  !
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+!
+  write(33,*)"saturation model geometry factor 1/(<phi|(B/(B_unit grad_r))**2\phi>/<phi|phi>) per mode:"
+  write(33,*)"index limits: nky"
+  write(33,*)n_ky
+!
+  do i=1,n_ky
+    write(33,*)(sat_geo_spectrum(i))
+  enddo
+  CLOSE(33)
+!
+ END SUBROUTINE write_qlgyro_sat_geo_spectrum
+!-----------------------------------------------------------------
+!
+
+   SUBROUTINE write_qlgyro_kxrms_spectrum
+!
+  USE qlgyro_globals
+ 
+  IMPLICIT NONE
+  CHARACTER(33) :: fluxfile="out.qlgyro.kxrms_spectrum"
+  INTEGER :: i
+  CHARACTER (126) :: full_fluxfile
+
+  full_fluxfile = trim(path)//trim(iter_path)//fluxfile
+  !
+  OPEN(unit=33,file=full_fluxfile,status='replace')
+!
+  write(33,*)"kx rms model used"
+  write(33,*)"index limits: nky"
+  write(33,*)n_ky
+!
+  do i=1,n_ky
+    write(33,*)(kxrms_spectrum(i))
+  enddo
+  CLOSE(33)
+!
+ END SUBROUTINE write_qlgyro_kxrms_spectrum
+!-----------------------------------------------------------------
+!
+
+ subroutine init_qlgyro_status
+   ! Reads in status file for a given ky
+   
+   use mpi
+   use qlgyro_globals
+   use tglf_interface
+   implicit none
+   
+   integer :: file_handle, i, colour
+   character(len=55) :: outstr
+   CHARACTER(18) :: statusfile="out.qlgyro.status"
+   CHARACTER(98) :: full_statusfile
+
+   full_statusfile = trim(path)//statusfile
+
+   call MPI_FILE_DELETE(full_statusfile, MPI_INFO_NULL, ierr)
+
+   call MPI_FILE_OPEN(QLGYRO_COMM_WORLD, full_statusfile, &
+        MPI_MODE_WRONLY+MPI_MODE_CREATE, MPI_INFO_NULL, file_handle, ierr)
+   
+   do i=1,n_kypx0
+
+      colour = -1
+      if (i .le. n_parallel) colour = i-1
+      write(outstr, 44) "KY = ", tglf_ky_spectrum_out(i_ky(i)), ", PX0 = ",&
+      px0_spectrum(i_px0(i)), ": fresh       ", 0, colour, NEW_LINE(' ')
+      
+      if (i_proc_global .eq. 0) then
+         call MPI_FILE_WRITE(file_handle, TRIM(outstr), LEN(TRIM(outstr)), &
+              MPI_CHARACTER, MPI_STATUS_IGNORE, ierr)
+      end if
+   end do
+   
+   statstr = LEN(TRIM(outstr))
+   call MPI_file_close(file_handle, ierr)
+   
+   
+44 format(A5, F7.3, A8, F7.3, A14, 2I4, A1)
+   
+ end subroutine init_qlgyro_status
+
+ 
+ subroutine write_qlgyro_status(runs, colors, i_kypx0, status, color_in)
+   ! Writes out status file for each ky value
+   ! ky_run :: integer(n_kypx0) status for each ky run
+   ! i_kypx0   :: indice where to overwrite value
+   ! status :: overwrite value
+   ! color  :: color of cores that ran this ky
+
+   
+   use qlgyro_globals
+   use tglf_interface
+   use mpi
+   implicit none
+   
+   CHARACTER(18) :: statusfile="out.qlgyro.status"
+   integer, dimension(n_kypx0), intent(inout) :: runs
+   integer, dimension(n_kypx0), intent(inout) :: colors
+   integer, intent(in) :: i_kypx0, status, color_in
+   integer :: file_handle
+   integer(kind=MPI_OFFSET_KIND) :: offset
+   CHARACTER(statstr) :: statusline
+   CHARACTER(98) :: full_statusfile
+   CHARACTER(14) :: ky_status
+
+   full_statusfile = trim(path)//statusfile
+
+   offset = (i_kypx0 - 1) * statstr
+
+   runs(i_kypx0) = status
+   colors(i_kypx0) = color_in
+
+   select case(runs(i_kypx0))
+
+   case (0)
+      ky_status = ": fresh       "
+   case (1)
+      ky_status = ": running     "
+   case (2)
+      ky_status = ": unconverged "
+   case (3)
+      ky_status = ": converged   "
+   end select
+
+   write(statusline, 44) "KY = ", tglf_ky_spectrum_out(i_ky(i_kypx0)), ", PX0 = ",&
+   px0_spectrum(i_px0(i_kypx0)), ky_status, runs(i_kypx0), colors(i_kypx0), NEW_LINE(' ')
+
+   call MPI_FILE_OPEN(qlgyro_comm, full_statusfile, &
+        MPI_MODE_WRONLY, MPI_INFO_NULL, file_handle, ierr)
+
+   call MPI_FILE_WRITE_AT(file_handle, offset, statusline, &
+           statstr, MPI_CHARACTER, &
+           MPI_STATUS_IGNORE, ierr)
+
+   call MPI_file_close(file_handle, ierr)
+   
+44 format(A5, F7.3, A8, F7.3, A14, 2I4, A1)
+    
+ end subroutine write_qlgyro_status
+
+ 
+ subroutine get_qlgyro_status(i_kypx0, status, loop_cycle)
+   
+   use mpi
+   use qlgyro_globals
+   use tglf_interface
+   implicit none
+      
+   integer :: file_handle
+   integer(kind=MPI_OFFSET_KIND) :: offset
+   integer, intent(in) :: i_kypx0
+   integer, intent(out) :: status
+   logical, intent(out) :: loop_cycle
+   CHARACTER(18) :: statusfile="out.qlgyro.status"
+   CHARACTER(1) :: outstr
+   CHARACTER(98) :: full_statusfile
+
+   full_statusfile = trim(path)//statusfile
+
+   offset = (i_kypx0-1) * statstr + 44
+   call MPI_FILE_OPEN(qlgyro_comm, full_statusfile, &
+        MPI_MODE_RDONLY, MPI_INFO_NULL, file_handle, ierr)
+
+   ! Location of run status
+   call MPI_FILE_READ_AT(file_handle, offset, outstr, &
+        1, MPI_CHARACTER, &
+        MPI_STATUS_IGNORE, ierr)
+
+   read(outstr, *) status
+   call MPI_file_close(file_handle, ierr)
+
+   loop_cycle = .true.
+   if (status .eq. 0) loop_cycle = .false.
+
+ end subroutine get_qlgyro_status
+
+ 
+ subroutine read_qlgyro_status(runs, cores)
+   ! Reads in status file for a given ky
+   ! i_kypx0 :: indice for ky run
+   ! status :: integer stating run status
+   
+   use qlgyro_globals
+   use tglf_interface
+   use mpi
+   implicit none
+
+   integer, dimension(n_kypx0), intent(out) :: runs, cores
+   integer :: file_handle
+   CHARACTER(18) :: statusfile="out.qlgyro.status"
+   CHARACTER(1) :: status_str
+   CHARACTER(3) :: core_str
+   INTEGER :: i_kypx0
+   INTEGER(kind=MPI_OFFSET_KIND) :: offset1, offset2
+   CHARACTER(98) :: full_statusfile
+
+   full_statusfile = trim(path)//statusfile
+
+   call MPI_FILE_OPEN(qlgyro_comm, full_statusfile, &
+        MPI_MODE_RDONLY, MPI_INFO_NULL, file_handle, ierr)
+
+   do i_kypx0=1,n_kypx0
+      
+      ! Location of run status
+      offset1 = (i_kypx0-1) * statstr + 44
+      call MPI_FILE_READ_AT(file_handle, offset1, status_str, &
+           1, MPI_CHARACTER, &
+           MPI_STATUS_IGNORE, ierr)
+      
+      read(status_str, *) runs(i_kypx0)
+
+      ! Location of run color
+      offset2 = offset1 + 2
+      call MPI_FILE_READ_AT(file_handle, offset2, core_str, &
+           3, MPI_CHARACTER, &
+           MPI_STATUS_IGNORE, ierr)
+      
+      read(core_str, *) cores(i_kypx0)
+      
+   end do
+   
+   call MPI_file_close(file_handle, ierr)
+
+end subroutine read_qlgyro_status
+
+ ! SUBROUTINE write_tglf_density_spectrum
+!   !
+!   USE tglf_dimensions
+!   USE tglf_global
+!   USE tglf_species
+!   USE tglf_kyspectrum
+!   !   
+!   IMPLICIT NONE
+!   CHARACTER(25) :: fluxfile="out.tglf.density_spectrum"
+!   INTEGER :: i,is,n
+!   REAL :: density(nsm)
+!   !
+!   if(new_start)then
+!      write(*,*)"error: tglf_TM must be called before write_tglf_density_spectrum"
+!      write(*,*)"       NN doesn't compute spectra -> if needed set tglf_nn_max_error_in=-1"
+!   endif
+!   !
+!   OPEN(unit=33,file=fluxfile,status='replace')
+! !
+!   write(33,*)"gyro-bohm normalized density fluctuation amplitude spectra"
+!   write(33,*)"ky,(density(is),is=1,ns_in)"
+!   do i=1,nky
+!     do is=1,ns
+!       density(is) = 0.0
+!       do n = 1,nmodes_in
+!         density(is) = density(is) + intensity_spectrum_out(1,is,i,n)
+!       enddo
+!       density(is) = SQRT(density(is))
+!     enddo
+!     write(33,*)ky_spectrum(i),(density(is),is=1,ns)
+!   enddo
+! !
+!   CLOSE(33)
+! !
+! END SUBROUTINE write_tglf_density_spectrum
+! !-----------------------------------------------------------------
+
+! SUBROUTINE write_tglf_temperature_spectrum
+!   !
+!   USE tglf_dimensions
+!   USE tglf_global
+!   USE tglf_species
+!   USE tglf_kyspectrum
+!   !   
+!   IMPLICIT NONE
+!   CHARACTER(29) :: fluxfile="out.tglf.temperature_spectrum"
+!   INTEGER :: i,is,n
+!   REAL :: temp(nsm)
+!   !
+!   if(new_start)then
+!      write(*,*)"error: tglf_TM must be called before write_tglf_temperature_spectrum"
+!      write(*,*)"       NN doesn't compute spectra -> if needed set tglf_nn_max_error_in=-1"
+!   endif
+!   !
+!   OPEN(unit=33,file=fluxfile,status='replace')
+! !
+!   write(33,*)"gyro-bohm normalized temperature fluctuation amplitude spectra"
+!   write(33,*)"ky,(temperature(is),is=1,ns_in)"
+!   do i=1,nky
+!     do is=1,ns
+!       temp(is) = 0.0
+!       do n = 1,nmodes_in
+!         temp(is) = temp(is) + intensity_spectrum_out(2,is,i,n)
+!       enddo
+!       temp(is) = SQRT(temp(is))
+!     enddo
+!     write(33,*)ky_spectrum(i),(temp(is),is=1,ns)
+!   enddo
+! !
+!   CLOSE(33)
+! !
+! END SUBROUTINE write_tglf_temperature_spectrum
+! !-----------------------------------------------------------------
+
+! SUBROUTINE write_tglf_intensity_spectrum
+!   !
+!   USE tglf_dimensions
+!   USE tglf_global
+!   USE tglf_species
+!   USE tglf_kyspectrum
+!   !   
+!   IMPLICIT NONE
+!   CHARACTER(27) :: fluxfile="out.tglf.intensity_spectrum"
+!   INTEGER :: i,is,n
+!   REAL :: den,tem, u_par, q_tot
+!   !
+!   if(new_start)then
+!      write(*,*)"error: tglf_TM must be called before write_tglf_intensity_spectrum"
+!      write(*,*)"       NN doesn't compute spectra -> if needed set tglf_nn_max_error_in=-1"
+!   endif
+!   !
+!   OPEN(unit=33,file=fluxfile,status='replace')
+! !
+!   write(33,*)"gyro-bohm normalized intensity fluctuation amplitude spectra"
+!   write(33,*)"ky,density,temperature,parallel velocity, parallel energy"
+!   do is=ns0,ns
+!     write(33,*)"species ",is
+!     do i=1,nky
+!       den = 0.0
+!       tem = 0.0
+!       u_par = 0.0
+!       q_tot = 0.0
+!       do n = 1,nmodes_in
+!         den = den + intensity_spectrum_out(1,is,i,n)
+!         tem = tem + intensity_spectrum_out(2,is,i,n)
+!         u_par = u_par + intensity_spectrum_out(3,is,i,n)
+!         q_tot = q_tot + intensity_spectrum_out(4,is,i,n)
+!       enddo
+!       write(33,*)ky_spectrum(i),den,tem,u_par,q_tot
+!     enddo
+!   enddo
+! !
+!   CLOSE(33)
+! !
+! END SUBROUTINE write_tglf_intensity_spectrum
+
+! !-----------------------------------------------------------------
+
+! SUBROUTINE write_tglf_intensity_spectrum_per_mode
+!   !
+!   USE tglf_dimensions
+!   USE tglf_global
+!   USE tglf_species
+!   USE tglf_kyspectrum
+!   !   
+!   IMPLICIT NONE
+!   CHARACTER(36) :: fluxfile="out.tglf.intensity_spectrum_per_mode"
+!   INTEGER :: i,is,n
+!   REAL :: den,tem, u_par, q_tot
+!   !
+!   if(new_start)then
+!      write(*,*)"error: tglf_TM must be called before write_tglf_intensity_spectrum_per_mode"
+!      write(*,*)"       NN doesn't compute spectra -> if needed set tglf_nn_max_error_in=-1"
+!   endif
+!   !
+!   OPEN(unit=33,file=fluxfile,status='replace')
+! !
+!   write(33,*)"gyro-bohm normalized intensity fluctuation amplitude spectra per mode"
+!   write(33,*)"density,temperature,parallel velocity,parallel energy"
+!   write(33,*)"index limits: ns,nky,nmodes"
+!   write(33,*)ns,nky,nmodes_in
+!   do is=ns0,ns
+!     do i=1,nky
+!       den = 0.0
+!       tem = 0.0
+!       u_par = 0.0
+!       q_tot = 0.0
+!       do n = 1,nmodes_in
+!         den = intensity_spectrum_out(1,is,i,n)
+!         tem = intensity_spectrum_out(2,is,i,n)
+!         u_par = intensity_spectrum_out(3,is,i,n)
+!         q_tot = intensity_spectrum_out(4,is,i,n)
+!         write(33,*) den
+!         write(33,*) tem
+!         write(33,*) u_par
+!         write(33,*) q_tot
+!       enddo      
+!     enddo
+!   enddo
+! !
+!   CLOSE(33)
+! !
+! END SUBROUTINE write_tglf_intensity_spectrum_per_mode
+
+! !-----------------------------------------------------------------
+
+! !-----------------------------------------------------------------
+
+! SUBROUTINE write_tglf_field_spectrum_per_mode
+!   !
+!   USE tglf_dimensions
+!   USE tglf_global
+!   USE tglf_species
+!   USE tglf_kyspectrum
+!   !   
+!   IMPLICIT NONE
+!   CHARACTER(36) :: fluxfile="out.tglf.field_spectrum_per_mode"
+!   INTEGER :: i,n
+!   REAL :: phi,a_par,b_par
+!   !
+!   if(new_start)then
+!      write(*,*)"error: tglf_TM must be called before write_tglf_field_spectrum_per_mode"
+!      write(*,*)"       NN doesn't compute spectra -> if needed set tglf_nn_max_error_in=-1"
+!   endif
+!   !
+!   OPEN(unit=33,file=fluxfile,status='replace')
+! !
+!   write(33,*)"gyro-bohm normalized field fluctuation intensity spectra per mode"
+!   write(33,*)"potential,A_par,B_par"
+!   write(33,*)"index limits: nky,nmodes"
+!   write(33,*)nky,nmodes_in
+!   if(use_bper_in)then
+!      write(33,*)"a_par_yes"
+!   else
+!      write(33,*)"a_par_no"
+!   endif
+!   if(use_bpar_in) then
+!      write(33,*)"b_par_yes"
+!   else
+!      write(33,*)"b_par_no"
+!   endif
+!   do i=1,nky
+!     phi = 0.0
+!     a_par=0.0
+!     b_par=0.0
+!     do n = 1,nmodes_in
+!       phi = field_spectrum_out(2,i,n)
+!       if(use_bper_in)a_par = field_spectrum_out(3,i,n)
+!       if(use_bpar_in)b_par = field_spectrum_out(4,i,n)
+!       write(33,*)phi
+!       if(use_bper_in)write(33,*)a_par
+!       if(use_bpar_in)write(33,*)b_par
+!     enddo
+!   enddo
+! !
+!   CLOSE(33)
+! !
+! END SUBROUTINE write_tglf_field_spectrum_per_mode
+! !-----------------------------------------------------------------
+
+
diff --git a/qlgyro/src/qlgyro_ky_spectrum.f90 b/qlgyro/src/qlgyro_ky_spectrum.f90
new file mode 100644
index 000000000..8c9fde35a
--- /dev/null
+++ b/qlgyro/src/qlgyro_ky_spectrum.f90
@@ -0,0 +1,24 @@
+      SUBROUTINE qlgyro_ky_spectrum(kymin)
+!
+      USE tglf_dimensions
+      USE tglf_global
+      USE tglf_species
+      USE tglf_kyspectrum
+      USE tglf_interface
+      IMPLICIT NONE
+
+      real, intent(in) :: kymin
+      real, dimension(12) :: n_tor
+      integer :: i_ky
+
+      call get_ky_spectrum
+
+      tglf_nky_in = nky
+      if (.not. allocated(tglf_ky_spectrum_out)) then
+         allocate(tglf_ky_spectrum_out(nky), tglf_dky_spectrum_out(nky))
+      end if
+
+      tglf_ky_spectrum_out = ky_spectrum(:nky)
+      tglf_dky_spectrum_out = dky_spectrum(:nky)
+
+    END SUBROUTINE qlgyro_ky_spectrum
diff --git a/qlgyro/src/qlgyro_px0_spectrum.f90 b/qlgyro/src/qlgyro_px0_spectrum.f90
new file mode 100644
index 000000000..a68cad4da
--- /dev/null
+++ b/qlgyro/src/qlgyro_px0_spectrum.f90
@@ -0,0 +1,32 @@
+      SUBROUTINE qlgyro_px0_spectrum
+!
+
+      USE qlgyro_globals
+      IMPLICIT NONE
+
+      integer :: i
+      
+      if (.not.allocated(px0_spectrum)) allocate(px0_spectrum(n_px0))
+
+      ! Set px0 values to scan through (currently 0 -> 0.5)
+      if (n_px0 .eq. 1) then
+         px0_spectrum(1) = 0.0
+      else if (px0grid_model .eq. 2) then
+         do i=1, n_px0 - 2
+            px0_spectrum(i) = ((i-1)*0.1) * 0.5
+         end do
+         px0_spectrum(n_px0-1) = 0.25
+         px0_spectrum(n_px0) = 0.5
+      else if (px0grid_model .eq. 3) then
+         do i=1, n_px0 - 2
+            px0_spectrum(i) = (i-1) * 0.016
+         end do
+         px0_spectrum(n_px0-1) = 0.2
+         px0_spectrum(n_px0) = 0.5
+      else
+         do i=1, n_px0
+            px0_spectrum(i) = (i-1.0) / (n_px0-1.0) * 0.5
+         end do
+      end if
+      
+    END SUBROUTINE qlgyro_px0_spectrum
diff --git a/qlgyro/src/qlgyro_read_input.f90 b/qlgyro/src/qlgyro_read_input.f90
new file mode 100644
index 000000000..16eebb05a
--- /dev/null
+++ b/qlgyro/src/qlgyro_read_input.f90
@@ -0,0 +1,117 @@
+!--------------------------------------------------------------
+! gyro_read_input.f90
+!
+! PURPOSE:
+!  Complete read of input parameters.
+!
+! NOTES:
+!  Input parameters are automatically broadcast 
+!  to entire GYRO_COMM_WORLD. 
+!
+!   =============================================
+!   HOW TO ADD INPUT VARIABLES 
+!
+!   Adding a new input variable is now simple.
+!   Just append a line analogous to one of those 
+!   below.  The variable will be read from the 
+!   file 'input.dat' and broadcast to all members 
+!   of GYRO_COMM_WORLD.
+!   =============================================
+!---------------------------------------------------------------
+
+subroutine qlgyro_read_input
+
+  use qlgyro_globals
+
+  !-------------------------
+  implicit none
+  !
+  integer :: i_kypx0
+  !-------------------------
+
+  if (i_proc_global == 0) open(unit=1,file=trim(path)//'input.qlgyro.gen',status='old')
+
+  !--------------------------------------------------------
+  ! BEGIN reading data:
+  !
+  call ql_readbc_int(n_parallel)
+  call ql_readbc_int(n_runs)
+  call ql_readbc_real(gamma_exb)
+  call ql_readbc_int(code)
+  call ql_readbc_int(kygrid_model)
+  call ql_readbc_real(ky_in)
+  call ql_readbc_int(n_ky)
+  call ql_readbc_int(xnu_model)
+  call ql_readbc_int(auto_box_size)
+  call ql_readbc_real(kx_max_box)
+  call ql_readbc_int(sat_rule)
+  call ql_readbc_int(n_px0)
+  call ql_readbc_int(px0grid_model)
+
+  ! DONE reading data.
+  !--------------------------------------------------------
+  if (mod(n_inst, n_parallel) .ne. 0) then
+     open(unit=1,file=trim(runfile),position='append')
+     write(1,*) '------------------------------------------------------------'
+     write(1,*) 'No. of processors cant be divided in number of parallel jobs'
+     write(1,*) '------------------------------------------------------------'
+     stop
+  end if
+
+  if (sat_rule .eq. 1 .and. n_px0 .ne. 1) then
+     open(unit=1,file=trim(runfile),position='append')
+     write(1,*) '---------------------------------------------------------'
+     write(1,*) 'Saturation rule 1 can only be run with a single PX0 value'
+     write(1,*) '---------------------------------------------------------'
+     stop
+  end if
+
+  if (gamma_exb .ne. 0.0) then
+     qlgyro_rotation_flag = 1
+  endif
+
+  procs = n_inst/n_parallel
+  
+  if (i_proc_global == 0) close(1)
+
+  if (debug_flag == 1 .and. i_proc_global == 0) then
+     print *,'[qlgyro_read_input done]'
+  endif
+
+end subroutine qlgyro_read_input
+
+!------------------------------------------------------------
+! Service routines: 
+!
+! (1) read and broadcast an integer:
+!
+subroutine ql_readbc_int(p)
+
+  use mpi
+  use qlgyro_globals
+
+  implicit none
+  integer, intent(inout) :: p
+
+  if (i_proc_global == 0) read(1,*) p
+
+  call MPI_BCAST(p,1,MPI_INTEGER,0,QLGYRO_COMM_WORLD,ierr)
+
+end subroutine ql_readbc_int
+!
+! (2) read and broadcast a real:
+!
+subroutine ql_readbc_real(x)
+  
+  use mpi
+  use qlgyro_globals
+
+  implicit none
+  real, intent(inout) :: x
+
+  if (i_proc_global == 0) read(1,*) x
+
+  call MPI_BCAST(x,1,MPI_DOUBLE,0,QLGYRO_COMM_WORLD,ierr)
+
+end subroutine ql_readbc_real
+!------------------------------------------------------------
diff --git a/qlgyro/src/qlgyro_run.f90 b/qlgyro/src/qlgyro_run.f90
new file mode 100644
index 000000000..ccf0b619c
--- /dev/null
+++ b/qlgyro/src/qlgyro_run.f90
@@ -0,0 +1,118 @@
+!-----------------------------------------------------------------
+! qlgyro_run.f90
+!
+! PURPOSE:
+!  Manage call to QLGYRO simulation for both standalone and
+!  TGYRO usage.
+!-----------------------------------------------------------------
+
+subroutine qlgyro_run(lpath_in, qlgyro_comm_in, i_tran_in)
+
+  use mpi
+  use qlgyro_globals
+  use qlgyro_cgyro_interface
+
+  !-----------------------------------------------------------------
+  implicit none
+  !
+  !-----------------------------------------------------------------
+
+  ! Input parameters (IN) - REQUIRED
+  character(len=*), intent(in) :: lpath_in
+  integer, intent(in) :: qlgyro_comm_in
+  integer, intent(in) :: i_tran_in
+  character(len=13) :: format_string
+
+  !-----------------------------------------------------------------
+  
+  !-----------------------------------------------------------------
+  ! Query MPI for dimensions
+  !
+  QLGYRO_COMM_WORLD = qlgyro_comm_in
+  !
+  ! Query rank and size
+  !
+  call MPI_COMM_RANK(QLGYRO_COMM_WORLD,i_proc_global,ierr)
+  call MPI_COMM_SIZE(QLGYRO_COMM_WORLD,n_proc_global,ierr)
+  n_inst = n_proc_global
+  !-----------------------------------------------------------------
+
+  !-----------------------------------------------------------------
+  ! Transport solver operation
+  transport_method = 1
+  tag_removal = 1
+  !
+  path = lpath_in
+  cgyro_path_in = path
+  i_tran = i_tran_in
+
+  call qlgyro_allocate_globals
+
+  call qlgyro_read_input
+
+  call qlgyro_comm_setup
+
+  CGYRO_COMM_WORLD = qlgyro_comm
+  call cgyro_init(path, CGYRO_COMM_WORLD)
+
+  if (cgyro_n_toroidal_in .gt. 1) then
+     call qlgyro_run_cgyro_fluxtube
+  else 
+     call qlgyro_run_cgyro_balloon
+  end if
+
+  ! Synchronise all cores
+  call qlgyro_comm_sync
+
+  ! Apply saturation rule
+  if (sat_rule .eq. 1) then
+     call qlgyro_sat1
+  else if (sat_rule .eq. -1) then
+     call qlgyro_sat_mg
+  else
+     open(unit=1,file=trim(runfile),position='append')
+     write(1,*) '-----------------------------------------'
+     write(1,*) 'Sat rule ', sat_rule, 'not a valid option'
+     write(1,*) '-----------------------------------------'
+     stop
+  end if
+
+  ! Sum flux over ky spectrum
+  call qlgyro_sum_fluxes
+
+  if (i_proc_global .eq. 0) then
+
+     if (transport_method .eq. 1) then
+        if (i_tran .lt. 10) then
+           format_string = "(A10, I1, A1)"
+        else if (i_tran .lt. 100) then
+           format_string = "(A10, I2, A1)"
+        else if (i_tran .lt. 1000) then
+           format_string = "(A10, I3, A1)"
+        else
+           write(*, *) "Too many iterations... over 1000..."
+           stop
+        end if
+
+        write(iter_path, format_string) "ITERATION_", i_tran, "/"
+        call system("mkdir -p "//trim(path)//trim(iter_path))
+     end if
+
+     call write_qlgyro_ky_spectrum
+     call write_qlgyro_QL_weight_spectrum
+     call write_qlgyro_eigenvalue_spectrum
+     call write_qlgyro_flux_spectrum
+     call write_qlgyro_field_spectrum
+     call write_qlgyro_gbflux
+     call write_qlgyro_units
+     call write_qlgyro_sat_geo_spectrum
+     call write_qlgyro_kxrms_spectrum
+
+     print*, 'Completed QLGYRO run'
+     
+  end if
+
+  ! Need to deallocate array which get re-allocated in next call
+  call tglf_deallocate
+
+end subroutine qlgyro_run
diff --git a/qlgyro/src/qlgyro_run_cgyro_balloon.f90 b/qlgyro/src/qlgyro_run_cgyro_balloon.f90
new file mode 100644
index 000000000..8fef13fb6
--- /dev/null
+++ b/qlgyro/src/qlgyro_run_cgyro_balloon.f90
@@ -0,0 +1,290 @@
+subroutine qlgyro_run_cgyro_balloon
+
+  use mpi
+  use qlgyro_globals
+  use qlgyro_cgyro_interface
+  use tglf_interface
+  
+  implicit none
+
+  integer :: i_ky_local, i_run, i_colour, i_theta, i_px0_local, i_kypx0
+  integer :: ios
+
+  character(len=5) :: kystr, px0str
+  real :: ky, timestep, maxtime, kx_max_default, px0
+
+  integer, dimension(:), allocatable :: ky_run, px0_run
+  integer, dimension(:), allocatable :: ky_px0_run
+  integer :: run_status, restart
+
+  logical :: loop_cycle
+
+  ! Read input.gacode in necessary
+  if (cgyro_profile_model_in .eq. 2) then
+     ! File needed for output 
+     open(unit=1,file=trim(path)//'out.cgyro.info',status='replace')
+     call cgyro_make_profiles
+     call qlgyro_cgyro_deallocate_arrays
+     call map_global2interface
+  end if
+
+  ! Maps (Physics) CGYRO interface to QLGYRO globals
+  call qlgyro_cgyro_map
+
+  ! Maps (Numerics) CGYRO globals (from input.cgyro file) to CGYRO interface
+  call map_global2interface
+
+  ! Maps (Physics) QLGYRO globals to back CGYRO interface
+  call cgyro_qlgyro_map
+
+  ! Map all to CGYRO interface to CGYRO globals
+  call map_interface2global
+
+  ! Maps QL-GYRO variable to TGLF
+  call qlgyro_tglf_map
+
+  call map_global2interface
+  call allocate_cgyro_interface
+  if (i_proc_global .eq. 0)  call tglf_dump_local
+  
+  call qlgyro_ky_spectrum(0.005)
+  call qlgyro_px0_spectrum
+
+  maxtime = cgyro_max_time_in
+  timestep = cgyro_delta_t_in
+
+  restart = cgyro_restart_flag_in
+  tglf_nmodes_in = n_px0
+
+  n_ky = tglf_nky_in
+  
+  ! Set up ky px0 grid
+  n_kypx0 = n_ky * n_px0
+  if (.not. allocated(i_ky)) allocate(i_ky(n_kypx0))
+  if (.not. allocated(i_px0)) allocate(i_px0(n_kypx0))
+
+  do i_kypx0=1, n_kypx0
+     i_ky(i_kypx0) = (i_kypx0-1) / n_px0 + 1
+     i_px0(i_kypx0) = modulo((i_kypx0-1), n_px0) + 1
+  end do
+
+  n_thetab = cgyro_n_theta_in * cgyro_n_radial_in
+  n_field = cgyro_n_field_in
+
+  ! Eigenvalues
+  if (.not.allocated(tglf_eigenvalue_spectrum_out)) allocate(tglf_eigenvalue_spectrum_out(2, tglf_nky_in, tglf_nmodes_in))
+  if (.not.allocated(qlgyro_eigenvalue_spectrum_out)) allocate(qlgyro_eigenvalue_spectrum_out(2, n_ky, n_px0))
+
+  ! Fields
+  if (.not.allocated(tglf_field_spectrum_out)) allocate(tglf_field_spectrum_out(4, tglf_nky_in, tglf_nmodes_in))
+  if (.not.allocated(qlgyro_field_spectrum_out)) allocate(qlgyro_field_spectrum_out(3, n_thetab, n_ky, n_px0))
+  if (.not.allocated(qlgyro_theta_ballooning)) allocate(qlgyro_theta_ballooning(n_thetab))
+  if (.not.allocated(qlgyro_k_perp)) allocate(qlgyro_k_perp(n_thetab, n_ky, n_px0))
+  if (.not.allocated(qlgyro_jacobian)) allocate(qlgyro_jacobian(n_thetab, n_ky, n_px0))
+
+  ! Fluxes
+  if (.not.allocated(tglf_flux_spectrum_out)) allocate(tglf_flux_spectrum_out(5, n_species, 3, tglf_nky_in, tglf_nmodes_in))
+  if (.not.allocated(qlgyro_flux_spectrum_out)) allocate(qlgyro_flux_spectrum_out(5, n_species, 3, n_ky, n_px0))
+
+  ! Array to check if simulation started for each ky
+  if (.not.allocated(ky_run)) allocate(ky_run(n_kypx0))
+  if (.not.allocated(ky_color)) allocate(ky_color(n_kypx0))
+
+  ! Grad r geometry factor
+  if (.not.allocated(sat_geo_spectrum)) allocate(sat_geo_spectrum(tglf_nky_in))
+  if (.not.allocated(kxrms_spectrum)) allocate(kxrms_spectrum(tglf_nky_in))
+
+  ! Initial status of each sim
+  ky_run = 0
+
+  ! Initial proc no. for ky run
+  ky_color = -1
+
+  ! Initialise status file with all zeros if doesnt exist
+  call init_qlgyro_status
+
+  call MPI_BCAST(ky_run, tglf_nky_in, MPI_INTEGER, 0, QLGYRO_COMM_WORLD, ierr)
+
+  tglf_elec_pflux_out = 0.0
+  tglf_elec_eflux_out = 0.0
+  tglf_elec_mflux_out = 0.0
+  tglf_elec_expwd_out = 0.0
+
+  tglf_ion_pflux_out = 0.0
+  tglf_ion_eflux_out = 0.0
+  tglf_ion_mflux_out = 0.0
+  tglf_ion_expwd_out = 0.0
+
+  tglf_particle_flux_out = 0.0
+  tglf_energy_flux_out = 0.0
+  tglf_stress_tor_out = 0.0
+  tglf_exchange_out = 0.0
+  tglf_eigenvalue_spectrum_out = 0.0
+  tglf_flux_spectrum_out = 0.0
+  tglf_field_spectrum_out = 0.0
+  qlgyro_eigenvalue_spectrum_out = 0.0
+  qlgyro_flux_spectrum_out = 0.0
+  qlgyro_field_spectrum_out = 0.0
+  qlgyro_k_perp = 0.0
+  qlgyro_jacobian = 0.0
+
+  call MPI_barrier(QLGYRO_COMM_WORLD, ierr)
+
+  do i_kypx0=1,n_kypx0
+
+     ! Initial assignment of jobs to cores
+     if (i_kypx0 .le. n_parallel .and. i_kypx0 .ne. color+1) then
+        cycle
+     end if
+
+     i_ky_local = i_ky(i_kypx0)
+     i_px0_local = i_px0(i_kypx0)
+     
+     call get_qlgyro_status(i_kypx0, run_status, loop_cycle)
+     
+     ! If run is being done then skip to next ky
+     if (loop_cycle) then
+        ! Give some time to allow for other statuses to be set
+        call sleep(2)
+        call MPI_barrier(CGYRO_COMM_WORLD, ierr)
+        cycle
+     end if
+     run_status = 1
+
+     call write_qlgyro_status(ky_run, ky_color, i_kypx0, run_status, color)
+
+     ky = tglf_ky_spectrum_out(i_ky_local)
+     px0 = px0_spectrum(i_px0_local)
+
+     ! Creates directory for each ky and changes into it for that run
+     write(kystr, '(F5.2)') ky
+     write(px0str, '(F5.2)') px0
+     runpath = trim(trim(path)//'/KY_'//trim(adjustl(kystr)))//"_PX0_"//trim(adjustl(px0str))//"/"
+
+     if (adjoint .eq. 0) then
+        call system("mkdir -p "//runpath)
+        write(*,*) ' '
+        write(*,21) 'Group ',  color, ' running in folder ', trim(runpath), ky_color(i_kypx0)
+     end if
+
+     call MPI_barrier(CGYRO_COMM_WORLD, ierr)
+
+     ! Ensure linear settings for CGYRO
+     cgyro_n_toroidal_in = 1
+     if (auto_box_size .eq. 1) then
+        kx_max_default = ((cgyro_n_radial_in /2) -1) * 2 * pi * ky * cgyro_s_in
+        if (kx_max_default .gt. kx_max_box) then
+           cgyro_box_size_in = int(kx_max_default / kx_max_box)
+        else
+           cgyro_box_size_in = 1
+        end if
+        if (adjoint .eq. 0) print*, 'New box size = ', cgyro_box_size_in, kx_max_default/cgyro_box_size_in, ky
+     else        
+        cgyro_box_size_in = 1
+     end if
+     
+     cgyro_nonlinear_flag_in = 0
+     
+     ! Change values after init
+     cgyro_ky_in = ky
+     cgyro_px0_in = px0
+
+     cgyro_integration_error_in = 0.0
+     cgyro_printout_in = .false.
+
+     if (ky .le. 1.0) then
+        cgyro_max_time_in = maxtime
+        cgyro_delta_t_in = timestep
+     else
+        cgyro_max_time_in = maxtime/ky
+        cgyro_delta_t_in = timestep/ky
+     end if
+
+     cgyro_path_in = trim(runpath)//'/'
+     
+     call MPI_barrier(CGYRO_COMM_WORLD, ierr)
+
+     cgyro_restart_flag_in = restart
+
+     ! Reset signal to 0
+     cgyro_signal_out = 0
+
+     call map_interface2global
+
+     do i_run=1, n_runs
+        call cgyro_init_kernel
+        call cgyro_kernel
+        call qlgyro_cgyro_cleanup
+        call cgyro_final_kernel
+
+        ! Check if converged
+        if (cgyro_signal_out .ne. 1) then
+
+           cgyro_restart_flag_in=1
+           
+           if ( i_run == n_runs) then
+              run_status = 2
+           end if
+        else
+           run_status = 3
+           exit
+        end if
+     end do
+
+     call write_qlgyro_status(ky_run, ky_color, i_kypx0, run_status, color)
+
+     ! Set run status
+     if (adjoint == 0 ) then
+        if (run_status .eq. 3) then
+           write(*,22) 'CGYRO run converged at ky/px0 =', ky,'/',px0
+        else if (run_status .eq. 2) then
+           write(*,22) 'CGYRO not converged at ky/px0 = ', ky,'/',px0
+        end if
+     end if
+
+     ! CGYRO eigenvalues
+     qlgyro_eigenvalue_spectrum_out(2,i_ky_local,i_px0_local) = real(cgyro_omega_out(1))
+     qlgyro_eigenvalue_spectrum_out(1,i_ky_local,i_px0_local) = aimag(cgyro_omega_out(1))
+
+     ! CGYRO has electrons at last index, TGLF has them in first so load them seperately
+     qlgyro_flux_spectrum_out(1:3, 1, :cgyro_n_field_in, i_ky_local, i_px0_local) =         &
+          cgyro_gbflux_out(1:3, elec_ind, :cgyro_n_field_in, 1) * cgyro_ky_in * (-cgyro_btccw_in)
+
+     qlgyro_flux_spectrum_out(1:3, 2:, :cgyro_n_field_in, i_ky_local, i_px0_local) = &
+          cgyro_gbflux_out(1:3, ion_start:ion_end, :cgyro_n_field_in, 1) * cgyro_ky_in * (-cgyro_btccw_in)
+
+     qlgyro_theta_ballooning = cgyro_thetab_out
+     qlgyro_field_spectrum_out(:, :, i_ky_local, i_px0_local) = cgyro_wavefunction_out(1, :, :)
+
+     qlgyro_k_perp(:, i_ky_local, i_px0_local) = cgyro_k_perp_out(:, 1)
+     qlgyro_jacobian(:, i_ky_local, i_px0_local) = cgyro_jacobian_out
+
+     ! If run hasn't converged, sent eigenvalue/growth to 0
+     if (run_status .eq. 2) then
+        qlgyro_eigenvalue_spectrum_out(:,i_ky_local,i_px0_local) = 0.0
+        
+        qlgyro_flux_spectrum_out(1:4, :, :cgyro_n_field_in, i_ky_local, i_px0_local) = 0.0
+
+     end if
+
+     call MPI_BARRIER(CGYRO_COMM_WORLD, ierr)
+  end do
+
+  call MPI_BARRIER(QLGYRO_COMM_WORLD, ierr)
+  
+  call read_qlgyro_status(ky_run, ky_color)
+ 
+  if (i_proc_global == 0) then
+     open(unit=1,file=trim(runfile),position='append')
+     write(1, *) 'INFO: Ran all kys'
+     write(1, *) 'B_unit = ', bunit
+     close(1)
+  endif
+
+  
+21 format(A6, I3, A24, A19, I3)
+22 format(A32, F5.2, A1, F5.2)
+end subroutine qlgyro_run_cgyro_balloon
+
+  
+    
diff --git a/qlgyro/src/qlgyro_run_cgyro_fluxtube.f90 b/qlgyro/src/qlgyro_run_cgyro_fluxtube.f90
new file mode 100644
index 000000000..68262a606
--- /dev/null
+++ b/qlgyro/src/qlgyro_run_cgyro_fluxtube.f90
@@ -0,0 +1,269 @@
+subroutine qlgyro_run_cgyro_fluxtube
+
+  use mpi
+  use qlgyro_globals
+  use qlgyro_cgyro_interface
+  use tglf_interface
+  
+  implicit none
+
+  integer :: i_ky_local, i_run, i_colour, i_theta, i_px0_local, i_kypx0
+  integer :: ios
+
+  character(len=5) :: kystr, px0str
+  real :: ky, timestep, maxtime, kx_max_default, px0
+
+  integer, dimension(:), allocatable :: ky_run, px0_run
+  integer, dimension(:), allocatable :: ky_px0_run
+  integer :: run_status, restart
+
+  logical :: loop_cycle
+
+  ! Read input.gacode in necessary
+  if (cgyro_profile_model_in .eq. 2) then
+     ! File needed for output 
+     open(unit=1,file=trim(path)//'out.cgyro.info',status='replace')
+     call cgyro_make_profiles
+     call qlgyro_cgyro_deallocate_arrays
+     call map_global2interface
+  end if
+
+  ! Maps (Physics) CGYRO interface to QLGYRO globals
+  call qlgyro_cgyro_map
+
+  ! Maps (Numerics) CGYRO globals (from input.cgyro file) to CGYRO interface
+  call map_global2interface
+
+  ! Maps (Physics) QLGYRO globals to back CGYRO interface
+  call cgyro_qlgyro_map
+
+  ! Map all to CGYRO interface to CGYRO globals
+  call map_interface2global
+
+  ! Maps QL-GYRO variable to TGLF
+  call qlgyro_tglf_map
+
+  call map_global2interface
+
+  call allocate_cgyro_interface
+  if (i_proc_global .eq. 0)  call tglf_dump_local
+
+  tglf_nky_in = cgyro_n_toroidal_in - 1
+
+  if (.not. allocated(tglf_ky_spectrum_out)) then
+     allocate(tglf_ky_spectrum_out(tglf_nky_in), tglf_dky_spectrum_out(tglf_nky_in))
+  end if
+  
+  do i_ky_local=1, cgyro_n_toroidal_in - 1
+     tglf_ky_spectrum_out(i_ky_local) = cgyro_ky_in * i_ky_local
+  end do
+  
+  tglf_dky_spectrum_out = cgyro_ky_in
+
+  call qlgyro_px0_spectrum
+
+  restart = cgyro_restart_flag_in
+  tglf_nmodes_in = n_px0
+
+  n_ky = tglf_nky_in
+
+  ! Set up ky px0 grid
+  n_kypx0 = n_ky * n_px0
+  if (.not. allocated(i_ky)) allocate(i_ky(n_kypx0))
+  if (.not. allocated(i_px0)) allocate(i_px0(n_kypx0))
+
+  do i_kypx0=1, n_kypx0
+     i_ky(i_kypx0) = (i_kypx0-1) / n_px0 + 1
+     i_px0(i_kypx0) = modulo((i_kypx0-1), n_px0) + 1
+  end do
+
+  n_thetab = cgyro_n_theta_in * cgyro_n_radial_in
+  n_field = cgyro_n_field_in
+
+  ! Eigenvalues
+  if (.not.allocated(tglf_eigenvalue_spectrum_out)) allocate(tglf_eigenvalue_spectrum_out(2, tglf_nky_in, tglf_nmodes_in))
+  if (.not.allocated(qlgyro_eigenvalue_spectrum_out)) allocate(qlgyro_eigenvalue_spectrum_out(2, n_ky, n_px0))
+
+  ! Fields
+  if (.not.allocated(tglf_field_spectrum_out)) allocate(tglf_field_spectrum_out(4, tglf_nky_in, tglf_nmodes_in))
+  if (.not.allocated(qlgyro_field_spectrum_out)) allocate(qlgyro_field_spectrum_out(3, n_thetab, n_ky, n_px0))
+  if (.not.allocated(qlgyro_theta_ballooning)) allocate(qlgyro_theta_ballooning(n_thetab))
+  if (.not.allocated(qlgyro_k_perp)) allocate(qlgyro_k_perp(n_thetab, n_ky, n_px0))
+  if (.not.allocated(qlgyro_jacobian)) allocate(qlgyro_jacobian(n_thetab, n_ky, n_px0))
+
+  ! Fluxes
+  if (.not.allocated(tglf_flux_spectrum_out)) allocate(tglf_flux_spectrum_out(5, n_species, 3, tglf_nky_in, tglf_nmodes_in))
+  if (.not.allocated(qlgyro_flux_spectrum_out)) allocate(qlgyro_flux_spectrum_out(5, n_species, 3, n_ky, n_px0))
+
+  ! Array to check if simulation started for each ky
+  if (.not.allocated(ky_run)) allocate(ky_run(n_kypx0))
+  if (.not.allocated(ky_color)) allocate(ky_color(n_kypx0))
+
+  ! Grad r geometry factor
+  if (.not.allocated(sat_geo_spectrum)) allocate(sat_geo_spectrum(tglf_nky_in))
+  if (.not.allocated(kxrms_spectrum)) allocate(kxrms_spectrum(tglf_nky_in))
+
+  ! Initial status of each sim
+  ky_run = 0
+
+  ! Initial proc no. for ky run
+  ky_color = -1
+
+  ! Initialise status file with all zeros if doesnt exist
+  call init_qlgyro_status
+
+  call MPI_BCAST(ky_run, tglf_nky_in, MPI_INTEGER, 0, QLGYRO_COMM_WORLD, ierr)
+
+  tglf_elec_pflux_out = 0.0
+  tglf_elec_eflux_out = 0.0
+  tglf_elec_mflux_out = 0.0
+  tglf_elec_expwd_out = 0.0
+
+  tglf_ion_pflux_out = 0.0
+  tglf_ion_eflux_out = 0.0
+  tglf_ion_mflux_out = 0.0
+  tglf_ion_expwd_out = 0.0
+
+  tglf_particle_flux_out = 0.0
+  tglf_energy_flux_out = 0.0
+  tglf_stress_tor_out = 0.0
+  tglf_exchange_out = 0.0
+  tglf_eigenvalue_spectrum_out = 0.0
+  tglf_flux_spectrum_out = 0.0
+  tglf_field_spectrum_out = 0.0
+  qlgyro_eigenvalue_spectrum_out = 0.0
+  qlgyro_flux_spectrum_out = 0.0
+  qlgyro_field_spectrum_out = 0.0
+  qlgyro_k_perp = 0.0
+  qlgyro_jacobian = 0.0
+
+  call MPI_barrier(QLGYRO_COMM_WORLD, ierr)
+
+  do i_px0_local=1,n_px0
+
+     ! Initial assignment of jobs to cores
+     if (i_px0_local .le. n_parallel .and. i_px0_local .ne. color+1) then
+        cycle
+     end if
+
+     do i_ky_local=1,tglf_nky_in
+        i_kypx0  = (tglf_nky_in * (i_px0_local-1)) + i_ky_local
+        call get_qlgyro_status(i_kypx0, run_status, loop_cycle)
+     end do
+     
+     ! If run is being done then skip to next ky
+     if (loop_cycle) then
+        ! Give some time to allow for other statuses to be set
+        call sleep(2)
+        call MPI_barrier(CGYRO_COMM_WORLD, ierr)
+        cycle
+     end if
+     run_status = 1
+
+     call write_qlgyro_status(ky_run, ky_color, i_px0_local, run_status, color)
+
+     px0 = px0_spectrum(i_px0_local)
+
+     ! Creates directory for each ky and changes into it for that run
+     write(px0str, '(F5.2)') px0
+     runpath = trim(trim(path)//"_PX0_"//trim(adjustl(px0str))//"/")
+
+     if (adjoint .eq. 0) then
+        call system("mkdir -p "//runpath)
+        write(*,*) ' '
+        write(*,21) 'Group ',  color, ' running in folder ', trim(runpath), ky_color(i_px0)
+     end if
+
+     call MPI_barrier(CGYRO_COMM_WORLD, ierr)
+
+     ! Ensure linear settings for CGYRO
+     cgyro_box_size_in = 1     
+     cgyro_nonlinear_flag_in = 0
+     
+     ! Change values after init
+     cgyro_px0_in = px0
+
+     cgyro_integration_error_in = 0.0
+     cgyro_printout_in = .false.
+
+     cgyro_path_in = trim(runpath)//'/'
+     
+     call MPI_barrier(CGYRO_COMM_WORLD, ierr)
+
+     cgyro_restart_flag_in = restart
+
+     ! Reset signal to 0
+     cgyro_signal_out = 0
+
+     call map_interface2global
+
+     do i_run=1, n_runs
+        call cgyro_init_kernel
+        call cgyro_kernel
+        call qlgyro_cgyro_cleanup
+        call cgyro_final_kernel
+        run_status = 2
+     end do
+
+     do i_ky_local=1, tglf_nky_in
+
+        ky = tglf_ky_spectrum_out(i_ky_local)
+
+        if (abs(cgyro_omega_error_out(i_ky_local+1)) .lt. cgyro_freq_tol_in) then
+           run_status = 3
+        end if
+
+        i_kypx0  = (tglf_nky_in * i_px0_local) + i_ky_local
+
+        call write_qlgyro_status(ky_run, ky_color, i_kypx0, run_status, color)
+
+        if (run_status .eq. 3) then
+
+           if (adjoint == 0 ) write(*,22) 'CGYRO run converged at ky/px0 =', ky,'/',px0
+
+           ! CGYRO eigenvalues
+           qlgyro_eigenvalue_spectrum_out(2,:,i_px0_local) = real(cgyro_omega_out(i_ky_local))
+           qlgyro_eigenvalue_spectrum_out(1,:,i_px0_local) = aimag(cgyro_omega_out(i_ky_local))
+           
+           ! CGYRO has electrons at last index, TGLF has them in first so load them seperately
+           qlgyro_flux_spectrum_out(1:3, 1, :cgyro_n_field_in, i_ky_local, i_px0_local) =         &
+                cgyro_gbflux_out(1:3, elec_ind, :cgyro_n_field_in, i_ky_local) * ky * i_ky_local * (-cgyro_btccw_in)
+           
+           qlgyro_flux_spectrum_out(1:3, 2:, :cgyro_n_field_in, i_ky_local, i_px0_local) = &
+                cgyro_gbflux_out(1:3, ion_start:ion_end, :cgyro_n_field_in, i_ky_local) * ky * i_ky_local * (-cgyro_btccw_in)
+           
+           qlgyro_theta_ballooning = cgyro_thetab_out
+           qlgyro_field_spectrum_out(:, :, i_ky_local, i_px0_local) = cgyro_wavefunction_out(i_ky_local, :, :)
+           
+           qlgyro_k_perp(:, i_ky_local, i_px0_local) = cgyro_k_perp_out(i_ky_local, :)
+           qlgyro_jacobian(:, i_ky_local, i_px0_local) = cgyro_jacobian_out
+           
+        ! If run hasn't converged, sent eigenvalue/growth to 0
+        else if (run_status .eq. 2) then
+           if (adjoint .eq. 0) write(*,22) 'CGYRO not converged at ky/px0 = ', ky,'/',px0
+           qlgyro_eigenvalue_spectrum_out(:,i_ky_local,i_px0_local) = 0.0
+           qlgyro_flux_spectrum_out(1:4, :, :cgyro_n_field_in, i_ky_local, i_px0_local) = 0.0
+        end if
+
+     end do
+     call MPI_BARRIER(CGYRO_COMM_WORLD, ierr)
+  end do
+
+  call MPI_BARRIER(QLGYRO_COMM_WORLD, ierr)
+  
+  call read_qlgyro_status(ky_run, ky_color)
+ 
+  if (i_proc_global == 0) then
+     open(unit=1,file=trim(runfile),position='append')
+     write(1, *) 'INFO: Ran all kys'
+     write(1, *) 'B_unit = ', bunit
+     close(1)
+  endif
+
+  
+21 format(A6, I3, A24, A19, I3)
+22 format(A32, F5.2, A1, F5.2)
+end subroutine qlgyro_run_cgyro_fluxtube
+
+  
+    
diff --git a/qlgyro/src/qlgyro_run_gyro.f90 b/qlgyro/src/qlgyro_run_gyro.f90
new file mode 100644
index 000000000..cd017246c
--- /dev/null
+++ b/qlgyro/src/qlgyro_run_gyro.f90
@@ -0,0 +1,364 @@
+!------------------------------------------------------------
+! qlgyro_run.f90
+!
+! PURPOSE:
+!  Driver for QLGYRO
+!  Runs GYRO for all the KYs specified
+!   
+!
+! 
+!------------------------------------------------------------
+
+subroutine qlgyro_run_gyro
+
+  use mpi
+  use qlgyro_globals
+  use gyro_interface
+  use tglf_interface
+  
+  implicit none
+  integer :: i_ky, i_run, i_colour
+  integer :: ios
+
+  character(len=5) :: kystr
+  real :: ky, timestep, maxtime, freq_tol
+
+  integer, dimension(:), allocatable :: ky_run
+  integer :: run_status
+
+  logical :: file_exists=.false.
+  
+  ! Map TGYRO parameters to GYRO
+  
+  gyrotest_flag=0
+
+  ! Reads in GYRO input and sets up GYRO variables
+  call gyro_read_input
+  call gyro_read_input_extra
+  call map_global2interface
+  
+  gyro_silent_flag_in=1
+
+  ! Maps GYRO variables to QL-GYRO
+  call qlgyro_gyro_map
+
+  ! Maps QL-GYRO variable to TGLF
+  call qlgyro_tglf_map
+
+  call tglf_dump_local()
+
+  call qlgyro_ky_spectrum
+
+  n_ky = tglf_nky_in
+
+  timestep = gyro_time_step_in
+  maxtime = gyro_time_max_in
+  freq_tol = abs(maxtime - int(maxtime))
+  
+  tglf_nmodes_in = n_modes
+
+  ! Ensure GYRO prints out wavefunction and flux data
+  gyro_plot_u_flag_in = 1
+  gyro_lindiff_method_in = 3
+
+  if (gyro_theta_plot_in .eq. 1) then
+     gyro_theta_plot_in = 64
+  end if
+  
+  if (i_tran == 1) then
+
+     ! Eigenvalues
+     allocate(tglf_eigenvalue_spectrum_out(2, tglf_nky_in, tglf_nmodes_in))
+     
+     ! Fields
+     allocate(tglf_field_spectrum_out(4, tglf_nky_in, tglf_nmodes_in))
+     
+     ! Fluxes
+     allocate(tglf_flux_spectrum_out(5, n_species, 3, tglf_nky_in, tglf_nmodes_in))
+     !allocate(gyro_fluxes_out(loc_n_ion+1, gyro_n_field_in, 4, gyro_radial_grid_in, tglf_nky_in, n_inst))
+
+     ! Array to check if simulation started for each ky
+     allocate(ky_run(tglf_nky_in), ky_color(tglf_nky_in))
+
+     ! Grad r geometry factor
+     allocate(sat_geo_spectrum(tglf_nky_in))
+     
+     ! Initial status of each sim
+     ky_run = 0
+
+     ! Initial proc no. for ky run
+     ky_color = -1
+     
+     inquire(file=trim(path)//'out.qlgyro.status', exist=file_exists)
+
+     ! Initialise status file with all zeros if doesnt exist
+     call init_qlgyro_status
+     
+  end if
+
+  call MPI_BCAST(ky_run, tglf_nky_in, MPI_INTEGER, 0, QLGYRO_COMM_WORLD, ierr)
+  
+  tglf_eigenvalue_spectrum_out = 0.0
+  tglf_flux_spectrum_out = 0.0
+  tglf_field_spectrum_out = 0.0
+
+  call MPI_barrier(QLGYRO_COMM_WORLD, ierr)
+
+  do i_ky=1,tglf_nky_in
+
+     ! Initial assignment of jobs to cores
+     if (i_ky .le. n_parallel .and. i_ky .ne. color+1) then
+        cycle
+     end if
+
+     call get_qlgyro_status(i_ky, run_status)
+  
+     ! If run is being done then skip to next ky
+     if (run_status .ne. 0) then
+        cycle
+     end if
+
+     run_status = 1
+     call read_qlgyro_status(ky_run, ky_color)
+     call write_qlgyro_status(ky_run, i_ky, run_status, color)
+
+     if (adjoint .eq. 0) then
+        
+        print*, ' '
+        write(*,21) 'Group ',  color, ' running ky = ', tglf_ky_spectrum_out(i_ky), ky_color(i_ky)
+     end if
+
+     ! Ensure linear settings for GYRO
+     gyro_toroidal_grid_in = 1
+     gyro_nonlinear_flag_in = 0
+     gyro_box_multiplier_in = -1
+     
+     ky = tglf_ky_spectrum_out(i_ky)
+     gyro_l_y_in = ky
+
+     ! Scales timestep by 1/ly if larger than 1.0
+     if (ky .le. 1.0) then
+        gyro_time_step_in = timestep
+        gyro_time_max_in  = maxtime
+     else
+        gyro_time_step_in = timestep * 1.0/ky
+        if (maxtime .gt. 0.0) then
+           gyro_time_max_in = int(maxtime * 1.0/ky) + freq_tol !- 1.0
+        else
+           gyro_time_max_in = int(maxtime * 1.0/ky) - freq_tol - 1.0
+        end if
+     end if
+
+     ! Creates directory for each ky and changes into it for that run
+     write(kystr, '(F5.2)') ky
+     runpath = 'KY_'//adjustl(kystr)
+     
+     call system("mkdir -p "//runpath)
+
+     inquire(file=trim(path)//'input.gacode', exist=file_exists)
+     if (file_exists .eqv. .true.) then        
+        call system("cp input.gacode  "//runpath)
+     end if
+     
+     gyro_path_in = trim(runpath)//'/'
+     
+     gyro_restart_method=1
+     call MPI_barrier(qlgyro_comm, ierr)
+     
+     do i_run=1,n_runs
+
+        ! Call GYRO
+        call gyro_run(gyrotest_flag,gyro_restart_method,transport_method)
+
+        call qlgyro_gyro_cleanup
+        
+        ! Check if converged
+        if (abs(gyro_omega_error_out) .gt. freq_tol) then
+
+           gyro_restart_method=1
+           
+           if ( i_run == n_runs) then
+              run_status = 2              
+           end if
+        else
+           run_status = 3           
+           exit
+        end if           
+     end do
+     
+     call read_qlgyro_status(ky_run, ky_color)
+     call write_qlgyro_status(ky_run, i_ky, run_status, color)
+
+     ! Set run status
+     if (adjoint == 0 ) then
+        if (run_status .eq. 3) then
+           write(*,22) 'GYRO run converged at ky =', ky
+        else if (run_status .eq. 2) then
+           write(*,22) 'GYRO not converged for ky = ', ky
+        end if
+     end if
+
+     ! GYRO eigenvalues
+     tglf_eigenvalue_spectrum_out(2,i_ky,1) = real(gyro_omega_out)
+     tglf_eigenvalue_spectrum_out(1,i_ky,1) = aimag(gyro_omega_out)
+
+     ! GYRO has electrons at last index, TGLF has them in first so load them seperately
+     tglf_flux_spectrum_out(1:4, 1, :gyro_n_field_in, i_ky, 1) = gyro_gbflux_out(1:4, n_species, :gyro_n_field_in) * gyro_l_y_in
+     
+     tglf_flux_spectrum_out(1:4, 2:, :gyro_n_field_in, i_ky, 1) = gyro_gbflux_out(1:4, 1:n_species-1, :gyro_n_field_in) * gyro_l_y_in
+     
+     !if (adjoint .eq. 0) print*, i_ky, tglf_flux_spectrum_out(2, :, 1, i_ky, 1)
+     ! If run hasn't converged, sent eigenvalue/growth to 0
+     if (run_status .eq. 2) then
+        tglf_eigenvalue_spectrum_out(2,i_ky,1) = 0.0
+        tglf_eigenvalue_spectrum_out(1,i_ky,1) = 0.0
+        
+        ! GYRO has electrons at last index, TGLF has them in first so load them seperately
+        tglf_flux_spectrum_out(1:4, :, :gyro_n_field_in, i_ky, 1) = 0.0
+     end if
+
+     call gyro_sat_geo_factor(sat_geo_spectrum(i_ky))
+
+     call MPI_BARRIER(qlgyro_comm, ierr)
+  end do
+
+  call MPI_BARRIER(QLGYRO_COMM_WORLD, ierr)
+
+  if (i_proc_global == 0) then
+     print*, 'Ran all kys'
+     open(unit=1,file=trim(runfile),position='append')
+     write(1, *) 'INFO: Ran all kys'
+     write(1, *) 'B_unit = ', bunit
+     close(1)
+  endif
+
+  
+21 format(A6, I3, A24, F5.2, I3)
+22 format(A30, F5.2)
+ 
+end subroutine qlgyro_run_gyro
+
+
+subroutine gyro_sat_geo_factor(sat_geo_phi_average)
+  
+  use tglf_interface
+  use tglf_max_dimensions
+  use tglf_sgrid
+  use qlgyro_globals
+  use gyro_interface
+  
+  implicit none
+
+  real :: drmindx, kx0
+
+  integer :: it, tglf_n_theta, jt, t1, t2
+
+  real :: sat_geo_phi_average, qrat_geo_phi, phi_norm
+  real :: qrat_1, qrat_2, gyro_theta
+
+  real, dimension(gyro_theta_plot_in*gyro_radial_grid_in) :: gyro_qrat_geo, gyro_int_factor
+
+  real, dimension(:), allocatable :: dR, dZ, dtheta, dl_dtheta, int_factor
+  real :: int_factor_1, int_factor_2, d_theta
+  
+  drmindx = 1.0
+  kx0 = 0.0
+  
+  CALL put_Miller_geometry(tglf_rmin_loc_in, &
+       tglf_rmaj_loc_in, &
+       tglf_zmaj_loc_in, &
+       drmindx, &
+       tglf_drmajdx_loc_in, &
+       tglf_dzmajdx_loc_in, &
+       tglf_kappa_loc_in, &
+       tglf_s_kappa_loc_in, &
+       tglf_delta_loc_in, &
+       tglf_s_delta_loc_in, &
+       tglf_zeta_loc_in, &
+       tglf_s_zeta_loc_in, &
+       tglf_q_loc_in, &
+       tglf_q_prime_loc_in, &
+       tglf_p_prime_loc_in, &
+       kx0)
+  
+  call tglf_setup_geometry
+
+  ! t_s contains data on theta
+  ! Now goes from 2*pi -> 0
+  t_s = t_s + 2*pi
+  
+  tglf_n_theta = ms+1
+
+  allocate(dR(0:ms), dZ(0:ms), dtheta(0:ms), int_factor(0:ms), &
+       dl_dtheta(0:ms))
+
+  ! Find integration factor, then interpolating. Not sure if correct order there
+  ! Shift arrays forward/back to find dl/dtheta
+
+  dZ = cshift(Z, -1) - cshift(Z, 1)
+  dR = cshift(R, -1) - cshift(R, 1)  
+  dtheta = cshift(t_s, -1) - cshift(t_s, 1)
+  
+  dtheta = modulo(dtheta, 2*pi)
+
+  dl_dtheta = sqrt( (dR/dtheta)**2 + (dZ/dtheta)**2)
+
+  ! Integration factor = dl/dtheta * B/Bp
+  int_factor = b_geo * dl_dtheta / Bp
+
+  ! Create qrat_geo and int_factor on GYRO thetab grid by interpolating
+  do it=1, gyro_theta_plot_in*gyro_radial_grid_in
+     gyro_theta = modulo(gyro_thetab_out(it), 2*pi)
+
+     ! Shift it to positive if negative
+     if (gyro_theta .lt. 0.0) gyro_theta = 2*pi - gyro_theta
+     
+     do jt=0, tglf_n_theta-1
+        if ( t_s(jt) .le. gyro_theta) then
+           ! Index of t_s above and below index of interest
+           t1 = jt-1
+           t2 = jt
+           exit
+        end if
+     end do
+        
+     ! TGLF uses qrat_geo**2
+     qrat_1 = qrat_geo(t1)**2
+     qrat_2 = qrat_geo(t2)**2
+
+     ! Integration measure interpolated
+     int_factor_1 = int_factor(t1)
+     int_factor_2 = int_factor(t2)
+     
+     ! Linearly extrapolate and multiply by |Phi|
+     gyro_qrat_geo(it) = (qrat_1 + (qrat_2 - qrat_1)*(gyro_theta - t_s(t1)) / &
+          (t_s(t2) - t_s(t1))) * abs(gyro_wavefunction_out(1, it))**2
+     
+     gyro_int_factor(it) = int_factor_1 + (int_factor_2 -int_factor_1) * &
+          (gyro_theta - t_s(t1)) / (t_s(t2) - t_s(t1))
+     
+  end do
+
+  qrat_geo_phi = 0.0
+  
+  ! Trapezoid rule
+  do it=1, gyro_theta_plot_in*gyro_radial_grid_in -1
+
+     ! dtheta
+     d_theta = gyro_thetab_out(it+1) - gyro_thetab_out(it)
+
+     ! Wavefunction average using composite trapezoidal rule
+     qrat_geo_phi = qrat_geo_phi +  d_theta * gyro_int_factor(it) * &
+          (gyro_qrat_geo(it+1) + gyro_qrat_geo(it))/2
+     
+     phi_norm = phi_norm + d_theta * gyro_int_factor(it) * &
+          (abs(gyro_wavefunction_out(1, it+1))**2 + abs(gyro_wavefunction_out(1, it))**2)/2
+
+  end do
+
+  ! SAT_geo is 1/qrat_geo
+  sat_geo_phi_average = 1.0 / (qrat_geo_phi / phi_norm)
+  
+end subroutine gyro_sat_geo_factor
+
+
diff --git a/qlgyro/src/qlgyro_sat1.f90 b/qlgyro/src/qlgyro_sat1.f90
new file mode 100644
index 000000000..df48d12db
--- /dev/null
+++ b/qlgyro/src/qlgyro_sat1.f90
@@ -0,0 +1,42 @@
+!
+!--------------------------------------------------------------
+!
+      SUBROUTINE qlgyro_sat1
+!
+!***********************************************************************
+!  questions  should be addressed to
+!  Gary Staebler 858-455-3466  or email: gary.staebler@gat.com
+!***********************************************************************
+!
+!  TGLF multiscale saturation rule: sat_rule_in = 1 option
+!  April 8, 2016: G.M. Staebler, J. Candy, N. T. Howard, and C. Holland
+!                  Physics of Plasmas, 23 (2016) 062518
+!  June 22, 2017: Retuned after coding error to Laplacian terms in Ampere 
+!                 and Poisson equations was fixed
+!
+!***********************************************************************
+!
+      USE tglf_dimensions
+      USE tglf_global
+      USE tglf_species
+      USE tglf_kyspectrum
+      USE tglf_xgrid
+      USE tglf_sgrid
+      USE tglf_interface
+      USE qlgyro_globals
+
+      ! CGYRO eigenvalues and fluxes - need to set these equal when
+      ! n_PX0 = 1
+      tglf_eigenvalue_spectrum_out = qlgyro_eigenvalue_spectrum_out
+      tglf_flux_spectrum_out = qlgyro_flux_spectrum_out
+
+      eigenvalue_spectrum_out(:, :nky, :1) = tglf_eigenvalue_spectrum_out
+      QL_flux_spectrum_out(:, :ns, :, :nky, :1) = tglf_flux_spectrum_out
+
+      call get_multiscale_spectrum
+
+      tglf_flux_spectrum_out = flux_spectrum_out(:, :ns, :, :nky, :1)
+      tglf_field_spectrum_out = field_spectrum_out
+
+    
+    END SUBROUTINE qlgyro_sat1
diff --git a/qlgyro/src/qlgyro_sat_mg.f90 b/qlgyro/src/qlgyro_sat_mg.f90
new file mode 100644
index 000000000..30a845b89
--- /dev/null
+++ b/qlgyro/src/qlgyro_sat_mg.f90
@@ -0,0 +1,226 @@
+!
+!--------------------------------------------------------------
+!
+      SUBROUTINE qlgyro_sat_mg
+!
+!***********************************************************************
+!  questions  should be addressed to
+!  Gary Staebler 858-455-3466  or email: gary.staebler@gat.com
+!***********************************************************************
+!
+!  TGLF multiscale saturation rule: sat_rule_in = 1 option
+!  April 8, 2016: G.M. Staebler, J. Candy, N. T. Howard, and C. Holland
+!                  Physics of Plasmas, 23 (2016) 062518
+!  June 22, 2017: Retuned after coding error to Laplacian terms in Ampere 
+!                 and Poisson equations was fixed
+!
+!***********************************************************************
+!
+
+        USE qlgyro_globals
+        USE tglf_interface
+        
+
+      implicit none
+      integer :: i_kypx0, px0_max_index, i_ky_local, i_px0_local, i_species, i_field, i_moment
+      real, dimension(n_ky, n_px0) :: ql_metric_ky_px0, species_sum_flux
+      real, dimension(n_ky) :: ql_metric_ky
+      real :: ql_metric
+      real :: px0_max, max_gam
+      real :: facnorm, b, a
+
+      call calculate_ql_metric(ql_metric_ky_px0)
+
+      ! Normalise fluxes to total heat flux
+      species_sum_flux = sum(sum(qlgyro_flux_spectrum_out(2, :, :, :, :), dim=2), dim=1)
+      
+      do i_ky_local=1, n_ky
+         do i_px0_local=1, n_px0
+            if (species_sum_flux(i_ky_local, i_px0_local) .eq. 0.0) then
+               ql_metric_ky_px0(i_ky_local, i_px0_local) = 0.0
+               species_sum_flux(i_ky_local, i_px0_local) = 1.0
+            end if
+         end do
+      end do
+
+      ! Re-scale fluxes
+      do i_moment=1, 3
+         do i_species=1, n_species
+            do i_field=1, n_field
+               qlgyro_flux_spectrum_out(i_moment, i_species, i_field, :, :) = &
+               qlgyro_flux_spectrum_out(i_moment, i_species, i_field, :, :) &
+               * ql_metric_ky_px0 / species_sum_flux
+            end do
+         end do
+      end do
+
+      ! DO PX0 average here!
+      if (n_px0 .eq. 1) then
+         ! CGYRO flux
+         tglf_flux_spectrum_out = qlgyro_flux_spectrum_out
+         ql_metric_ky(:) = ql_metric_ky_px0(:, 1)
+      else
+         do i_ky_local=1, n_ky
+            max_gam = maxval(qlgyro_eigenvalue_spectrum_out(1, i_ky_local, :))
+
+            if (max_gam < abs(gamma_exb) / 10) then
+               ! Set all to 0 
+               tglf_flux_spectrum_out(:, :, :, i_ky_local, 1) = qlgyro_flux_spectrum_out(:, :, :, i_ky_local, 1) * 0.0
+               ql_metric_ky(i_ky_local) = 0.0
+            else
+               px0_max = min(abs(gamma_exb / (s * max_gam * 2 * pi)), 0.5)
+               px0_max = max(px0_max, px0_spectrum(2))
+
+               do i_px0_local = 1, n_px0
+                  if (px0_spectrum(i_px0_local) .le. px0_max) then
+                     px0_max_index = i_px0_local
+                  else
+                     exit
+                  end if
+               end do
+               
+               call trapezoid_flux(px0_spectrum, px0_max_index, qlgyro_flux_spectrum_out(:, :, :, i_ky_local, :) &
+               , tglf_flux_spectrum_out(:, :, :, i_ky_local, 1))
+               call trapezoid_metric_px0(px0_spectrum, px0_max_index, ql_metric_ky_px0(i_ky_local, :), ql_metric_ky(i_ky_local))
+            end if
+         end do 
+      end if
+ 
+      call trapezoid_ky(tglf_ky_spectrum_out, ql_metric_ky, ql_metric)
+
+      a = 2.1
+
+      ! Convert from using rho_s(B0) to rho_s(Bunit) by (bgs2**-2)
+      facnorm = bgs2**(-2)
+
+      b = exp(3.0)
+      tglf_flux_spectrum_out = tglf_flux_spectrum_out * facnorm * b * ql_metric ** (a-1)
+      tglf_eigenvalue_spectrum_out = qlgyro_eigenvalue_spectrum_out
+
+    END SUBROUTINE qlgyro_sat_mg
+
+
+    subroutine calculate_ql_metric(ql_metric_local)
+
+      use qlgyro_globals
+      implicit none
+
+      integer :: i_field, i_thetab
+      
+      real, dimension(3, n_thetab, n_ky, n_px0) :: field_sq, numer, denom
+      real, dimension(3, n_ky, n_px0) :: max_field, numer_trapz, denom_trapz
+      real, intent(out), dimension(n_ky, n_px0) :: ql_metric_local
+      
+      field_sq = abs(qlgyro_field_spectrum_out)**2
+
+      numer = 0.0
+      denom = 0.0
+      do i_thetab=1, n_thetab
+         do i_field=1, n_field
+            numer(i_field, i_thetab, :, :) = field_sq(i_field, i_thetab, :, :) * qlgyro_jacobian(i_thetab, :, :)
+            denom(i_field, i_thetab, :, :) = numer(i_field, i_thetab, :, :) * qlgyro_k_perp(i_thetab, :, :)**2
+         end do
+      end do
+      
+      max_field = maxval(field_sq, dim=2)
+      
+      call trapezoid_field(qlgyro_theta_ballooning, numer, numer_trapz)
+      call trapezoid_field(qlgyro_theta_ballooning, denom, denom_trapz)
+
+      ql_metric_local = 0.0
+      do i_field=1, n_field
+         ql_metric_local = ql_metric_local + (qlgyro_eigenvalue_spectrum_out(1, :, :) * numer_trapz(i_field, :, :)&
+         / denom_trapz(i_field, :, :) * (max_field(i_field, :, :) / max_field(1, :, :)) ** 0.5)
+
+      end do
+
+    end subroutine calculate_ql_metric
+
+
+    subroutine trapezoid_field(thetab, integrand, integral)
+
+      use qlgyro_globals
+      implicit none
+
+      real, dimension(n_thetab), intent(in) :: thetab
+      real, dimension(3, n_thetab, n_ky, n_px0), intent(in) :: integrand
+      real, dimension(3, n_ky, n_px0), intent(out) :: integral
+      integer :: i_thetab
+      real :: dthetab
+      
+      integral = 0.0
+
+      do i_thetab=1, n_thetab - 1
+         dthetab = thetab(i_thetab+1) - thetab(i_thetab)
+         integral = integral + dthetab * (integrand(:, i_thetab+1, :, :) + integrand(:, i_thetab, :, :)) / 2
+      end do
+
+    end subroutine trapezoid_field
+      
+    
+    subroutine trapezoid_flux(px0, px0_max, integrand, integral)
+
+      use qlgyro_globals
+      implicit none
+
+      real, dimension(n_px0), intent(in) :: px0
+      real, dimension(5, n_species, n_field, n_px0), intent(in) :: integrand
+      real, dimension(5, n_species, n_field), intent(out) :: integral
+      integer, intent(in) :: px0_max
+      integer :: i_px0_local
+      real :: dpx0
+      
+      integral = 0.0
+
+      do i_px0_local=1, px0_max - 1
+         dpx0 = px0(i_px0_local+1) - px0(i_px0_local)
+         integral = integral + dpx0 * (integrand(:, :, :, i_px0_local+1) + integrand(:, :, :, i_px0_local)) / 2
+      end do
+
+      integral = integral / px0(px0_max)
+
+    end subroutine trapezoid_flux
+    
+    subroutine trapezoid_metric_px0(px0, px0_max, integrand, integral)
+
+      use qlgyro_globals
+      implicit none
+
+      real, dimension(n_px0), intent(in) :: px0
+      real, dimension(n_px0), intent(in) :: integrand
+      real, intent(out) :: integral
+      integer, intent(in) :: px0_max
+      integer :: i_px0_local
+      real :: dpx0
+      
+      integral = 0.0
+      
+      do i_px0_local=1, px0_max - 1
+         dpx0 = px0(i_px0_local+1) - px0(i_px0_local)
+         integral = integral + dpx0 * (integrand(i_px0_local+1) + integrand(i_px0_local)) / 2
+      end do
+
+      integral = integral / px0(px0_max)
+
+    end subroutine trapezoid_metric_px0
+    
+    subroutine trapezoid_ky(ky_local, integrand, integral)
+
+      use qlgyro_globals
+      implicit none
+
+      real, dimension(n_ky), intent(in) :: ky_local
+      real, dimension(n_ky), intent(in) :: integrand
+      real, intent(out) :: integral
+      integer :: i_ky_local
+      real :: dky
+      
+      integral = 0.0
+
+      do i_ky_local=1, n_ky - 1
+         dky = ky_local(i_ky_local+1) - ky_local(i_ky_local)
+         integral = integral + dky * (integrand(i_ky_local+1) + integrand(i_ky_local)) / 2
+      end do
+
+    end subroutine trapezoid_ky
+    
diff --git a/qlgyro/src/qlgyro_sum_fluxes.f90 b/qlgyro/src/qlgyro_sum_fluxes.f90
new file mode 100644
index 000000000..fe971707a
--- /dev/null
+++ b/qlgyro/src/qlgyro_sum_fluxes.f90
@@ -0,0 +1,175 @@
+SUBROUTINE qlgyro_sum_fluxes
+!
+!  computes spectral integrals of field, intensity and fluxes.
+!
+      USE tglf_dimensions
+      USE tglf_global
+      USE tglf_species
+      USE tglf_kyspectrum
+      USE tglf_interface
+      USE qlgyro_globals
+      IMPLICIT NONE
+!
+      INTEGER :: i,j,is,imax
+      REAL :: dky, qlgyro_ky_in
+      REAL :: phi_bar0,phi_bar1
+      REAl :: v_bar0,v_bar1
+      REAL :: dky0,dky1,ky0,ky1
+      REAL :: pflux0(nsm,3),eflux0(nsm,3)
+      REAL :: stress_par0(nsm,3),stress_tor0(nsm,3)
+      REAL :: exch0(nsm,3)
+      REAL :: nsum0(nsm),tsum0(nsm)
+      REAL :: pflux1(nsm,3),eflux1(nsm,3)
+      REAL :: stress_par1(nsm,3),stress_tor1(nsm,3)
+      REAL :: exch1(nsm,3)
+      REAL :: nsum1(nsm),tsum1(nsm)
+!
+!      CALL tglf_startup  
+!
+! initialize fluxes
+!
+      do is=1,tglf_ns_in
+        do j=1,3 
+          pflux0(is,j) = 0.0
+          eflux0(is,j) = 0.0
+          stress_par0(is,j) = 0.0
+          stress_tor0(is,j) = 0.0
+          exch0(is,j) = 0.0
+        enddo
+        n_bar_sum_out(is) = 0.0
+        t_bar_sum_out(is) = 0.0
+        q_low_out(is) = 0.0
+        nsum0(is) = 0.0
+        tsum0(is) = 0.0
+      enddo
+      phi_bar_sum_out = 0.0
+      v_bar_sum_out = 0.0
+      v_bar0 = 0.0
+      phi_bar0 = 0.0     
+!
+! compute the flux spectrum
+!
+!      CALL get_bilinear_spectrum_mpi
+!
+! sum over ky spectrum
+!
+      iflux_in=.TRUE. 
+      dky0=0.0
+      ky0=0.0 
+      do i=1,nky
+        qlgyro_ky_in = tglf_ky_spectrum_out(i)
+        dky = tglf_dky_spectrum_out(i)
+        ky1=qlgyro_ky_in
+        if(i.eq.1)then
+          dky1=ky1
+        else
+          dky = LOG(ky1/ky0)/(ky1-ky0)
+          dky1 = ky1*(1.0 - ky0*dky)
+          dky0 = ky0*(ky1*dky - 1.0)
+        endif
+! normalize the ky integral to make it independent of the 
+! choice of temperature and mass scales 
+        dky0 = dky0*SQRT(tglf_taus_in(1)*tglf_mass_in(2))
+        dky1 = dky1*SQRT(tglf_taus_in(1)*tglf_mass_in(2))
+!
+! compute the field integrals
+!
+        v_bar1 = 0.0
+        phi_bar1 = 0.0
+        do imax = 1,tglf_nmodes_in
+          v_bar1 = v_bar1 + field_spectrum_out(1,i,imax)
+          phi_bar1 = phi_bar1 + field_spectrum_out(2,i,imax)
+        enddo
+        phi_bar_sum_out = phi_bar_sum_out + dky0*phi_bar0 + dky1*phi_bar1
+        v_bar_sum_out = v_bar_sum_out + dky0*v_bar0 + dky1*v_bar1
+        phi_bar0 = phi_bar1
+        v_bar0 = v_bar1
+!
+! compute the intensity integrals
+!
+!        do is=1,ns
+!          nsum1(is) = 0.0
+!          tsum1(is) = 0.0
+!          do imax = 1,tglf_nmodes_in
+!            nsum1(is) = nsum1(is) + intensity_spectrum_out(1,is,i,imax)
+!            tsum1(is) = tsum1(is) + intensity_spectrum_out(2,is,i,imax)
+!          enddo
+!          n_bar_sum_out(is) = n_bar_sum_out(is) &
+!              + dky0*nsum0(is) + dky1*nsum1(is)
+!          t_bar_sum_out(is) = t_bar_sum_out(is) &
+!              + dky0*tsum0(is) + dky1*tsum1(is)
+!          nsum0(is) = nsum1(is)
+!          tsum0(is) = tsum1(is)
+!        enddo
+!
+! compute the flux integrals
+!
+        do is=1,tglf_ns_in
+          do j=1,3
+            pflux1(is,j) = 0.0
+            eflux1(is,j) = 0.0
+            stress_tor1(is,j) = 0.0
+            stress_par1(is,j) = 0.0
+            exch1(is,j) = 0.0
+            do imax = 1,tglf_nmodes_in
+              pflux1(is,j) = pflux1(is,j) + tglf_flux_spectrum_out(1,is,j,i,imax)
+              eflux1(is,j) = eflux1(is,j) + tglf_flux_spectrum_out(2,is,j,i,imax)
+              stress_tor1(is,j) = stress_tor1(is,j) + &
+                 tglf_flux_spectrum_out(3,is,j,i,imax)
+              stress_par1(is,j) = stress_par1(is,j) + &
+                 tglf_flux_spectrum_out(4,is,j,i,imax)
+              exch1(is,j) = exch1(is,j) + tglf_flux_spectrum_out(5,is,j,i,imax)
+           enddo !imax
+            tglf_particle_flux_out(is,j) = tglf_particle_flux_out(is,j) &
+              + dky0*pflux0(is,j) + dky1*pflux1(is,j)
+            tglf_energy_flux_out(is,j) = tglf_energy_flux_out(is,j) &
+              + dky0*eflux0(is,j) + dky1*eflux1(is,j)
+            tglf_stress_tor_out(is,j) = tglf_stress_tor_out(is,j) &
+              + dky0*stress_tor0(is,j) + dky1*stress_tor1(is,j)
+            tglf_stress_par_out(is,j) = tglf_stress_par_out(is,j) &
+              + dky0*stress_par0(is,j) + dky1*stress_par1(is,j)
+            tglf_exchange_out(is,j) = tglf_exchange_out(is,j) &
+              + dky0*exch0(is,j) + dky1*exch1(is,j)
+!            write(*,*)is,j,i
+!            write(*,*)"ky0=",ky0,"ky1=",ky1
+!            write(*,*)"pflux0=",pflux0,"pflux1=",pflux1
+!            write(*,*)"eflux0=",eflux0,"eflux1=",eflux1
+!            write(*,*)dky0*pflux0+dky1*pflux1
+!            write(*,*)dky0*eflux0+dky1*eflux1
+!            write(*,*)"tglf_stress_tor_out=",tglf_stress_tor_out(is,1)
+             pflux0(is,j) = pflux1(is,j)
+             eflux0(is,j) = eflux1(is,j)
+             stress_par0(is,j) = stress_par1(is,j)
+             stress_tor0(is,j) = stress_tor1(is,j)
+             exch0(is,j) = exch1(is,j)
+           enddo  ! j
+           if(qlgyro_ky_in*SQRT(tglf_taus_in(2)*tglf_mass_in(2)).le.1.0)then
+             q_low_out(is) = tglf_energy_flux_out(is,1)+tglf_energy_flux_out(is,2)
+           endif
+         enddo  ! is 
+!
+        ky0 = ky1
+      enddo  ! i
+!
+!      CALL tglf_shutdown
+      !
+
+      tglf_elec_pflux_out  = sum(tglf_particle_flux_out(1, :))
+      tglf_elec_eflux_out  = sum(tglf_energy_flux_out(1, :))
+      tglf_elec_mflux_out  = sum(tglf_stress_tor_out(1, :))
+      tglf_elec_expwd_out  = sum(tglf_exchange_out(1, :))
+
+      do i=2,tglf_ns_in
+         tglf_ion_pflux_out(i-1)  = sum(tglf_particle_flux_out(i, :))
+         tglf_ion_eflux_out(i-1)  = sum(tglf_energy_flux_out(i, :))
+         tglf_ion_mflux_out(i-1)  = sum(tglf_stress_tor_out(i, :))
+         tglf_ion_expwd_out(i-1)  = sum(tglf_exchange_out(i, :))
+      end do
+
+      if (i_proc_global == 0) then
+         write(*,*) 'QLGYRO Heat     fluxes (Qe, Qi): ', tglf_elec_eflux_out, tglf_ion_eflux_out(1)
+         write(*,*) 'QLGYRO Particle fluxes (Qe, Qi): ', tglf_elec_pflux_out, tglf_ion_pflux_out(1)
+      end if
+21 format(A35, F8.3, F8.3)
+    END SUBROUTINE qlgyro_sum_fluxes
+
diff --git a/qlgyro/src/qlgyro_tglf_map.f90 b/qlgyro/src/qlgyro_tglf_map.f90
new file mode 100644
index 000000000..93b684898
--- /dev/null
+++ b/qlgyro/src/qlgyro_tglf_map.f90
@@ -0,0 +1,438 @@
+!------------------------------------------------------------
+! tgyro_tglf_map.f90
+!
+! PURPOSE:
+!  Mapping from TGYRO internal variables to TGLF interface.
+!------------------------------------------------------------
+
+subroutine qlgyro_tglf_map
+
+  use qlgyro_globals
+  use tglf_interface
+  USE tglf_kyspectrum
+  
+  implicit none
+
+  ! Local variables
+  integer :: i0
+  real :: q_abs
+  real :: q_prime
+  real :: p_prime
+
+  q_abs = abs(q)
+
+  ! Initialize TGLF
+  call tglf_init('.', qlgyro_comm)
+
+  ! Are we just testing (to get dump file, for example)?
+  tglf_test_flag_in = gyrotest_flag
+
+  ! Want fluxes from TGLF
+  tglf_use_transport_model_in = .true.
+
+  tglf_path_in='./'
+  !----------------------------------------------------------------
+  ! Signs of toroidal magnetic field and current 
+  tglf_sign_bt_in = -1.0*signb
+  tglf_sign_it_in = -1.0*signb*signq
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! No. of modes
+  tglf_nmodes_in = n_modes
+
+  !----------------------------------------------------------------
+  ! Sat rule
+  tglf_sat_rule_in = sat_rule
+
+  !----------------------------------------------------------------
+  ! Ky grid model
+
+  tglf_kygrid_model_in = kygrid_model
+  tglf_ky_in = ky_in
+  tglf_nky_in = n_ky
+  
+  !----------------------------------------------------------------
+  ! No. of fields
+  if (n_field .eq. 2) tglf_use_bper_in = .true.
+  if (n_field .eq. 3) tglf_use_bpar_in = .true.
+  
+  !----------------------------------------------------------------
+  ! Number of species (max=6)
+  tglf_ns_in = n_ion+1
+
+  if (tglf_ns_in > nsm) then
+     call qlgyro_catch_error('ERROR: (qlgyro_tglf_map) Too many ions in TGLF.')
+  endif
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Species loop:
+  !
+  ! Charges: e,i,z
+  tglf_zs_in(1) = -1.0
+  !
+  ! Mass ratios: me/mi(1),mi(1)/mi(1),m(2)/mi(1), ... 
+  !              [assume mi(1) is normalizing mass]
+  tglf_mass_in(1) = me
+  !
+  ! Density ratios: ne/ne,ni(1)/ne,ni(2)/ne, ...
+  tglf_as_in(1) = ne
+  !
+  ! Density gradients (e,i,z)
+  tglf_rlns_in(1) = dlnnedr
+  !
+  ! Temperature gradients (e,i,z)
+  tglf_rlts_in(1) = dlntedr
+  !
+  ! Temperature ratios: Te/Te,Ti(1)/Te,Ti(2)/Te
+  tglf_taus_in(1) = te
+
+  i0 = 1
+  do i_ion=1,n_ion
+     i0 = i0+1 
+     tglf_zs_in(i0)   = zi_vec(i_ion)
+     tglf_mass_in(i0) = mi(i_ion)
+     tglf_as_in(i0)   = ni(i_ion)
+     tglf_rlns_in(i0) = dlnnidr(i_ion)
+     tglf_rlts_in(i0) = dlntidr(i_ion)
+     tglf_taus_in(i0) = ti(i_ion)
+  enddo
+  
+ 
+  !----------------------------------------------------------------
+  !   Debye length/rhos   te in ev, rho_s in cm ne in 10^13/cm^3
+ ! tglf_debye_in = 7.43e2*sqrt(te/(ne))/abs(rho_s)
+
+  !----------------------------------------------------------------
+  ! TGLF-specific quantities
+  q_prime = (q_abs/r_min)**2*s
+  p_prime = (q_abs/r_min)*(beta_unit/(8*pi))*(-dlnpdr)
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Geometry parameters:
+  !
+  ! s-alpha (not really needed)
+  tglf_rmin_sa_in     = r_min
+  tglf_rmaj_sa_in     = r_maj
+  tglf_q_sa_in        = q_abs
+  tglf_shat_sa_in     = s
+  tglf_alpha_sa_in    = r_maj*beta_unit*dlnpdr*q_abs**2
+  tglf_xwell_sa_in    = 0.0
+  tglf_theta0_sa_in   = 0.0
+  tglf_b_model_sa_in  = 0
+  tglf_ft_model_sa_in = 1
+
+  if (qlgyro_num_equil_flag == 1) then
+
+     ! Numerical (Fourier) shape
+     tglf_geometry_flag_in = 2
+
+     tglf_q_fourier_in       = q_abs
+     tglf_q_prime_fourier_in = q_prime
+     tglf_p_prime_fourier_in = p_prime
+     tglf_nfourier_in        = n_fourier_geo
+     tglf_fourier_in(:,0:n_fourier_geo) = a_fourier_geo(:,0:n_fourier_geo)
+
+  else
+
+     ! Model (Miller) shape
+     tglf_geometry_flag_in = 1 
+
+     tglf_rmin_loc_in    = r_min
+     tglf_rmaj_loc_in    = r_maj
+     tglf_zmaj_loc_in    = zmag
+     tglf_drmajdx_loc_in = shift
+     tglf_dzmajdx_loc_in = dzmag
+     tglf_kappa_loc_in   = kappa
+     tglf_s_kappa_loc_in = s_kappa
+     tglf_delta_loc_in   = delta
+     tglf_s_delta_loc_in = s_delta
+     tglf_zeta_loc_in    = zeta
+     tglf_s_zeta_loc_in  = s_zeta
+     tglf_q_loc_in       = q_abs
+     tglf_q_prime_loc_in = q_prime
+     tglf_p_prime_loc_in = p_prime
+     tglf_beta_loc_in = betae_unit
+
+  endif
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Electron beta used for electromagnetic calculations
+  tglf_betae_in = betae_unit
+  !----------------------------------------------------------------
+  !----------------------------------------------------------------
+  ! Collisions:
+  !
+  ! Electron collision frequency
+  tglf_xnue_in = nue
+  tglf_xnu_model_in = xnu_model
+  !
+  ! Zeff
+  tglf_zeff_in = z_eff
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Gamma_ExB (ExB shearing rate, units of a/cs)
+  if (qlgyro_rotation_flag == 1) then
+     ! Currently TGLF uses toroidal current as reference direction
+     ! Overall minus sign is due to QLGYRO toroidal angle in CW direction
+     !tglf_vexb_shear_in    = -tglf_sign_it_in*gamma_eb0*a_min/c_s  
+     !tglf_vpar_shear_in(:) = -tglf_sign_it_in*gamma_p0*a_min/c_s
+     !tglf_vpar_in(:)       = -tglf_sign_it_in*r_maj*w0/c_s
+     ! Currently GAMMA_EB in input.qlgyro reads in TGLF_VEB_SHEAR
+     tglf_vexb_shear_in = -tglf_sign_it_in*gamma_exb
+     tglf_alpha_quench_in = 1.0
+  endif
+  !----------------------------------------------------------------
+  ! set ky_in to value for n=1
+  if (tglf_kygrid_model_in == 3) tglf_ky_in = abs(rho_s*q/r_min)
+  !-----------------------------------
+  ! Number of high-k modes
+  !  nky=12 (default to include ETG)
+  !  nky=0  (low-k only)
+  !  tglf_nky_in = 12
+  !-----------------------------------
+
+  !----------------------------------------------------------------
+  ! Linear mode selection
+  !
+  ! i_branch_tg = -1: use nmodes_tg modes (default for transport)
+  ! i_branch_tg =  0: most unstable electron mode (1) and ion mode (2)
+  !
+  tglf_ibranch_in = -1
+  !
+  ! Number of modes in transport calculation;
+  ! should be 2-4.
+  !tglf_nmodes_in = 4
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! Width selection parameters
+  !
+  ! Use bisection method to determine Gaussian width;
+  ! bisection is better, faster.
+  !  tglf_use_bisection_in = .true.
+  !
+  ! Number of Hermite functions to determine Gaussian Width (1-2)
+  !  tglf_nbasis_min_in = 1
+  !
+  ! Number of Hermite function in full expansion (4 or more, even)
+  !  tglf_nbasis_max_in = 4
+  !
+  ! Number of Hermite quadrature nodes
+  ! tglf_nxgrid_in = 16
+  !
+  ! Maximum number of widths sampled (could be higher than 21)
+  !  tglf_nwidth_in = 21
+  !
+  ! Bisection search interval; must increase nwidth_tg if
+  ! increasing this interval to maintain accuracy:
+  !
+  !  accuracy ~ (width_max_tg-width_min_tg)/nwidth_tg
+  !
+  !  tglf_width_min_in = 0.3
+  !  tglf_width_in = 1.65
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! CONTROL PARAMETERS
+  !
+  ! Use adiabatic electrons
+  tglf_adiabatic_elec_in = .false.
+  !
+  ! Compute eikonal (use stored value if false)
+  tglf_new_eikonal_in = .true.
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! OTHER DEFAULT CONTROL PARAMETERS
+  !
+  !  tglf_find_width_in    = .true.
+  !  tglf_iflux_in         = .true.
+  !  tglf_theta_trapped_in = 0.7
+  !  tglf_xnu_factor_in    = 1.0
+  !  tglf_debye_factor_in  = 1.0
+  !  tglf_filter_in        = 2.0
+  !----------------------------------------------------------------
+
+  !----------------------------------------------------------------
+  ! NEW TGLF SETTINGS
+  !
+  ! select case (qlgyro_tglf_revision)
+
+  ! case(0)
+
+  !    ! use defaults and overwrites
+
+  ! case (1)
+
+  !    ! APS07 
+
+  !    tglf_alpha_quench_in = 1.0
+  !    tglf_xnu_model_in    = 1
+
+  ! case (2)
+
+  !    ! Summer 2009
+
+  !    tglf_alpha_quench_in = 1.0
+  !    tglf_xnu_model_in    = 2
+
+  ! case (3)
+
+  !    ! IAEA-2012 with spectral shift ExB shear model
+
+  !    tglf_alpha_quench_in = 0.0
+  !    tglf_xnu_model_in    = 2
+  !    tglf_alpha_e_in = 1.0
+  !    tglf_alpha_p_in = 1.0
+
+  ! end select
+
+  
+  !----------------------------------------------------------------
+  ! DUMP PARAMETERS
+  !
+  if (qlgyro_tglf_dump_flag == 0) then
+     tglf_dump_flag_in   = .false.
+  else
+     tglf_dump_flag_in = .true.
+  endif
+
+  !----------------------------------------------------------------
+  ! VERBOSITY
+  !
+  tglf_quiet_flag_in = .true.
+
+  !----------------------------------------------------------------
+  ! TGLFNN ACTIVATION THRESHOLD
+  !
+  tglf_nn_max_error_in = qlgyro_tglf_nn_max_error
+
+  if (flux_method == 6) then
+     
+  end if
+
+  call put_units(tglf_units_in)
+
+  call put_signs(tglf_sign_Bt_in,tglf_sign_It_in)
+
+  call put_species(tglf_ns_in, &
+       tglf_zs_in, &
+       tglf_mass_in)
+
+  call put_kys(tglf_ky_in)
+
+  call put_gaussian_width(tglf_width_in, &
+       tglf_width_min_in, &
+       tglf_nwidth_in, &
+       tglf_find_width_in)
+
+  call put_eikonal(tglf_new_eikonal_in)
+
+  call put_gradients(tglf_rlns_in, &
+       tglf_rlts_in, &
+       tglf_vpar_shear_in, &
+       tglf_vexb_shear_in)
+
+  call put_averages(tglf_taus_in, &
+       tglf_as_in, &
+       tglf_vpar_in, &
+       tglf_vexb_in, &
+       tglf_betae_in, &
+       tglf_xnue_in, &
+       tglf_zeff_in, &
+       tglf_debye_in)
+
+  call put_switches(tglf_iflux_in, &
+       tglf_use_bper_in, &
+       tglf_use_bpar_in, &
+       tglf_use_mhd_rule_in, &
+       tglf_use_bisection_in, &
+       tglf_use_inboard_detrapped_in, &
+       tglf_ibranch_in, &
+       tglf_nmodes_in, &
+       tglf_nbasis_max_in, &
+       tglf_nbasis_min_in, &
+       tglf_nxgrid_in, &
+       tglf_nky_in, &
+       tglf_use_ave_ion_grid_in)  
+
+  call put_rare_switches(tglf_theta_trapped_in, &
+       tglf_wdia_trapped_in, &
+       tglf_park_in, &
+       tglf_ghat_in, &
+       tglf_gchat_in, &
+       tglf_wd_zero_in, &
+       tglf_linsker_factor_in, &
+       tglf_gradB_factor_in, &
+       tglf_filter_in, &
+       tglf_damp_psi_in, &
+       tglf_damp_sig_in)
+
+  call put_model_parameters(tglf_adiabatic_elec_in, &
+       tglf_alpha_e_in, &
+       tglf_alpha_p_in, &
+       tglf_alpha_mach_in, &
+       tglf_alpha_quench_in, &
+       tglf_alpha_zf_in, &
+       tglf_xnu_factor_in, &
+       tglf_debye_factor_in, &
+       tglf_etg_factor_in, &
+       tglf_rlnp_cutoff_in, &
+       tglf_sat_rule_in, &
+       tglf_kygrid_model_in, &
+       tglf_xnu_model_in, &
+       tglf_vpar_model_in, &
+       tglf_vpar_shear_model_in)
+
+  tglf_kygrid_model_in = kygrid_model
+
+  if (tglf_geometry_flag_in == 1 ) then
+
+     call put_miller_geometry(tglf_rmin_loc_in, &
+          tglf_rmaj_loc_in, &
+          tglf_zmaj_loc_in, &
+          tglf_drmindx_loc_in, &
+          tglf_drmajdx_loc_in, &
+          tglf_dzmajdx_loc_in, &
+          tglf_kappa_loc_in, &
+          tglf_s_kappa_loc_in, &
+          tglf_delta_loc_in, &
+          tglf_s_delta_loc_in, &
+          tglf_zeta_loc_in, &
+          tglf_s_zeta_loc_in, &
+          tglf_q_loc_in, &
+          tglf_q_prime_loc_in, &
+          tglf_p_prime_loc_in, &
+          tglf_beta_loc_in,  &
+          tglf_kx0_loc_in)
+
+  elseif (tglf_geometry_flag_in == 2)then
+
+     call put_fourier_geometry(tglf_q_fourier_in,  &
+          tglf_q_prime_fourier_in, &
+          tglf_p_prime_fourier_in, &
+          tglf_nfourier_in, &
+          tglf_fourier_in)
+
+  else
+
+     call put_s_alpha_geometry(tglf_rmin_sa_in, &
+          tglf_rmaj_sa_in, &
+          tglf_q_sa_in, &
+          tglf_shat_sa_in, &
+          tglf_alpha_sa_in, &
+          tglf_xwell_sa_in, &
+          tglf_theta0_sa_in, &
+          tglf_b_model_sa_in, &
+          tglf_ft_model_sa_in)
+
+  endif
+
+  call tglf_startup
+
+end subroutine qlgyro_tglf_map
diff --git a/qlgyro/src/qlgyro_trap_component_error.f90 b/qlgyro/src/qlgyro_trap_component_error.f90
new file mode 100644
index 000000000..82fbe9030
--- /dev/null
+++ b/qlgyro/src/qlgyro_trap_component_error.f90
@@ -0,0 +1,58 @@
+!-----------------------------------------------------------------
+! qlgyro_trap_component_error.f90
+!
+! PURPOSE:
+!  Manage return status from components (NEO, TGLF, GYRO).
+! 
+!  success:
+!   status=0
+!   message='null'
+!
+!  failure
+!   status=1
+!   message=<error description>
+!
+!  warning
+!   status=2
+!   message=<warning description>
+!-------------------------------------------------------------------
+
+subroutine qlgyro_trap_component_error(status,message)
+
+  use mpi
+  use qlgyro_globals
+
+  implicit none
+
+  integer :: i
+  ! INPUT
+  integer, intent(in) :: status
+  character (len=80), intent(in) :: message
+  ! INTERNAL
+  integer, dimension(n_inst) :: status_vec
+  character (len=80), dimension(n_inst) :: message_vec
+
+
+  ! Collect distributed error messages into global vectors
+  call MPI_ALLGATHER(status,1,MPI_INTEGER,status_vec,1,MPI_INTEGER,qlgyro_adj,ierr)
+  call MPI_ALLGATHER(message,80,MPI_CHARACTER,message_vec,80,MPI_CHARACTER,qlgyro_adj,ierr)
+
+  ! Broadcast vectors to all members of a given instance 
+  ! (Required for GYRO runs, not NEO or TGLF):
+  call MPI_BCAST(status_vec,n_inst,MPI_INTEGER,0,qlgyro_comm,ierr)
+  call MPI_BCAST(message_vec,80*n_inst,MPI_CHARACTER,0,qlgyro_comm,ierr)
+  
+ ! Serial logic from here onward
+
+  
+  if (sum(status_vec) > 0) then
+     if (i_proc_global == 0) then
+        open(unit=1,file=trim(runfile),position='append')
+        do i=1,n_inst
+           write(1,*) trim(path),": ",trim(message_vec(i))
+        enddo
+        close(1)
+     endif
+  endif
+
+end subroutine qlgyro_trap_component_error
diff --git a/shared/bin/gacode_qsub b/shared/bin/gacode_qsub
index 47cb649d4..937bf8357 100755
--- a/shared/bin/gacode_qsub
+++ b/shared/bin/gacode_qsub
@@ -30,7 +30,7 @@ then
   echo "         Run <code> using input.<code> in <simdir>."
   echo
   echo "         -code <code>"
-  echo "         <code>=tgyro,gyro,neo"
+  echo "         <code>=tgyro,cgyro,neo"
   echo
   echo "         -n <MPI tasks>" 
   echo "         Number of MPI tasks."
@@ -50,7 +50,7 @@ then
   echo "         Default unit MB. Slurm recognizes [K|M|G|T]"
   echo "         No space beween number and unit."
   echo "         Precedence is User then -mem"
-  echo "         (default --mem=16GB)."
+  echo "         (default set in platform/qsub/qsub.<PLATFORM>)."
   echo
   echo "         -queue"
   echo "         Queue name"
@@ -75,6 +75,7 @@ SUB_FLAG=0
 NO_LOGIN=0
 QUEUE=null_queue
 WALLTIME=0:59:00
+
 if hash getnim 2> /dev/null; then
    # NERSC
    x=`getnim -U $user -D`
@@ -104,9 +105,8 @@ numa=0
 mpinuma=0
 
 #Default Memory Per Node
-MEMPERNODE=16G
+MEMPERNODE=
 MEMPERCPU=
-USERMPN=false
 
 #=============================================================
 # Parse command line options
@@ -130,7 +130,7 @@ while [[ $# -gt 0 ]] ; do
 
   -numa) shift ; numa=$1 ;;
 
-  -mem) shift ; MEMPERNODE=$1 ; USERMPN=true;;
+  -mem) shift ; MEMPERNODE=$1 ;;
 
   -mem-per-cpu) shift ; MEMPERCPU=$1 ;;
 
@@ -151,14 +151,11 @@ done
 #==============================================================
 # Resolve double specification of memory
 #
-if [[ $USERMPN == true && -n $MEMPERCPU ]]; then
+if [[ -n $MEMPERNODE && -n $MEMPERCPU ]]; then
   echo "WARNING: Both -mem and -mem-per-cpu specified."
   echo "Applying Precedence -mem=$MEMPERNODE."
   MEMPERCPU=
-elif [[ $USERMPN == false ]]; then
-  MEMPERNODE=
 fi
-export MEMP
 
 #==============================================================
 # Manage paths
@@ -171,14 +168,6 @@ fi
 SIMDIR=$SIMROOT/$LOCDIR
 #=============================================================
 
-# Manage execution on ORNL SUMMIT
-if [[ $GACODE_PLATFORM == SUMMI* ]]; then
-    . $GACODE_ROOT/platform/qsub/qsub.$GACODE_PLATFORM
-    cat $SIMDIR/batch.src
-    $GACODE_ROOT/platform/exec/exec.$GACODE_PLATFORM $SIMDIR $nmpi $CODE 0 1 $mpinuma 
-    exit 0
-fi
-
 echo $SIMDIR
 # Extract CORES_PER_NODE and NUMAS_PER_NODE
 export `grep _NODE $GACODE_ROOT/platform/build/make.inc.$GACODE_PLATFORM`
@@ -195,7 +184,6 @@ echo " cores used              : $cores_used"
 echo " total MPI tasks         : $nmpi"
 echo " MPI tasks/node          : $mpinode"
 echo " OpenMP threads/MPI task : $nomp"
-echo " MPI tasks per numa node : $mpinuma"
 echo
 . $GACODE_ROOT/platform/qsub/qsub.$GACODE_PLATFORM
 
@@ -239,8 +227,6 @@ else
        sbatch $bfile 
     elif hash qsub 2> /dev/null ; then
        qsub $bfile
-    elif hash bsub 2> /dev/null ; then
-       bsub $bfile
     else
        echo "ERROR: (gacode_qsub) No batch command recognized."
     fi 
diff --git a/shared/bin/gacode_setup b/shared/bin/gacode_setup
index 2ccbe3b16..37c7b51f6 100755
--- a/shared/bin/gacode_setup
+++ b/shared/bin/gacode_setup
@@ -13,13 +13,13 @@ export PATH=$GACODE_ROOT/le3/bin:${PATH}
 export PATH=$GACODE_ROOT/profiles_gen/bin:${PATH}
 export PATH=$GACODE_ROOT/shared/bin:${PATH}
 export PATH=$GACODE_ROOT/gftm/bin:${PATH}
+export PATH=$GACODE_ROOT/qlgyro/bin:${PATH}
 
 if [ -d $GACODE_ROOT/../gacode_add ] 
 then
    export GACODE_ADD_ROOT=$GACODE_ROOT/../gacode_add
    export PATH=$GACODE_ADD_ROOT/freya/bin:${PATH}
    export PATH=$GACODE_ADD_ROOT/prefreya/bin:${PATH}
-   export PATH=$GACODE_ADD_ROOT/qlgyro/bin:${PATH}
 fi
 
 export PYTHONPATH=$GACODE_ROOT/f2py:${PYTHONPATH}
diff --git a/shared/hybridtest/Makefile b/shared/hybridtest/Makefile
new file mode 100644
index 000000000..087e46015
--- /dev/null
+++ b/shared/hybridtest/Makefile
@@ -0,0 +1,16 @@
+include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
+
+ifeq ($(OPT),debug)
+   FFLAGS=${FDEBUG}
+else
+   FFLAGS=${FOPT}
+endif
+
+FC += ${FOMP} ${FACC}
+
+all:
+	$(FC) $(FMATH) $(FFLAGS) -c hybrid.f90
+	$(FC) $(FMATH) $(FFLAGS) -o hybrid hybrid.o $(LMATH)
+
+clean:
+	rm -f *.o *~ hybrid
diff --git a/shared/hybridtest/hybrid.f90 b/shared/hybridtest/hybrid.f90
new file mode 100644
index 000000000..b63fad5e4
--- /dev/null
+++ b/shared/hybridtest/hybrid.f90
@@ -0,0 +1,62 @@
+program hybrid
+  
+  use mpi
+
+  implicit none
+ 
+  integer :: ierr,iproc
+  integer :: nmpi,nomp,ntot
+  integer :: i,j
+  integer,external :: omp_get_max_threads
+  integer,external :: omp_get_thread_num
+  integer :: supported
+
+  real :: mysum,mysums,total
+  real, dimension(3,3) :: a
+  real, dimension(3) :: b
+  integer, dimension(3) :: work
+  
+  nomp = omp_get_max_threads()
+
+  if (nomp > 1) then
+     call MPI_INIT_THREAD(MPI_THREAD_FUNNELED,supported,ierr)
+     if (supported < MPI_THREAD_FUNNELED) then
+        print *, "ERROR: Multi-threaded MPI not supported." 
+     endif
+  else 
+     call MPI_INIT_THREAD(MPI_THREAD_SINGLE,supported,ierr)
+  endif
+
+  call MPI_COMM_SIZE(MPI_COMM_WORLD,nmpi,ierr)
+  call MPI_COMM_RANK(MPI_COMM_WORLD,iproc,ierr)
+
+  mysum = 0.0
+  
+!$omp parallel do private (i,a,b,work,ierr) reduction(+:mysum)
+  do i=0,nomp-1
+   
+     a(:,:) = 0.0
+     a(1,1) = 1.0
+     a(2,2) = 1.0
+     a(3,3) = 1.0
+     
+     b(:) = omp_get_thread_num()+iproc*nmpi
+ 
+     call DGESV(3,1,a,3,work,b,3,ierr)
+
+     mysum = mysum+sum(b)
+  enddo
+
+  call MPI_ALLREDUCE(mysum,mysums,1,MPI_DOUBLE_PRECISION,MPI_SUM,MPI_COMM_WORLD,ierr)
+  call MPI_FINALIZE(ierr)
+
+  ntot = nomp*nmpi
+  if (iproc == 0) then
+     if (int(3*ntot*(ntot-1)/2-mysums) == 0) then
+        print *,'Success'
+     else
+        print *,'Fail'
+     endif
+  endif
+  
+end program hybrid
diff --git a/shared/hybridtest/test b/shared/hybridtest/test
new file mode 100755
index 000000000..6be845aee
--- /dev/null
+++ b/shared/hybridtest/test
@@ -0,0 +1 @@
+$GACODE_ROOT/platform/exec/exec.$GACODE_PLATFORM "." 4 ./hybrid 4 0 0
diff --git a/shared/math/Makefile b/shared/math/Makefile
index 57af0bb80..378669d06 100644
--- a/shared/math/Makefile
+++ b/shared/math/Makefile
@@ -3,7 +3,7 @@ include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
 ifeq ($(OPT),debug)
    FFLAGS=${FDEBUG}
 else
-   FFLAGS=${FOPT} -fPIC
+   FFLAGS=${FOPT}
 endif
 
 LLIB=math_lib
diff --git a/shared/nclass/Makefile b/shared/nclass/Makefile
index 39b47702c..cd7b24d5a 100644
--- a/shared/nclass/Makefile
+++ b/shared/nclass/Makefile
@@ -15,7 +15,7 @@ OBJECTS = nclass_mod.o \
           u_erf.o \
           u_lu_backsub.o \
           u_lu_decomp.o \
-          write_mod.o 
+          write_mod.o
 
 .SUFFIXES : .o .f90 .f
 
@@ -26,6 +26,6 @@ lib: $(OBJECTS)
 
 .f.o :
 	$(F77) $(FMATH) $(FFLAGS) -c $<
- 
+
 clean:
 	rm -rf *.o nclass_lib.a *~
diff --git a/tgyro/Makefile b/tgyro/Makefile
index 872909259..37ee6ae7b 100644
--- a/tgyro/Makefile
+++ b/tgyro/Makefile
@@ -2,8 +2,17 @@
 # Toplevel makefile for tgyro
 #----------------------------
 
-include ../platform/build/make.inc.${GACODE_PLATFORM}
-include Makefile.extra
+include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
+
+export EXTRA_LIBS = \
+       ${GACODE_ROOT}/neo/src/neo_lib.a \
+       ${GACODE_ROOT}/shared/nclass/nclass_lib.a \
+       ${GACODE_ROOT}/tglf/src/tglf_lib.a \
+       ${GACODE_ROOT}/cgyro/src/cgyro_lib.a \
+       ${GACODE_ROOT}/f2py/expro/expro_lib.a \
+       ${GACODE_ROOT}/f2py/geo/geo_lib.a \
+       ${GACODE_ROOT}/shared/math/math_lib.a \
+       ${GACODE_ROOT}/shared/UMFPACK/UMFPACK_lib.a
 
 all:
 	gacode_getversion > .VERSION
diff --git a/tgyro/Makefile.extra b/tgyro/Makefile.extra
deleted file mode 100644
index 22d8f7f9e..000000000
--- a/tgyro/Makefile.extra
+++ /dev/null
@@ -1,10 +0,0 @@
-export EXTRA_LIBS = \
-       ${GACODE_ROOT}/neo/src/neo_lib.a \
-       ${GACODE_ROOT}/shared/nclass/nclass_lib.a \
-       ${GACODE_ROOT}/tglf/src/tglf_lib.a \
-       ${GACODE_ROOT}/cgyro/src/cgyro_lib.a \
-       ${GACODE_ROOT}/f2py/expro/expro_lib.a \
-       ${GACODE_ROOT}/f2py/geo/geo_lib.a \
-       ${GACODE_ROOT}/shared/math/math_lib.a \
-       ${GACODE_ROOT}/shared/UMFPACK/UMFPACK_lib.a
-
diff --git a/tgyro/src/Makefile b/tgyro/src/Makefile
index 550e00c05..42d431b7e 100644
--- a/tgyro/src/Makefile
+++ b/tgyro/src/Makefile
@@ -1,5 +1,4 @@
 include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
-include ../Makefile.extra
 
 ifeq ($(OPT),debug)
    FFLAGS=${FDEBUG}