diff --git a/gftm/Makefile b/gftm/Makefile
deleted file mode 100644
index 7f53599db..000000000
--- a/gftm/Makefile
+++ /dev/null
@@ -1,7 +0,0 @@
-include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
-
-all:
-	cd src ; make
-
-clean:
-	cd src ; make clean
diff --git a/gftm/bin/gene_defaults.py b/gftm/bin/gene_defaults.py
deleted file mode 100644
index ded2575c4..000000000
--- a/gftm/bin/gene_defaults.py
+++ /dev/null
@@ -1,52 +0,0 @@
-# file processed by 2to3
-from __future__ import print_function, absolute_import
-from builtins import map, filter, range
-#-------------------------------------------------------------------
-# gene_defaults.py
-#
-# PURPOSE
-# define defaults for inputs to GENE that are needed for TGLF
-#
-# AUTHORS:
-# Gary Staebler
-#--------------------------------------------------------------------
-import sys
-from gacodeinput import *
-gene = SimpleInput()
-# note the namelist parser f90nml converts everything to lower case
-def set_defaults() :
-# box namelist
-     gene.add('nky0','16')
-     gene.add('kymin','0.05')
-     gene.add('n_spec','2')
-# general namelist
-     gene.add('nonlinear','True')
-     gene.add('collision_op','pitch-angle')
-     gene.add('coll','0.0')
-     gene.add('beta','0.0')
-     gene.add('debye2','0.0')
-     gene.add('bpar','T')
-     gene.add('zeff','1.0')
-#  external_contr namelist
-     gene.add('exbrate','0.0')
-     gene.add('pfsrate','0.0')
-# geometry namelist
-     gene.add('magn_geometry','miller')
-     gene.add('shat','1.0')
-     gene.add('q0','2.0')
-     gene.add('major_r','3.0')
-     gene.add('minor_r','1.0')
-     gene.add('major_z','0.0')
-     gene.add('trpeps','0.167')
-     gene.add('amhd','0.0')
-     gene.add('kappa','1.0')
-     gene.add('delta','0.0')
-     gene.add('s_kappa','0.0')
-     gene.add('s_delta','0.0')
-     gene.add('drr','0.0')
-     gene.add('drz','0.0')
-     gene.add('zeta','0.0')
-     gene.add('s_zeta','0.0')
-     gene.add('dpdx_term','full-drift')
-     gene.add('dpdx_pm','0.0')     
-     return gene
diff --git a/gftm/bin/gftm b/gftm/bin/gftm
deleted file mode 100755
index 13590ae5d..000000000
--- a/gftm/bin/gftm
+++ /dev/null
@@ -1,227 +0,0 @@
-#!/bin/bash
-#=============================================================
-# gftm
-#
-# PURPOSE:
-#  Top-level script controlling execution of GFTM.
-#=============================================================
-
-#=============================================================
-# Syntax validity check and help message
-#
-n=$#
-
-if [ $n -eq 0 ]
-then
-  echo
-  echo "Usage:   gftm [options]"
-  echo
-  echo "         -p <path>"
-  echo "         Set optional path to simulation directory."
-  echo "         [The default path is the current directory]" 
-  echo
-  echo "EXECUTE MODE (single core)"
-  echo
-  echo "         -e <simdir>" 
-  echo "         Run GFTM using input.gftm data in <simdir>."
-  echo
-  echo "         -n <MPI tasks>" 
-  echo "         Number of MPI tasks."
-  echo
-  echo "INITIALIZE ONLY"
-  echo
-  echo "         -i <simdir>" 
-  echo "         Process input.gftm only."
-  echo
-  echo "REGRESSION TESTING"
-  echo
-  echo "         -rc <simdir>"
-  echo "         Check <simdir> for regression pass/fail."
-  echo
-  echo "         -r"
-  echo "         Run full regression suite."
-  echo 
-  echo "         -reset"
-  echo "         Reset regression data."
-  echo 
-  echo "TEMPLATE GENERATION"
-  echo
-  echo "         -g"
-  echo "         List available simulation templates."
-  echo
-  echo "         -g <template>"
-  echo "         Copy <template> into simulation path."
-  echo
-  echo "UTILITIES"
-  echo
-  echo "         -h" 
-  echo "         Version and platform information."
-  echo
-  echo "         -c" 
-  echo "         Clean out current directory."
-
-  exit 1
-fi
-#=============================================================
- 
-#=============================================================
-# Define variables for flag capture
-#
-RUNBASE='out.gftm.run'
-VERBASE='out.gftm.version'
-#
-SIMROOT=$PWD
-GFTM_DIR=$GACODE_ROOT/gftm
-# Parallelization parameters
-NPROC=1
-NOMP=1
-NUMA=0
-MPINUMA=0
-# Execute/test mode flags
-EXEC_FLAG=0
-INIT_FLAG=0
-GENERATE_FLAG=0
-REGRESS=0
-REGRESS_RESET=0
-#=============================================================
-
-#=============================================================
-# Parse command line options
-#
-while [ $# -gt 0 ] ; do
-  case "$1" in
-
-  -p) shift ; SIMROOT=$1 ;;
-
-  -e) shift ; LOCDIR=$1 ; EXEC_FLAG=1 ;;
-
-  -n) shift ; NPROC=$1 ;;
-
-  -g) shift ; LOCDIR=$1 ; GENERATE_FLAG=1 ;;
-
-  -i) shift ; LOCDIR=$1 ; INIT_FLAG=1 ;;
-
-  -r) REGRESS=1 ;;
-
-  -rc) shift ; LOCDIR=$1 ; REGRESS=2 ;;
-
-  -reset) REGRESS_RESET=1 ;;
-
-  -c) rm -f out.* ; exit 0 ;;
-
-  -h) gftm_version_message ; exit 0 ;;
-
-  *) echo "ERROR: incorrect gftm syntax." ; exit 1 ;;
- 
-  esac
-  shift
-done
-#=============================================================
-
-if [ "$LOCDIR" == "." ]
-then
-   SIMDIR=$PWD
-   cd .. ; LOCDIR=$PWD
-else
-   SIMDIR=$SIMROOT/$LOCDIR
-fi
-
-#============================================================
-# Check for inconsistent flags:
-if [ $REGRESS -eq 0 ] ; then
-   REGRESS_FLAG=0
-else
-   REGRESS_FLAG=1
-fi
-FLAG_SUM=$[$EXEC_FLAG+$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 [ $GENERATE_FLAG -eq 1 ]
-then
-   if [ ! -f "${GFTM_DIR}/tools/input/$LOCDIR/input.gftm" ]
-   then
-      cat ${GFTM_DIR}/tools/input/simdir_list
-   else
-      cp -ai ${GFTM_DIR}/tools/input/$LOCDIR $SIMDIR
-   fi
-   exit 0
-fi
-#============================================================
-
-#============================================================
-# Do the regression test if -r set, then exit.
-#
-if [ $REGRESS -eq 1 ] 
-then 
-   gacode_reg_do 1 1 $REGRESS_RESET gftm 1e-5
-   exit 0
-fi
-if [ $REGRESS -eq 2 ] 
-then 
-   gacode_reg $LOCDIR $GACODE_ROOT/gftm/tools/input out.gftm.prec 1e-6
-   exit 0
-fi
-#============================================================
-
-#============================================================
-# Everything else must be done in $SIMDIR; so ensure existence 
-# of $SIMDIR (needed at this point) and go there: 
-#
-if ! gftm_sim_warn $SIMDIR
-then
-   exit 1 
-fi 
-
-cd $SIMDIR
-#============================================================
-
-#==========================================================
-# echo number of tasks, then parse INPUT
-#
-echo "[Parsing data in input.gftm]" > $RUNBASE
-
-python $GFTM_DIR/bin/gftm_parse.py >> $RUNBASE
-if [ $? -eq 1 ] 
-then
-   cat $RUNBASE
-   exit 1
-fi
-#==========================================================
-
-#===========================================================
-# RUN GFTM
-#
-
-# Execute:
-if [ $EXEC_FLAG -eq 1 ]
-then
-
-   # Version stamp:
-   echo `gacode_getversion` > $VERBASE
-   echo $GACODE_PLATFORM >> $VERBASE
-   date >> $VERBASE
-
-   if [ $NPROC -eq 1 ]
-   then
-     echo 'no mpi'  >> $RUNBASE
-     cd $SIMDIR
-     export OMP_NUM_THREADS=$NOMP
-     $GFTM_DIR/src/gftm >> $RUNBASE
-   else
-     $GACODE_ROOT/platform/exec/exec.$GACODE_PLATFORM \
-     $SIMDIR $NPROC $GFTM_DIR/src/gftm_mpi $NOMP $NUMA $MPINUMA >> $RUNBASE
-   fi
-   gacode_printversion GFTM
-
-   cat $RUNBASE
-
-fi
-#===========================================================
diff --git a/gftm/bin/gftm_defaults.py b/gftm/bin/gftm_defaults.py
deleted file mode 100755
index 4b6759295..000000000
--- a/gftm/bin/gftm_defaults.py
+++ /dev/null
@@ -1,170 +0,0 @@
-#-------------------------------------------------------------------
-# tglf_defaults.py
-#
-# PURPOSE
-# define defaults for inputs to GFTM
-#
-# AUTHORS:
-# Gary Staebler
-# Jeff Candy
-#--------------------------------------------------------------------
-from gacodeinput import *
-import sys
-
-def set_defaults() :
-     t = SimpleInput()
-     t.add('UNITS','GYRO')
-     t.add('USE_TRANSPORT_MODEL','.true.')
-     t.add('GEOMETRY_FLAG','1')
-     t.add('WRITE_WAVEFUNCTION_FLAG','0')
-     t.add('SIGN_BT','1.0')
-     t.add('SIGN_IT','1.0')
-     t.add('THETA_TRAPPED','0.7')
-     t.add('WDIA_TRAPPED','0.0')
-     t.add('PARK','1.0')
-     t.add('GHAT','1.0')
-     t.add('GCHAT','1.0')
-     t.add('WD_ZERO','0.1')
-     t.add('LINSKER_FACTOR','0.0')
-     t.add('GRADB_FACTOR','0.0')
-     t.add('FILTER','2.0')
-     t.add('DAMP_PSI','0.0')
-     t.add('DAMP_SIG','0.0')
-     t.add('IFLUX','.true.')
-     t.add('USE_BPER','.false.')
-     t.add('USE_BPAR','.false.')
-     t.add('USE_MHD_RULE','.true.')
-     t.add('USE_BISECTION','.true.')
-     t.add('USE_INBOARD_DETRAPPED','.false.')
-     t.add('IBRANCH','-1')
-     t.add('NMODES','2')
-     t.add('NBASIS_MAX','4')
-     t.add('NBASIS_MIN','2')
-     t.add('NXGRID','16')
-     t.add('NKY','12')
-     t.add('USE_AVE_ION_GRID','.false.')
-     t.add('ADIABATIC_ELEC','.false.')
-     t.add('ALPHA_MACH','0.0')
-     t.add('ALPHA_E','1.0')
-     t.add('ALPHA_P','1.0')
-     t.add('ALPHA_QUENCH','0.0')
-     t.add('ALPHA_ZF','1.0')
-     t.add('XNU_FACTOR','1.0')
-     t.add('DEBYE_FACTOR','1.0')
-     t.add('ETG_FACTOR','1.25')
-     t.add('RLNP_CUTOFF','18.0')
-     t.add('SAT_RULE','0')
-     t.add('KYGRID_MODEL','1')
-     t.add('XNU_MODEL','2')
-     t.add('VPAR_MODEL','0')
-     t.add('VPAR_SHEAR_MODEL','1')
-     t.add('NS','2')
-     t.add('MASS_1','2.723e-4')
-     t.add('MASS_2','1.0')
-     t.add('MASS_3','0.0')
-     t.add('MASS_4','0.0')
-     t.add('MASS_5','0.0')
-     t.add('MASS_6','0.0')
-     t.add('MASS_7','0.0')
-     t.add('ZS_1','-1.0')      
-     t.add('ZS_2','1.0') 
-     t.add('ZS_3','0.0')
-     t.add('ZS_4','0.0')
-     t.add('ZS_5','0.0')
-     t.add('ZS_6','0.0')
-     t.add('ZS_7','0.0')
-     t.add('KY','0.3')
-     t.add('WIDTH','1.65')
-     t.add('WIDTH_MIN','0.3')
-     t.add('NWIDTH','21')
-     t.add('FIND_WIDTH','.true.')
-     t.add('RLNS_1','1.0')
-     t.add('RLNS_2','1.0') 
-     t.add('RLNS_3','0.0')
-     t.add('RLNS_4','0.0')
-     t.add('RLNS_5','0.0')
-     t.add('RLNS_6','0.0')
-     t.add('RLNS_7','0.0')
-     t.add('RLTS_1','3.0')
-     t.add('RLTS_2','3.0')
-     t.add('RLTS_3','0.0')
-     t.add('RLTS_4','0.0')
-     t.add('RLTS_5','0.0')
-     t.add('RLTS_6','0.0')
-     t.add('RLTS_7','0.0')
-     t.add('VPAR_SHEAR_1','0.0')
-     t.add('VPAR_SHEAR_2','0.0')
-     t.add('VPAR_SHEAR_3','0.0')
-     t.add('VPAR_SHEAR_4','0.0')
-     t.add('VPAR_SHEAR_5','0.0')
-     t.add('VPAR_SHEAR_6','0.0')
-     t.add('VPAR_SHEAR_7','0.0')
-     t.add('VEXB_SHEAR','0.0')
-     t.add('VNS_SHEAR_1','0.0')
-     t.add('VNS_SHEAR_2','0.0')
-     t.add('VNS_SHEAR_3','0.0')
-     t.add('VNS_SHEAR_4','0.0')
-     t.add('VNS_SHEAR_5','0.0')
-     t.add('VNS_SHEAR_6','0.0')
-     t.add('VNS_SHEAR_7','0.0')
-     t.add('VTS_SHEAR_1','0.0')
-     t.add('VTS_SHEAR_2','0.0')
-     t.add('VTS_SHEAR_3','0.0')
-     t.add('VTS_SHEAR_4','0.0')
-     t.add('VTS_SHEAR_5','0.0')
-     t.add('VTS_SHEAR_6','0.0')
-     t.add('VTS_SHEAR_7','0.0')
-     t.add('TAUS_1','1.0')
-     t.add('TAUS_2','1.0')
-     t.add('TAUS_3','0.0')
-     t.add('TAUS_4','0.0')
-     t.add('TAUS_5','0.0')
-     t.add('TAUS_6','0.0')
-     t.add('TAUS_7','0.0')
-     t.add('AS_1','1.0')
-     t.add('AS_2','1.0')
-     t.add('AS_3','0.0')
-     t.add('AS_4','0.0')
-     t.add('AS_5','0.0')
-     t.add('AS_6','0.0')
-     t.add('AS_7','0.0')
-     t.add('VPAR_1','0.0')
-     t.add('VPAR_2','0.0')
-     t.add('VPAR_3','0.0')
-     t.add('VPAR_4','0.0')
-     t.add('VPAR_5','0.0')
-     t.add('VPAR_6','0.0')
-     t.add('VPAR_7','0.0')
-     t.add('VEXB','0.0')
-     t.add('BETAE','0.0')
-     t.add('XNUE','0.0')
-     t.add('ZEFF','1.0')
-     t.add('DEBYE','0.0')
-     t.add('NEW_EIKONAL','.true.')
-     t.add('RMIN_SA','0.5')
-     t.add('RMAJ_SA','3.0')
-     t.add('Q_SA','2.0')
-     t.add('SHAT_SA','1.0')
-     t.add('ALPHA_SA','0.0')
-     t.add('XWELL_SA','0.0')
-     t.add('THETA0_SA','0.0')
-     t.add('B_MODEL_SA','1')
-     t.add('FT_MODEL_SA','1')
-     t.add('RMIN_LOC','0.5')
-     t.add('RMAJ_LOC','3.0')
-     t.add('ZMAJ_LOC','0.0')
-     t.add('DRMINDX_LOC','1.0')
-     t.add('DRMAJDX_LOC','0.0')
-     t.add('DZMAJDX_LOC','0.0')
-     t.add('KAPPA_LOC','1.0')
-     t.add('S_KAPPA_LOC','0.0')
-     t.add('DELTA_LOC','0.0')
-     t.add('S_DELTA_LOC','0.0')
-     t.add('ZETA_LOC','0.0')
-     t.add('S_ZETA_LOC','0.0')
-     t.add('Q_LOC','2.0')
-     t.add('Q_PRIME_LOC','16.0')
-     t.add('P_PRIME_LOC','0.0')
-     t.add('KX0_LOC','0.0')
-     # Deprecated parameters
-     return t
diff --git a/gftm/bin/gftm_input_gene.py b/gftm/bin/gftm_input_gene.py
deleted file mode 100644
index 7ed98795f..000000000
--- a/gftm/bin/gftm_input_gene.py
+++ /dev/null
@@ -1,226 +0,0 @@
-# file processed by 2to3
-from __future__ import print_function, absolute_import
-from builtins import map, filter, range
-#-------------------------------------------------------------------
-# tglf_input_gene.py
-#
-# PURPOSE
-# read GENE parameters_gene.txt file, map it to TGLF inputs and write input.tglf
-# this conversion uses the GENE chioces for Tref, Lref, mref
-# even if they are not the usual choices for TGLF. The conversion between B_unit and Bref
-# will be done inside TGLF so that the output from TGLF stand alone will be in GENE units Bref
-#
-# AUTHORS:
-# Gary Staebler
-# Orso Meneghini
-#--------------------------------------------------------------------
-#!/usr/bin/env python
-from gacodeinput import *
-import sys
-import tglf_defaults
-import gene_defaults
-import f90nml
-from pprint import pprint
-
-# read the file parameters_gene.txt file
-
-genenamelists = f90nml.read('./parameters_gene.txt')
-# pprint(genenamelists)
-# unpack the namelist
-geneinput={}
-# box namelist
-geneinput.update(genenamelists['box'])
-# general namelist
-geneinput.update(genenamelists['general'])
-#  external_contr namelist
-geneinput.update(genenamelists['external_contr'])
-# geometry namelist
-geneinput.update(genenamelists['geometry'])
-# pprint(geneinput)
-# species namelist
-species = genenamelists['species']
-#pprint(species)
-# use the geneinputs and the defaults gend to make a composite genein
-gend = SimpleInput()
-gened = gene_defaults.set_defaults()
-genein = {}
-for item in gened.data_dict :
-    genein[item] = gened.data_dict[item]
-    if item in geneinput :
-        genein[item] = geneinput[item]
-if genein['exbrate'] == -1111 :
-    print('warning: exbrate value not specified')
-    genein['exbrate'] = 0.0
-if genein['pfsrate'] == -1111 :
-    print('warning: pfsrate value not specified')
-    genein['pfsrate'] = 0.0
-#pprint(genein)
-# map genein to tglf
-tg = {}
-# set the units flag to GENE
-tg['UNITS'] = 'GENE'
-# ky-grid
-tg['KYGRID_MODEL'] = 0
-tg['NKY'] = genein['nky0']
-tg['KY'] = genein['nky0']*genein['kymin']
-if tg['KY'] <= 0.0 :
-    print('error: KY invalid ',KY)
-#control switches
-if(genein['nonlinear']=='True') :
-    tg['USE_TRANSPORT_MODEL'] = 'T'
-if genein['magn_geometry'] =='s-alpha' :
-    tg['GEOMETRY_FLAG']= 0
-if genein['magn_geometry'] == 'miller' :
-    tg['GEOMETRY_FLAG']= 1
-if genein['beta'] > 0.0 :
-    tg['USE_BPER'] = 'T'
-    tg['USE_BPAR'] = 'T'
-if genein['bpar'] == 'False' :
-    tg['USE_BPAR'] = 'F'
-
-tg['USE_MHD_RULE'] = 'F'
-if genein['dpdx_term'] == 'gradB_eq_curv' :
-    tg['USE_MHD_RULE'] = 'T'
-if genein['collision_op'] != 'pitch-angle' :
-    print('warning: TGLF only has pitch-angle collisions')
-# pprint(species[2]['name'])
-print('ZEFF in GENE file is ',genein['zeff'])
-tg['VEXB_SHEAR'] = genein['exbrate']
-# MILLER GEOMETRY
-tg['RMIN_LOC'] = genein['trpeps']*genein['major_r']
-tg['RMAJ_LOC'] = genein['major_r']
-tg['ZMAJ_LOC'] = genein['major_z']
-tg['DRMINDX_LOC'] = 1.0
-tg['DRMAJDX_LOC'] = genein['drr']
-tg['DZMAJDX_LOC'] = genein['drz']
-tg['KAPPA_LOC'] = genein['kappa']
-tg['S_KAPPA_LOC'] = genein['s_kappa']
-tg['DELTA_LOC'] = genein['delta']
-tg['S_DELTA_LOC'] = genein['s_delta']*(1.0-genein['delta']**2.0)**0.5
-tg['ZETA_LOC'] = genein['zeta']
-tg['S_ZETA_LOC'] = genein['s_zeta']
-tg['Q_LOC'] = genein['q0']
-if tg['Q_LOC'] < 0.0 :
-    tg['Q_LOC'] = -tg['Q_LOC']
-tg['Q_PRIME_LOC'] = genein['shat']*(tg['Q_LOC']/tg['RMIN_LOC'])**2
-tg['P_PRIME_LOC'] = -genein['amhd']/(8.0*3.14159265*tg['Q_LOC']*tg['RMAJ_LOC']*tg['RMIN_LOC'])
-tg['KX0_LOC'] = 0.0
-#S-ALPHA GEOMETRY
-tg['RMIN_SA'] = genein['trpeps']*genein['major_r']
-tg['RMAJ_SA'] = genein['major_r']
-tg['Q_SA'] = genein['q0']
-if tg['Q_SA'] < 0.0 :
-    tg['Q_SA'] = -tg['Q_SA']
-tg['SHAT_SA'] = genein['shat']
-tg['ALPHA_SA'] = genein['amhd']
-tg['XWELL_SA'] = 0.0
-tg['THETA0_SA'] = 0.0
-tg['B_MODEL_SA'] = 1
-tg['FT_MODEL_SA'] = 1
-# plasma species data
-nspecies = genein['n_spec']
-nions = 0
-for i in range(0, nspecies) :
-    passive = 'F'
-    if 'passive' in species[i] :
-        if species[i]['passive'] == 'True' :
-          passive = 'T'
-    if species[i]['charge'] == -1:
-# electrons
-       if passive == 'T' :
-          tg['ADIABATIC_ELEC'] = 'T'
-       tg['ZS_1'] = -1.0
-       tg['MASS_1'] = species[i]['mass']
-       tg['RLNS_1'] = species[i]['omn']
-       tg['RLTS_1'] = species[i]['omt']
-       tg['TAUS_1'] = species[i]['temp']
-       tg['AS_1'] = species[i]['dens']
-       tg['VPAR_1'] = '0.0'
-       tg['VPAR_SHEAR_1'] = genein['pfsrate']
-    if species[i]['charge'] > 0:
-        # skip passive species
-       if passive == 'F' :
-           nions = nions + 1
-           if nions == 1 :
-             tg['ZS_2'] = species[i]['charge']
-             tg['MASS_2'] = species[i]['mass']
-             tg['RLNS_2'] = species[i]['omn']
-             tg['RLTS_2'] = species[i]['omt']
-             tg['TAUS_2'] = species[i]['temp']
-             tg['AS_2'] = species[i]['dens']
-             tg['VPAR_2'] = 0.0
-             tg['VPAR_SHEAR_2'] = genein['pfsrate']
-             tg['ZEFF'] = tg['AS_2']*tg['ZS_2']**2
-           if nions == 2 :
-             tg['ZS_3'] = species[i]['charge']
-             tg['MASS_3'] = species[i]['mass']
-             tg['RLNS_3'] = species[i]['omn']
-             tg['RLTS_3'] = species[i]['omt']
-             tg['TAUS_3'] = species[i]['temp']
-             tg['AS_3'] = species[i]['dens']
-             tg['VPAR_3'] = 0.0
-             tg['VPAR_SHEAR_3'] = genein['pfsrate']
-             tg['ZEFF'] = tg['ZEFF']+tg['AS_3']*tg['ZS_3']**2
-           if nions == 3 :
-             tg['ZS_4'] = species[i]['charge']
-             tg['MASS_4'] = species[i]['mass']
-             tg['RLNS_4'] = species[i]['omn']
-             tg['RLTS_4'] = species[i]['omt']
-             tg['TAUS_4'] = species[i]['temp']
-             tg['AS_4'] = species[i]['dens']
-             tg['VPAR_4'] = 0.0
-             tg['VPAR_SHEAR_4'] = genein['pfsrate']
-             tg['ZEFF'] = tg['ZEFF']+tg['AS_4']*tg['ZS_4']**2
-           if nions == 4 :
-             tg['ZS_5'] = species[i]['charge']
-             tg['MASS_5'] = species[i]['mass']
-             tg['RLNS_5'] = species[i]['omn']
-             tg['RLTS_5'] = species[i]['omt']
-             tg['TAUS_5'] = species[i]['temp']
-             tg['AS_5'] = species[i]['dens']
-             tg['VPAR_5'] = '0.0'
-             tg['VPAR_SHEAR_5'] = genein['pfsrate']
-             tg['ZEFF'] = tg['ZEFF']+tg['AS_5']*tg['ZS_5']**2
-           if nions == 5 :
-             tg['ZS_6'] = species[i]['charge']
-             tg['MASS_6'] = species[i]['mass']
-             tg['RLNS_6'] = species[i]['omn']
-             tg['RLTS_6'] = species[i]['omt']
-             tg['TAUS_6'] = species[i]['temp']
-             tg['AS_6'] = species[i]['dens']
-             tg['VPAR_6'] = '0.0'
-             tg['VPAR_SHEAR_6'] = genein['pfsrate']
-             tg['ZEFF'] = tg['ZEFF']+tg['AS_6']*tg['ZS_6']**2
-           if nions > 5 :
-               print('warning: TGLF stand alone version can only have 5 kinetic ion species')
-               nions = 5
-tg['NS'] = nions + 1
-print('number of kinetic ions = ',nions)
-print('ZEFF in TGLF file is : ',tg['ZEFF'])
-# set TGLF parameters that need electron units
-# note beta,debye2 and amhd are wrt Bref so TGLF will convert to B_unit internally
-tg['BETAE'] = genein['beta']*tg['TAUS_1']*tg['AS_1']
-tg['DEBYE'] = genein['debye2']**0.5
-# note Cref=(Tref/mref)**0.5 the XNUE = nue*Lref/Cref in GENE units
-tg['XNUE'] = genein['coll']*(4.0/tg['MASS_1']**0.5)*tg['AS_1']/tg['TAUS_1']**1.5
-#print(tg)
-#transfer overwrites to input.tglf dictionary tin
-t = SimpleInput()
-t = tglf_defaults.set_defaults()
-
-t.set_extension('')
-
-tin = {}
-
-for item in tg:
-    if tg[item] != t.data_dict[item] :
-        tin[item] = tg[item]
-
-#print(tin)
-# write input.tglf
-with open('input.tglf','w') as f:
-    for item in tin:
-        f.write(item+'='+str(tin[item]))
-        f.write('\n')
-
-print('parameters_gene.txt succesfully converted to input.tglf')
diff --git a/gftm/bin/gftm_input_gyro.py b/gftm/bin/gftm_input_gyro.py
deleted file mode 100755
index a4ac1770d..000000000
--- a/gftm/bin/gftm_input_gyro.py
+++ /dev/null
@@ -1,200 +0,0 @@
-# file processed by 2to3
-from __future__ import print_function, absolute_import
-from builtins import map, filter, range
-#-------------------------------------------------------------------
-# tglf_input_gyro.py
-#
-# PURPOSE
-# read input.gyro.gen,  map it to TGLF inputs and write input.tglf
-#
-# AUTHORS:
-# Gary Staebler
-# Orso Meneghini
-#--------------------------------------------------------------------
-#!/usr/bin/env python
-from gacodeinput import *
-import sys
-import tglf_defaults
-
-# read the input.gyro file
-
-g = {}
-with open('input.gyro.gen','r') as f:
-    for line in f.readlines():
-
-       # Remove leading and trailing whitespace from line
-        line = line.strip()
-    #    print(line)
-        # Skip blank lines
-        if len(line) > 0 :
-            tmp = line.split('  ')
-            if len(tmp) == 2 :
-                val = eval(tmp[0])
-                arg = tmp[1]
-                g[arg] = val
-
-#print(g)
-
-# map gyro to tglf
-tg = {}
-
-# ky-grid
-tg['KYGRID_MODEL'] = 0
-tg['NKY'] = g['TOROIDAL_GRID']-1
-tg['KY'] = tg['NKY']*g['TOROIDAL_SEP']*g['RHO_STAR']*g['SAFETY_FACTOR']/g['RADIUS']
-if tg['KY'] < 0.0 :
-    tg['KY'] = -tg['KY']
-
-#control switches
-if g['RADIAL_PROFILE_METHOD'] == 1 :
-    tg['GEOMETRY_FLAG']= 0
-if g['RADIAL_PROFILE_METHOD'] == 5 :
-    tg['GEOMETRY_FLAG']= 1
-if g['RADIAL_PROFILE_METHOD' ]== 3 :
-    print('error gyro RADIAL_PROFILE_METHOD = 3')
-if g['N_FIELD'] >= 2 :
-    tg['USE_BPER'] = 'T'
-if g['N_FIELD'] == 3 :
-    tg['USE_BPAR'] = 'T'
-if g['ELECTRON_METHOD'] == 1 :
-    tg['ADIABATIC_ELECT'] = 'T'
-if g['GEO_GRADBCURV_FLAG'] == 0 :
-    tg['USE_MHD_RULE'] = 'F'
-tg['ALPHA_E'] = g['GAMMA_E_SCALE']
-tg['ALPHA_P'] = g['GAMMA_P_SCALE']
-tg['ALPHA_MACH'] = g['MACH_SCALE']
-tg['DEBYE_FACTOR'] = g['LAMBDA_DEBYE_SCALE']
-tg['XNU_FACTOR'] = g['NU_EI_SCALE']
-if g['NU_II_SCALE'] > 0.0 :
-    print('error GYRO ion collisions turned on')
-nion = 1
-if g['NI_OVER_NE_2'] > 0.0 :
-    nion = nion + 1
-if g['NI_OVER_NE_3'] > 0.0:
-    nion = nion + 1
-if g['NI_OVER_NE_4'] > 0.0:
-    nion = nion + 1
-if g['NI_OVER_NE_5'] > 0.0:
-    nion = nion + 1
-tg['NS'] = nion + 1
-
-# plasma data
-tg['SIGN_BT'] = g['BTCCW']
-tg['SIGN_IT'] = g['IPCCW']
-tg['ZS_1'] = -1.0
-tg['ZS_2'] = g['Z']
-tg['ZS_3'] = g['Z_2']
-tg['ZS_4'] = g['Z_3']
-tg['ZS_5'] = g['Z_4']
-tg['ZS_6'] = g['Z_5']
-tg['MASS_1'] = 1.0/(g['MU_ELECTRON']**2)
-tg['MASS_2'] = 1.0/(g['MU'])**2
-tg['MASS_3'] = (g['MU']/g['MU_2'])**2
-tg['MASS_4'] = (g['MU']/g['MU_3'])**2
-tg['MASS_5'] = (g['MU']/g['MU_4'])**2
-tg['MASS_6'] = (g['MU']/g['MU_5'])**2
-tg['RLNS_1'] = g['DLNNDR_ELECTRON']*(1.0-g['EPS_DLNNDR_ELECTRON'])
-tg['RLNS_2'] = g['DLNNDR']*(1.0-g['EPS_DLNNDR'])
-tg['RLNS_3'] = g['DLNNDR_2']*(1.0-g['EPS_DLNNDR_2'])
-tg['RLNS_4'] = g['DLNNDR_3']*(1.0-g['EPS_DLNNDR_3'])
-tg['RLNS_5'] = g['DLNNDR_4']*(1.0-g['EPS_DLNNDR_4'])
-tg['RLNS_6'] = g['DLNNDR_5']*(1.0-g['EPS_DLNNDR_5'])
-tg['RLTS_1'] = g['DLNTDR_ELECTRON']*(1.0-g['EPS_DLNTDR_ELECTRON'])
-tg['RLTS_2'] = g['DLNTDR']*(1.0-g['EPS_DLNTDR'])
-tg['RLTS_3'] = g['DLNTDR_2']*(1.0-g['EPS_DLNTDR_2'])
-tg['RLTS_4'] = g['DLNTDR_3']*(1.0-g['EPS_DLNTDR_3'])
-tg['RLTS_5'] = g['DLNTDR_4']*(1.0-g['EPS_DLNTDR_4'])
-tg['RLTS_6'] = g['DLNTDR_5']*(1.0-g['EPS_DLNTDR_5'])
-tg['TAUS_1'] = 1.0
-tg['TAUS_2'] = g['TI_OVER_TE']
-tg['TAUS_3'] = g['TI_OVER_TE_2']
-tg['TAUS_4'] = g['TI_OVER_TE_3']
-tg['TAUS_5'] = g['TI_OVER_TE_4']
-tg['TAUS_6'] = g['TI_OVER_TE_5']
-tg['AS_1'] = 1.0
-tg['AS_2'] = g['NI_OVER_NE']
-tg['AS_3'] = g['NI_OVER_NE_2']
-tg['AS_4'] = g['NI_OVER_NE_3']
-tg['AS_5'] = g['NI_OVER_NE_4']
-tg['AS_6'] = g['NI_OVER_NE_5']
-tg['VPAR_1'] = -tg['SIGN_IT']*g['MACH']
-tg['VPAR_2'] = -tg['SIGN_IT']*g['MACH']
-tg['VPAR_3'] = -tg['SIGN_IT']*g['MACH']
-tg['VPAR_4'] = -tg['SIGN_IT']*g['MACH']
-tg['VPAR_5'] = -tg['SIGN_IT']*g['MACH']
-tg['VPAR_6'] = -tg['SIGN_IT']*g['MACH']
-tg['VPAR_SHEAR_1'] = -tg['SIGN_IT']*g['GAMMA_P']
-tg['VPAR_SHEAR_2'] = -tg['SIGN_IT']*g['GAMMA_P']
-tg['VPAR_SHEAR_3'] = -tg['SIGN_IT']*g['GAMMA_P']
-tg['VPAR_SHEAR_4'] = -tg['SIGN_IT']*g['GAMMA_P']
-tg['VPAR_SHEAR_5'] = -tg['SIGN_IT']*g['GAMMA_P']
-tg['VPAR_SHEAR_6'] = -tg['SIGN_IT']*g['GAMMA_P']
-tg['VEXB_SHEAR'] = -tg['SIGN_BT']*g['GAMMA_E']
-tg['BETAE'] = g['BETAE_UNIT']*g['AMPERE_SCALE']
-tg['ZEFF'] = g['Z_EFF']
-tg['DEBYE'] = g['LAMBDA_DEBYE']/g['RHO_STAR']
-tg['XNUE'] = g['NU_EI']
-#S-ALPHA GEOMETRY
-tg['RMIN_SA'] = g['RADIUS']
-tg['RMAJ_SA'] = g['ASPECT_RATIO']
-tg['Q_SA'] = g['SAFETY_FACTOR']
-if tg['Q_SA'] < 0.0 :
-   tg['Q_SA'] = -tg['Q_SA']
-tg['SHAT_SA'] = g['SHEAR']
-tg['ALPHA_SA'] = g['SHIFT']
-tg['XWELL_SA'] = 0.0
-tg['THETA0_SA'] = 0.0
-tg['B_MODEL_SA'] = 1
-tg['FT_MODEL_SA'] = 1                   
-# MILLER GEOMETRY
-tg['RMIN_LOC'] = g['RADIUS']
-tg['RMAJ_LOC'] = g['ASPECT_RATIO']
-tg['ZMAJ_LOC'] = g['ZMAG']
-tg['DRMINDX_LOC'] = 1.0
-tg['DRMAJDX_LOC'] = g['SHIFT']
-tg['DZMAJDX_LOC'] = g['DZMAG']
-tg['KAPPA_LOC'] = g['KAPPA']
-tg['S_KAPPA_LOC'] = g['S_KAPPA']
-tg['DELTA_LOC'] = g['DELTA']
-tg['S_DELTA_LOC'] = g['S_DELTA']
-tg['ZETA_LOC'] = g['ZETA']
-tg['S_ZETA_LOC'] = g['S_ZETA']
-tg['Q_LOC'] = g['SAFETY_FACTOR']
-if tg['Q_LOC'] < 0.0 :
-   tg['Q_LOC'] = -tg['Q_LOC']
-tg['Q_PRIME_LOC'] = g['SHEAR']*(tg['Q_LOC']/tg['RMIN_LOC'])**2
-tg['KX0_LOC'] = 0.0
-# compute P_PRIME_LOC
-scale = g['GEO_BETAPRIME_SCALE']/(8.0*3.1415927)
-betae = g['BETAE_UNIT']
-rloc = g['RADIUS']
-qloc = tg['Q_LOC']
-dpdr = g['DLNNDR_ELECTRON'] + g['DLNTDR_ELECTRON'] +                              \
-            g['NI_OVER_NE']*g['TI_OVER_TE']*(g['DLNTDR'] + g['DLNNDR']) +          \
-            g['NI_OVER_NE_2']*g['TI_OVER_TE_2']*(g['DLNTDR_2'] + g['DLNNDR_2']) +  \
-            g['NI_OVER_NE_3']*g['TI_OVER_TE_3']*(g['DLNTDR_3'] + g['DLNNDR_3']) +  \
-            g['NI_OVER_NE_4']*g['TI_OVER_TE_4']*(g['DLNTDR_4'] + g['DLNNDR_4']) +  \
-            g['TI_OVER_TE_5']*g['NI_OVER_NE_5']*(g['DLNTDR_5'] + g['DLNNDR_5'])  
-tg['P_PRIME_LOC'] = -scale*betae*(qloc/rloc)*dpdr
-
-#print(tg)                   
-#transfer overwrites to input.tglf dictionary tin
-t = SimpleInput()
-t = tglf_defaults.set_defaults()
-
-t.set_extension('')
-
-tin = {}
-
-for item in tg:
-    if tg[item] != t.data_dict[item] :
-        tin[item] = tg[item]
-
-#print(tin)
-# write input.tglf
-with open('input.tglf','w') as f:
-    for item in tin:
-        f.write(item+'='+str(tin[item]))
-        f.write('\n')
-
-print('input.gyro succesfully converted to input.tglf')
diff --git a/gftm/bin/gftm_parse.py b/gftm/bin/gftm_parse.py
deleted file mode 100755
index e1f1410a2..000000000
--- a/gftm/bin/gftm_parse.py
+++ /dev/null
@@ -1,16 +0,0 @@
-from gacodeinput import *
-import sys
-import gftm_defaults
-
-# fill x with the GFTM defaults
-x = gftm_defaults.set_defaults()
-
-x.set_extension('.gen')
-
-# Perform the parsing
-x.read_input('input.gftm')
-
-x.printmsg()        
-
-sys.exit(x.error)
-
diff --git a/gftm/bin/gftm_sim_warn b/gftm/bin/gftm_sim_warn
deleted file mode 100755
index b151026d7..000000000
--- a/gftm/bin/gftm_sim_warn
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/bin/sh
-#
-# SCRIPT:
-#  gftm_sim_warn
-#
-# FUNCTION:
-#  Check for existence of sim directory
-#-------------------------------------------------------------
-
-if [ $1 = $PWD ]
-  then
-  echo "Error: missing simdir"
-  exit 1
-fi
-
-if [ ! -d "$1" ]
-  then
-  echo "$1 is not a valid simulation directory."
-  echo "Please create the directory first, or use [gftm -g]."
-  exit 1
-fi
-
-if [ ! -f "$1/input.gftm" ]
-  then
-  echo "input.gftm not found."
-  exit 1
-fi
-
-exit 0
diff --git a/gftm/bin/gftm_version_message b/gftm/bin/gftm_version_message
deleted file mode 100755
index 8ebc6175e..000000000
--- a/gftm/bin/gftm_version_message
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/sh
-#
-# SCRIPT:
-#  tglf_version_message
-#
-# FUNCTION:
-#  Echo version message.
-#------------------------------
-
-VERSION=`gacode_getversion`
-
-echo "=========================================================="
-echo "TGLF" `echo $VERSION` `echo $GACODE_PLATFORM` `uname -s` `uname -m`
-echo "=========================================================="
diff --git a/gftm/install/make.ext.EDISON_CRAY b/gftm/install/make.ext.EDISON_CRAY
deleted file mode 100644
index 7debc5609..000000000
--- a/gftm/install/make.ext.EDISON_CRAY
+++ /dev/null
@@ -1 +0,0 @@
-TGLFISNAN=tglf_isnan_cray.o
diff --git a/gftm/install/make.ext.SATURN b/gftm/install/make.ext.SATURN
deleted file mode 100644
index 7129a87fa..000000000
--- a/gftm/install/make.ext.SATURN
+++ /dev/null
@@ -1 +0,0 @@
-TGLFISNAN=tglf_isnan_ieee.o
diff --git a/gftm/install/make.ext.TITAN_CRAY b/gftm/install/make.ext.TITAN_CRAY
deleted file mode 100644
index 7debc5609..000000000
--- a/gftm/install/make.ext.TITAN_CRAY
+++ /dev/null
@@ -1 +0,0 @@
-TGLFISNAN=tglf_isnan_cray.o
diff --git a/gftm/src/Makefile b/gftm/src/Makefile
deleted file mode 100644
index 93eb7263c..000000000
--- a/gftm/src/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
-
-ifeq ($(OPT),debug)
-   FFLAGS=${FDEBUG}
-else
-   FFLAGS=${FOPT}
-endif
-
-EXEC1=gftm
-EXEC2=gftm_mpi
-
-LLIB=gftm_lib
-
-OBJECTS = gftm_isnan.o      \
-          gftm_modules.o    \
-          gftm_pkg.o        \
-          gftm_allocate.o   \
-          gftm_deallocate.o \
-          gftm_startup.o    \
-          gftm_hermite.o    \
-          gftm_inout.o      \
-          gftm_setup_geometry.o \
-          gftm_LS.o         \
-          gftm_eigensolver.o \
-          gftm_geometry.o   \
-          gftm_matrix.o     \
-          gftm_max.o        \
-          gftm_interface.o  \
-          gftm_error.o      \
-          gftm_isinf.o      \
-          gftm_shutdown.o   \
-          gftm_read_input.o \
-          gftm_multiscale_spectrum.o \
-          gftm_kygrid.o     \
-          gftm_run.o        \
-          gftm_TM.o         \
-          gftm_init_mpi.o   \
-          gftm_run_mpi.o    \
-          gftm_TM_mpi.o     \
-          gftm_collision1.o     \
-          gftm_collision2.o
-
-
-.SUFFIXES : .o .f90 .F90
-
-all: $(LLIB).a $(EXEC1) $(EXEC2) Makefile
-
-$(EXEC1): $(LLIB).a $(EXEC1).o
-	$(FC) $(FFLAGS) -o $(EXEC1) $(EXEC1).o $(LLIB).a $(LMATH) 
-$(EXEC2): $(LLIB).a $(EXEC2).o
-	$(FC) $(FFLAGS) -o $(EXEC2) $(EXEC2).o $(LLIB).a $(LMATH)
-
-$(LLIB).a: $(OBJECTS)
-	$(ARCH) $(LLIB).a $(OBJECTS)
-
-gftm_run_mpi.o: gftm_run.F90
-	$(FC) -o gftm_run_mpi.o $(FMATH) $(FFLAGS) -DMPI_GFTM=1 -c $<
-
-.f90.o:
-	$(FC) $(FMATH) $(FFLAGS) -c $<
-.F90.o:
-	$(FC) $(FMATH) $(FFLAGS) -c $<
-
-clean:
-	rm -f *.o *.lst $(LLIB).a $(EXEC1) $(EXEC2)
-	rm -f ${GACODE_ROOT}/modules/gftm*.mod
-
--include ${GACODE_ROOT}/platform/build/make.inc.${GACODE_PLATFORM}
diff --git a/gftm/src/gftm b/gftm/src/gftm
deleted file mode 100755
index f2db88b39..000000000
Binary files a/gftm/src/gftm and /dev/null differ
diff --git a/gftm/src/gftm.f90 b/gftm/src/gftm.f90
deleted file mode 100644
index 1e156a11e..000000000
--- a/gftm/src/gftm.f90
+++ /dev/null
@@ -1,166 +0,0 @@
-!---------------------------------------------------------
-! gftm_run.f90
-!
-! PURPOSE:
-!  Manage standalone gftm run by calling
-!
-!    call gftm_read_input()
-!    call gftm_run()
-!
-!  and then adding extra I/O. 
-!---------------------------------------------------------
-
-program gftm
-
-  use gftm_pkg
-  use gftm_interface
-  use gftm_global
-  use gftm_dimensions
-
-  implicit none
-
-  integer :: i
-  integer :: n
-  character (len=4) :: tag(6)=(/'ion1','ion2','ion3','ion4','ion5','ion6'/)
-  real :: prec
-
-  call gftm_read_input()
-  call gftm_run()
-  call gftm_dump_global()
-  if(units_in.eq.'GENE')then
-     print 30,'GENE reference units used'
-     print 30,'Conversion to gftm units:'
-     print 30,'Bunit/Bref = ',1.0/Bref_out
-     print 30,'Te/Tref = ',taus_in(1)
-     print 30,'mi/mref = ',mass_in(2)
-     print 30,'a/Lref = ',1.0
-     print 30,'cs/cref = ',SQRT(taus_in(1)/mass_in(2))
-     print 30,'rhos/rhoref = ',SQRT(mass_in(2)*taus_in(1))*Bref_out
-  endif
-  if(alpha_zf_in.lt.0.0)print 30,' kx_geo0_out = ',kx_geo0_out, &
-      ' SAT_geo0_out = ',SAT_geo0_out
-
-! write interchange stability criteria with ELITE conventions
-  Print 30,'  D(R) = ',-interchange_DR,'  D(I) = ',0.25-interchange_DM
-!  write species info
-  print 40,'  kinetic species = ',ns_in,'  non-kinetic species = ',nstotal_in - ns_in
-
-  if (gftm_use_transport_model_in) then
-
-     ! Output to screen
-
-     print 20,'Gam/Gam_GB','    Q/Q_GB','Q_low/Q_GB','  Pi/Pi_GB', '    S/S_GB'
-     print 10,'elec',&
-          gftm_elec_pflux_out,&
-          gftm_elec_eflux_out,&
-          gftm_elec_eflux_low_out,&
-          gftm_elec_mflux_out,&
-          gftm_elec_expwd_out
-
-     prec = abs(gftm_elec_pflux_out)+&
-          abs(gftm_elec_eflux_out)+&
-          abs(gftm_elec_eflux_low_out)+&
-          abs(gftm_elec_mflux_out)
-
-     do i=1,gftm_ns_in-1
-        print 10,tag(i),&
-             gftm_ion_pflux_out(i),&
-             gftm_ion_eflux_out(i),&
-             gftm_ion_eflux_low_out(i),&
-             gftm_ion_mflux_out(i),&
-             gftm_ion_expwd_out(i)
-
-        prec = prec+&
-             abs(gftm_ion_pflux_out(i))+&
-             abs(gftm_ion_eflux_out(i))+&
-             abs(gftm_ion_eflux_low_out(i))+&
-             abs(gftm_ion_mflux_out(i))
-     enddo
-
-     ! Output to file
-
-     n = gftm_ns_in-1
-     open(unit=1,file='out.gftm.gbflux',status='replace')
-     write(1,'(32(1pe11.4,1x))') gftm_elec_pflux_out,gftm_ion_pflux_out(1:n),&
-          gftm_elec_eflux_out,gftm_ion_eflux_out(1:n),&
-          gftm_elec_mflux_out,gftm_ion_mflux_out(1:n),&
-          gftm_elec_expwd_out,gftm_ion_expwd_out(1:n)
-     close(1)
-
-     open(unit=1,file='out.gftm.grid',status='replace')
-     write(1,'(i2)') gftm_ns_in,gftm_nxgrid_in
-     close(1)
-
-     write(*,*)"nbasis = ",nbasis,"  nu = ",nu,"  ne = ",ne
-
-     ! write ky spectrum to file out.gftm.ky_spectrum
-     CALL write_gftm_ky_spectrum
-
-     ! write flux spectrum summed over nmodes to file out.gftm.sum_flux_spectrum
-     ! this can be compared directly with the flux spectrum from CGYRO 
-
-     CALL write_gftm_sum_flux_spectrum
-
-     ! write density fluctuation amplitude spectrum to file out.gftm.density_spectrum
-     CALL write_gftm_density_spectrum
-
-     ! write temperature fluctuation amplitude spectrum to file out.gftm.temperature_spectrum
-     CALL write_gftm_temperature_spectrum
-
-     ! write intensity fluctuation amplitude spectrum per mode to file out.gftm.intensity_spectrum
-     CALL write_gftm_intensity_spectrum
-
-     ! write field fluctuation amplitude per mode spectrum to file out.gftm.field_spectrum
-     CALL write_gftm_field_spectrum
-
-     ! write eigenvalue spectrum to file out.gftm.eigenvalue_spectrum
-     CALL write_gftm_eigenvalue_spectrum
-
-     ! write ne-te crossphase spectrum to file out.gftm.nete_crossphase_spectrum
-     CALL write_gftm_nete_crossphase_spectrum
-
-     ! write ns-ts crossphase spectrum to file out.gftm.nsts_crossphase_spectrum
-     CALL write_gftm_nsts_crossphase_spectrum
-
-     ! write QL flux (weight) spectrum per mode to file out.gftm.QL_weight_spectrum
-     CALL write_gftm_QL_flux_spectrum
-
-     ! write kx/ky-spectral shift spectrum to file out.gftm.spectral_shift
-     CALL write_gftm_spectral_shift_spectrum
-
-     ! write ave_p0 spectrum to file out.gftm.ave_p0_spectrum
-     CALL write_gftm_ave_p0_spectrum
-
-     ! write intensity fluctuation amplitude spectrum per mode to file out.gftm.scalar_saturation_parameters
-     CALL write_gftm_scalar_saturation_parameters
-
-     ! write Gaussian width spectrum to file out.gftm.width_spectrum
-     CALL write_gftm_width_spectrum
-
-  else
-
-     print 10,'     ky:',gftm_ky_in
-     print 10,'     ft:',get_ft()
-     print 10,'Guassian width = ',get_gaussian_width()
-     ! Collect linear eigenvalues
-     do i=1,gftm_nmodes_in
-        print 10,'(wr,wi):',gftm_eigenvalue_out(i)
-     enddo
-
-     prec = sum(abs(gftm_eigenvalue_out))
-
-    ! write single ky-eigenmode wavefunction to file
-    CALL write_wavefunction_out('out.gftm.wavefunction')
-
-  endif
-
-  open(unit=1,file=trim(gftm_path_in)//'out.gftm.prec')
-  write(1,*) prec
-  close(1)
-
-10 format(a,10(1x,1pe11.4))
-20 format(t7,a,t19,a,t31,a,t43,a,t55,a)
-30 format(a,1pe11.4,a,1pe11.4)
-40 format(a,I10,a,I10)
-
-end program gftm
diff --git a/gftm/src/gftm_LS.f90 b/gftm/src/gftm_LS.f90
deleted file mode 100644
index af9084050..000000000
--- a/gftm/src/gftm_LS.f90
+++ /dev/null
@@ -1,829 +0,0 @@
-!
-!--------------------------------------------------------------
-!
-      SUBROUTINE gftm_LS
-!
-!***********************************************************************
-! questions  should be addressed to
-!  Gary Staebler 858-455-3466  or email: gary.staebler@gat.com
-!***********************************************************************
-!  gftm Linear Stability driver computes all quasilinear quantities
-!  for a single ky
-!
-!***********************************************************************
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_eigen
-      USE gftm_GFS
-      USE gftm_weight
-!
-      IMPLICIT NONE
-      REAL,PARAMETER :: epsilon1 = 1.E-12
-      INTEGER :: info
-      INTEGER :: j1, j, i, iroot, jmax(maxmodes)
-      INTEGER :: imax,is
-      INTEGER :: mi,me
-      INTEGER :: ip,jp
-      REAL :: zgamax
-      REAL :: phi2_bar,kyi
-      REAL :: sum_v_bar, sum_modB_bar
-      REAL :: one, henorm
-      COMPLEX :: testhe
-!  ZGESV storage
-      REAL :: small = 1.0E-10
-      REAL :: get_gamma_net
-!
-!      cputime0=MPI_WTIME()
-!
-! set ky in units of k_theta*rho_s  rho_s=C_s/omega_s
-! C_s=sqrt(Te/mi), omega_s=eB/(mi c)
-!
-      ky = ky_s
-!      write(*,*)"ky = ",ky
-      !
-      ! check co-dependencies
-      !
-      if(new_geometry)new_width=.TRUE.
-      if(new_width)new_matrix=.TRUE.
-!      write(*,*)"new_start=",new_start
-!      write(*,*)"new_geometry=",new_geometry
-!      write(*,*)"new_width=",new_width
-!      write(*,*)"new_matrix=",new_matrix
-!      write(*,*)"width_in=",width_in
-!      write(*,*)"nbasis_max_in=",nbasis_max_in
-!      write(*,*)"new_eikonal_in=",new_eikonal_in
-!      write(*,*)"betae_in=",betae_in
-!      write(*,*)"debye_in=",debye_in
-!      write(*,*)"xnue_in=",xnue_in
-!      write(*,*)"zeff_in=",zeff_in
-!      write(*,*)"filter_in=",filter_in
-!      write(*,*)"park_in=",park_in
-!      write(*,*)"ghat_in=",ghat_in
-!      write(*,*)"wd_zero_in=",wd_zero_in
-!      write(*,*)"Linsker_factor_in=",Linsker_factor_in
-!      write(*,*)"gradB_factor_in=",gradB_factor_in
-!      write(*,*)"xnu_factor_in=",xnu_factor_in
-!      write(*,*)"debye_factor_in=",debye_factor_in
-!      write(*,*)"theta_trapped_in=",theta_trapped_in
-!      write(*,*)"alpha_p_in=",alpha_p_in
-!      write(*,*)"alpha_e_in=",alpha_e_in
-!
-      ky = ky_s
-!
-      if(new_eikonal_in)then
-        if(new_geometry)then
-          if(igeo.eq.1)then
-! set up MILLER geometry
-            trace_path(4)=1
-            call miller_geo
-          elseif(igeo.eq.2)then
-! set up FOURIER geometry
-            trace_path(5)=1
-            call fourier_geo
-          elseif(igeo.eq.3)then
-! set up ELITE geometry
-            trace_path(8)=1
-            call ELITE_geo
-          endif
-!        write(*,*)"geometry done"
-!
-! compute the eikonal functions for general geometry (igeo>0)
-!
-          if(igeo.gt.0)call mercier_luc 
-!
-        endif ! new_geometry
-        new_geometry=.FALSE.
-!
-!  load the x-grid eikonal functions wdx,b0x
-!
-        if(new_width)then
-          trace_path(6)=1
-          call get_xgrid_functions
-        endif
-!       write(*,*)"ft=",ft
-      endif  !new_eikonal_in
-!      write(*,*)"eikonal done"
-!
-if(new_matrix)then
-        trace_path(7)=1
-        call get_matrix
-      endif
-!      write(*,*)"matrix done"
-!
-! allocate eigenvalues, eigenvectors
-!
-!      write(*,*)"eigen allocation done"
-!
-!  solver for linear eigenmodes of gftm equations
-!
-      call gftm_eigensolver
-!      write(*,*)"eigensolver done"
-!
-!      initalize output to zero
-!
-      do j1=1,maxmodes
-        jmax(j1) = 0
-        gamma_out(j1) = 0.0
-        freq_out(j1) = 0.0
-        v_QL_out(j1) = 0.0
-        a_par_QL_out(j1) = 0.0
-        b_par_QL_out(j1) = 0.0
-        phi_bar_out(j1) = 0.0
-        a_par_bar_out(j1) = 0.0
-        b_par_bar_out(j1) = 0.0
-        v_bar_out(j1) = 0.0
-        do is=1,nsm
-          particle_QL_out(j1,is) = 0.0
-          energy_QL_out(j1,is) = 0.0
-          stress_par_QL_out(j1,is) = 0.0
-          stress_tor_QL_out(j1,is) = 0.0
-          exchange_QL_out(j1,is) = 0.0
-          N_QL_out(j1,is) = 0.0
-          T_QL_out(j1,is) = 0.0
-          U_QL_out(j1,is) = 0.0
-          Q_QL_out(j1,is) = 0.0
-          N_bar_out(j1,is) = 0.0
-          T_bar_out(j1,is) = 0.0
-          U_bar_out(j1,is) = 0.0
-          Q_bar_out(j1,is) = 0.0
-          Ns_Ts_phase_out(j1,is) = 0.0
-        enddo
-        ne_te_phase_out(j1) = 0.0
-      enddo
-!
-      if(ibranch_in.eq.0)then
-!       write(*,*)"nmodes_in=",nmodes_in
-      nmodes_out = nmodes_in
-!
-! sort the unstable modes into electron and ion frequencies
-      mi = 0
-      me = 0
-      do j1=1,ntot
-        if(ri(j1).gt.epsilon1)then
-         if(rr(j1).lt.0.0)then
-           mi = mi+1
-           di(mi)=j1
-         else
-           me = me+1
-           de(me)=j1
-         endif
-!          write(*,*)"debug sort",j1,rr(j1),ri(j1),me,mi
-        endif
-      enddo
-! find the most unstable mode for each branch
-      if(me.gt.0)then
-        zgamax = 0.0
-        do iroot=1,me
-         if(ri(de(iroot)).gt.zgamax)then
-           zgamax = ri(de(iroot))
-           jmax(1) = de(iroot)
-         endif
-        enddo
-        gamma_out(1)=ri(jmax(1))
-        freq_out(1)=rr(jmax(1))
-      endif
-      if(mi.gt.0)then
-        zgamax = 0.0
-        do iroot=1,mi
-          if(ri(di(iroot)).gt.zgamax)then
-           zgamax = ri(di(iroot))
-           jmax(2) = di(iroot)
-         endif
-        enddo
-        gamma_out(2)=ri(jmax(2))
-        freq_out(2)=rr(jmax(2))
-      endif
-!        write(*,*)"debug sort", ky
-!        write(*,*)"nmodes_out = ",nmodes_out,nmodes_in
-!        write(*,*)"me = ",me,"mi = ",mi
-!        write(*,*)"gamma_out=",gamma_out(1),gamma_out(2)
-!        write(*,*)"freq_out=",freq_out(1),freq_out(2)
-      endif ! ibranch_in .eq.0 
-      if(ibranch_in.eq.-1)then
-!
-!  find the top nmodes most unstable modes
-       CALL sort_eigenvalues(nmodes_in,jmax)
-        nmodes_out = 0
-         do j1=1,nmodes_in 
-          if(jmax(j1).ne.0)then
-            nmodes_out = nmodes_out + 1
-            gamma_out(j1)=ri(jmax(j1))
-            freq_out(j1)=rr(jmax(j1))
-          endif
-        enddo
-!       write(*,*)"gamma_out = ",gamma_out(1)," freq_out = ", freq_out(1)
-!      write(*,*)"debug jmax =",jmax(1),jmax(2)
-!      write(*,*)"debug nmodes_out = ",nmodes_out
-      endif ! ibranch_in .eq. -1
-!
-      if(alpha_quench_in.ne.0.0)then
-! apply quench rule
-        do j1=1,nmodes_in
-          gamma_out(j1) = get_gamma_net(gamma_out(j1))
-        enddo
-      elseif(vexb_shear_s.ne.0.0)then
-! use spectral shift model for second pass
-       do j1=1,nmodes_in
-          gamma_out(j1) = gamma_reference_kx0(j1)
-          freq_out(j1) = freq_reference_kx0(j1)
-        enddo
-      endif
-!      
-!  get the fluxes for the most unstable modes
-!
-         do imax=1,nmodes_out
-         if(jmax(imax).gt.0)then
-!  alpha/beta=-(frequency+xi*growthrate)
-           we = alpha(jmax(imax))/beta(jmax(imax))
-!          write(*,*)"eigenvalue=",we,jmax(imax)
-          if(iflux_in)then
-           he(:) = hetot(:,jmax(imax))
-          else
-            do i=1,ntot
-            he(i) = small
-            do j=1,ntot
-              emat(i,j) = we*bmat(i,j) - amat(i,j) + small*one(i,j)
-            enddo
-           enddo
-!  find the eigenvector he correponding to we eigenvalue
-          call zgesv(ntot,1,emat,ntot,ipive,he,ntot,info)
-
-          ! Check for clean exit from ZGESV
-!          write(*,*)" info = ",info
-!          write(*,*)" amat(1,1) = ",amat(1,1)," bmat(1,1) = ",bmat(1,1), "zmat(1,1) = ",zmat(1,1)
-          if (info /= 0)CALL gftm_error(1,"1st call to ZGESV failed in gftm_LS")
-!
-          endif  ! iflux_in
-! debug
-          go to 10
-          henorm = 0.0
-          do i=1,ntot
-            henorm = henorm + REAL(CONJG(he(i))*he(i))
-          enddo
-          henorm = SQRT(henorm)
-          write(*,*)" henorm = ",henorm
-          do i=1,ntot
-             he(i) = he(i)/henorm
-             write(*,*)i,"  he = ",he(i)
-           enddo
-           do i=1,ntot
-           testhe = 0.0
-           do j=1,ntot
-              testhe = testhe + (we*bmat(i,j) - amat(i,j))*he(j)
-           enddo
-            write(*,*)i,"  test he = ", testhe
-           enddo
-     10   continue
-!
-!  compute propagator gmatinv for the eigenvalue we
-!  separate in to species block diagonal form before inverting
-!
-         
-          do is=1,ns
-            do ip=1,nphase
-            do jp=1,nphase
-              gmatinv(is,ip,jp) = 0.0
-              i = ip + nphase*(is-1)
-              j = jp + nphase*(is-1)
-               gmat(ip,jp) = one(ip,jp)
-               zmat(ip,jp) = we*one(i,j) - mateq(i,j)
-!            write(*,*)i,j,"  zmat = ",zmat(i,j)
-            enddo
-            enddo
-            call zgesv(nphase,nphase,zmat,nphase,ipiv,gmat,nphase,info)
-! Check for clean exit from ZGESV
-            if (info /= 0)CALL gftm_error(1,"2nd call to ZGESV failed in gftm_LS")
-!
-            do ip=1,nphase
-            do jp=1,nphase
-              gmatinv(is,ip,jp) = gmat(ip,jp)
-            enddo
-            enddo
-          enddo  ! is
-! debug
-!          do i=1,ntot
-!          do j=1,ntot
-!            write(*,*)i,j,"  gmatinv = ",gmatinv(i,j)
-!          enddo
-!          enddo
-!
-!  compute the response matrix and QL weights for this eigenvalue
-!
-          call get_QL_weights
-!
-!  save the results for output
-!
-          wd_bar_out(imax)=wd_bar
-          b0_bar_out(imax)=b0_bar
-          modB_bar_out(imax)=modB_bar
-          v_QL_out(imax)=v_weight
-          a_par_QL_out(imax)=a_par_weight
-          b_par_QL_out(imax)=b_par_weight
-          kx_bar_out(imax)=kx_bar
-          kpar_bar_out(imax)=kpar_bar/(R_unit*q_unit*width_in)
-          do i=1,nbasis
-            do j=1,3
-             field_weight_out(imax,j,i)=field_weight_QL_out(j,i)
-            enddo
-          enddo
-!
-          do is=ns0,ns
-            particle_QL_out(imax,is)=flux_out(is,1)
-            energy_QL_out(imax,is)=taus(is)*(flux_out(is,2)/sqrt_two+flux_out(is,3)+1.5*flux_out(is,1))
-!            stress_par_QL_out(imax,is)=stress_par_weight(is)
-            stress_tor_QL_out(imax,is) = mass(is)*taus(is)*flux_out(is,4)
-            exchange_QL_out(imax,is) = delta_out(is)
-            N_QL_out(imax,is)=N_weight(is)
-            T_QL_out(imax,is)=T_weight(is)
-            U_QL_out(imax,is)=U_weight(is)
-            Q_QL_out(imax,is)=Q_weight(is)
-            Ns_Ts_phase_out(imax,is)=Ns_Ts_phase(is)
-          enddo
-          ne_te_phase_out(imax) = Ne_Te_phase
-          phi_bar_out(imax) = phi2_bar
-          a_par_bar_out(imax) = phi2_bar*a_par_QL_out(imax)
-          b_par_bar_out(imax) = phi2_bar*b_par_QL_out(imax)
-          do is=ns0,ns
-            N_bar_out(imax,is)=phi2_bar*N_QL_out(imax,is)
-            T_bar_out(imax,is)=phi2_bar*T_QL_out(imax,is)
-            U_bar_out(imax,is)=phi2_bar*U_QL_out(imax,is)
-            Q_bar_out(imax,is)=phi2_bar*Q_QL_out(imax,is)
-          enddo
-         endif
-        enddo !imax
-!
-!
-      END SUBROUTINE gftm_LS
-!
-!--------------------------------------------------------------
-!
-      REAL FUNCTION get_gamma_net(gp)
-!
-      USE gftm_global
-      USE gftm_species
-!
-      REAL,INTENT(IN) :: gp
-      REAL :: alpha_exb
-!
-      alpha_exb = 0.3
-      if(igeo.eq.1)alpha_exb=0.3*SQRT(kappa_loc)
-      get_gamma_net =  MAX(gp - ABS(alpha_exb*alpha_quench_in*vexb_shear_s),0.0)
-!
-      END FUNCTION get_gamma_net
-!
-!--------------------------------------------------------------
-!
-      REAL FUNCTION get_GAM_freq()
-!
-      USE gftm_global
-      USE gftm_species
-!
-      REAL :: elong=1.0
-!
-      if(igeo.eq.1)elong = kappa_loc
-!      get_GAM_freq = SQRT(3.5*taus(2)+2.0*taus(1))/R_unit
-      get_GAM_freq = (2.0/(1.0+elong))*SQRT(taus(2)+taus(1))/R_unit
-!
-      END FUNCTION get_GAM_freq
-!
-!--------------------------------------------------------------
-!
-!
-      SUBROUTINE sort_eigenvalues(nsorted,sorted_index)
-!
-      USE gftm_dimensions
-      USE gftm_eigen
-!
-      IMPLICIT NONE
-      INTEGER :: i, j, ngrow,imid, iend, it, nsorted
-      INTEGER :: sorted_index(maxmodes)
-      REAL,PARAMETER ::  epsilon1=1.0E-12
-!
-!  find all of the unstable modes and the most unstable
-!
-      ngrow = 0
-!      write(*,*)ntot,"eigenvalues"
-      do i=1,ntot
-!        growthrate(i)=0.0
-!        frequency(i)=0.0
-        grow_index(i)=0
-        if(ri(i).gt.epsilon1)then
-          ngrow = ngrow + 1
-          grow_index(ngrow) = i
-!          write(*,*)
-!     >    ngrow,grow_index(ngrow),ri(grow_index(ngrow))
-        endif 
-      enddo
-!
-      if(ngrow.le.1)go to 30
-!
-! put the unstable modes in ascending order by growthrate
-! using a heapsort algorithm 
-!
-      imid = ngrow/2 + 1
-      iend = ngrow
-!      write(*,*)"imid = ",imid,"iend = ",iend
- 10   continue
-        if(imid.gt.1)then
-          imid = imid-1
-          it = grow_index(imid)
-        else
-          it = grow_index(iend)
-          grow_index(iend) = grow_index(1)
-          iend = iend-1
-          if(iend.eq.1)then
-            grow_index(1)=it
-          do i=1,ngrow
-!           write(*,*)i,grow_index(i),ri(grow_index(i))
-          enddo
-            go to 30
-         endif
-        endif
-        i=imid
-        j = imid+imid
-!        write(*,*)"i = ",i,"j = ",j
- 20     if(j.le.iend)then
-          if(j.lt.iend)then
-           if(ri(grow_index(j)).gt.ri(grow_index(j+1)))j=j+1
-          endif
-          if(ri(it).gt.ri(grow_index(j)))then
-            grow_index(i)=grow_index(j)
-            i=j
-            j=j+j
-          else
-            j = iend+1
-          endif
-        go to 20
-        endif
-        grow_index(i)=it
-      go to 10
- 30   continue
-      do i=1,nsorted
-        sorted_index(i)=0
-        if(i.le.ngrow)sorted_index(i)=grow_index(i)
-      enddo
-! debug
-!      do i=1,ngrow
-!        growthrate(i)=ri(grow_index(i))
-!        frequency(i)=rr(grow_index(i))
-!      enddo
-!      do i=1,ngrow
-!      write(*,*)i,growthrate(i),frequency(i),grow_index(i)
-!      enddo
-!
-      END SUBROUTINE sort_eigenvalues
-!
-      SUBROUTINE get_QL_weights
-! **************************************************************
-!
-! compute the quasilinear weights for a single eigenmode
-! with eigenvector v. All of the QL weights are normalized to phi_norm
-!
-!
-!***************************************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-!      USE gftm_hermite
-      USE gftm_eigen
-      USE gftm_coeff
-      USE gftm_weight
-      USE gftm_sgrid
-      USE gftm_gyro_average
-      USE gftm_GFS
-! 
-      IMPLICIT NONE
-!
-      INTEGER :: ib,jb,is,iu,ie,k1,k2,kp
-      INTEGER :: i,j,k, ip,jp
-!
-      COMPLEX :: n(nsm,nb)
-      COMPLEX :: u_par(nsm,nb)
-      COMPLEX :: t_par(nsm,nb)
-      COMPLEX :: t_per(nsm,nb)
-      COMPLEX :: q_par(nsm,nb)
-      COMPLEX :: q_per(nsm,nb)
-      COMPLEX :: temp(nsm,nb)
-      COMPLEX :: stress_par(nsm,nb,3),stress_per(nsm,nb,3)
-      COMPLEX :: phi_wd_phi,wd_phi
-      COMPLEX :: phi_b0_phi,b0_phi
-      COMPLEX :: phi_modB_phi,modB_phi
-      COMPLEX :: phi_kx_phi,kx_phi
-      COMPLEX :: phi_kpar_phi,kpar_phi
-      REAL :: betae_psi,betae_sig
-      REAL :: phi_norm,psi_norm,sig_norm,vnorm
-      REAL :: epsilon1
-      REAL :: stress_correction,wp
-      REAL :: one
-!
-      epsilon1 = 1.E-12
-!
-!  compute the electromagnetic potentials
-!
-      betae_psi = 0.0
-      if(use_bper_in)betae_psi = betae_s
-      betae_sig = 0.0
-      if(use_bpar_in)betae_sig = betae_s
-      do ib=1,nbasis
-        phi(ib)=0.0
-        psi(ib)=0.0
-        sig(ib)=0.0
-        do k1=1,ntot
-          phi(ib) = phi(ib) + phib(ib,k1)*he(k1)
-          psi(ib) = psi(ib) + psib(ib,k1)*he(k1)
-          sig(ib) = sig(ib) + sigb(ib,k1)*he(k1)
-        enddo
-      enddo
-!
-!  compute phi_norm, psi_norm, sig_norm
-!
-      phi_norm = 0.0
-      psi_norm = 0.0
-      sig_norm = 0.0
-      do ib=1,nbasis
-        phi_norm = phi_norm + REAL(phi(ib)*CONJG(phi(ib)))
-        psi_norm = psi_norm + REAL(psi(ib)*CONJG(psi(ib)))
-        sig_norm = sig_norm + REAL(sig(ib)*CONJG(sig(ib)))
-      enddo
-      if(phi_norm.lt.epsilon1)phi_norm = epsilon1
-!      write(*,*)"phi_norm =",phi_norm
-!       write(*,*)" phinorm = ",phi_norm
-!       write(*,*)" psinorm = ",psi_norm
-!       write(*,*)" signorm = ",sig_norm
-!
-! save the field weights
-      do i=1,nbasis
-        field_weight_QL_out(1,i) = phi(i)/SQRT(phi_norm)
-        field_weight_QL_out(2,i) = psi(i)/SQRT(phi_norm)
-        field_weight_QL_out(3,i) = sig(i)/SQRT(phi_norm)
-!        write(*,*)i,"field_weight=",field_weight_QL_out(1,i),field_weight_QL_out(2,i),field_weight_QL_out(3,i)
-       enddo
-!
-! compute <phi|*|phi> averages
-      phi_wd_phi = 0.0
-      phi_b0_phi = 0.0
-      phi_modB_phi = 0.0
-      phi_kx_phi = 0.0
-      phi_kpar_phi = 0.0
-      do i=1,nbasis
-         wd_phi = 0.0
-         b0_phi = 0.0
-         modB_phi = 0.0
-         kx_phi = 0.0
-         kpar_phi = 0.0
-         do j=1,nbasis
-           wd_phi = wd_phi +ave_wdpar(i,j)*phi(j)
-           b0_phi = b0_phi +ave_b0(i,j)*phi(j)
-           modB_phi = modB_phi +ave_c_par_par(i,j)*phi(j)
-           kx_phi = kx_phi +ave_kx(i,j)*phi(j)
-           kpar_phi = kpar_phi +xi*ave_kpar(i,j)*phi(j)
-         enddo
-         phi_wd_phi = phi_wd_phi + CONJG(phi(i))*wd_phi
-         phi_b0_phi = phi_b0_phi + CONJG(phi(i))*b0_phi
-         phi_modB_phi = phi_modB_phi + CONJG(phi(i))*modB_phi
-         phi_kx_phi = phi_kx_phi + CONJG(phi(i))*kx_phi
-         phi_kpar_phi = phi_kpar_phi + CONJG(phi(i))*kpar_phi
-      enddo
-      wd_bar = REAL(phi_wd_phi)/phi_norm
-      b0_bar = REAL(phi_b0_phi)/phi_norm
-      modB_bar = ABS(REAL(phi_modB_phi)/phi_norm)
-      kx_bar = REAL(phi_kx_phi)/phi_norm
-      kpar_bar = REAL(phi_kpar_phi)/phi_norm
-!      write(*,*)"wd_bar = ",wd_bar
-!      write(*,*)"b0_bar = ",b0_bar
-!       write(*,*)"modB_bar = ",modB_bar
-!      write(*,*)"kx_bar = ",kx_bar
-!      write(*,*)"kpar_bar = ",kpar_bar
-!
-! fill the moments
-!
-      do is=1,ns
-      do ie=1,ne
-      do ib=1,nbasis
-        pe1j0phi(is,ie,ib)=0.0
-        pe1j0psi(is,ie,ib)=0.0
-        pe1j1sig(is,ie,ib)=0.0
-        pe2j0phi(is,ie,ib)=0.0
-        pe2j0psi(is,ie,ib)=0.0
-        pe2j1sig(is,ie,ib)=0.0
-        do jb=1,nbasis
-          pe1j0phi(is,ie,ib) = pe1j0phi(is,ie,ib) + mat_pe1j0s(is,ie,ib,jb)*phi(jb)
-          pe1j0psi(is,ie,ib) = pe1j0psi(is,ie,ib) + mat_pe1j0s(is,ie,ib,jb)*psi(jb)
-          pe1j1sig(is,ie,ib) = pe1j1sig(is,ie,ib) + mat_pe1j1s(is,ie,ib,jb)*sig(jb)
-          pe2j0phi(is,ie,ib) = pe2j0phi(is,ie,ib) + mat_pe2j0s(is,ie,ib,jb)*phi(jb)
-          pe2j0psi(is,ie,ib) = pe2j0psi(is,ie,ib) + mat_pe2j0s(is,ie,ib,jb)*psi(jb)
-          pe2j1sig(is,ie,ib) = pe2j1sig(is,ie,ib) + mat_pe2j1s(is,ie,ib,jb)*sig(jb)
-        enddo
-      enddo
-      enddo
-      enddo
-!
-! now summ the gyro-average Maxwell fields
-!
-     do is = 1,ns
-     do ie = 1,ne
-     do iu = 1,nu
-     do ib = 1,nbasis
-         kp = ib+nbasis*(iu-1)+nbasis*nu*(ie-1)
-         k1 = kp + nphase*(is-1)
-         hes(is,kp) = he(k1)
-         pwns(is,kp) = one(1,iu)*pe1j0phi(is,ie,ib)                             &
-               - vs(is)*one(2,iu)*pe1j0psi(is,ie,ib)                            &
-               + 2.0*(taus(is)/zs(is))*one(1,iu)*pe1j1sig(is,ie,ib)
-         pwtpars(is,kp) = one(3,iu)*pe1j0phi(is,ie,ib)                          &
-               - vs(is)*sqrt_two*matu(3,iu)*pe1j0psi(is,ie,ib)                  &
-               + 2.0*(taus(is)/zs(is))*one(3,iu)*pe1j1sig(is,ie,ib)
-         pwtpers(is,kp) = one(1,iu)*pe2j0phi(is,ie,ib)                          &
-               - vs(is)*one(2,iu)*pe2j0psi(is,ie,ib)                            &
-               + 2.0*(taus(is)/zs(is))*one(1,iu)*pe2j1sig(is,ie,ib)
-         pwps(is,kp) = one(2,iu)*pe1j0phi(is,ie,ib)                             &
-               - vs(is)*sqrt_two*matu(2,iu)*pe1j0psi(is,ie,ib)                  &
-               + 2.0*(taus(is)/zs(is))*one(2,iu)*pe1j1sig(is,ie,ib)
-     enddo
-     enddo
-     enddo
-     enddo
-     do is=1,ns
-     do ip=1,nphase
-       hwns(is,ip) = 0.0
-       hwtpars(is,ip) = 0.0
-       hwtpers(is,ip) = 0.0
-       hwes(is,ip) = 0.0
-       hwps(is,ip) = 0.0
-       do jp=1,nphase
-         hwns(is,ip) = hwns(is,ip) + gmatinv(is,ip,jp)*pwns(is,jp)
-         hwtpars(is,ip) = hwtpars(is,ip) + gmatinv(is,ip,jp)*pwtpars(is,jp)
-         hwtpers(is,ip) = hwtpers(is,ip) + gmatinv(is,ip,jp)*pwtpers(is,jp)
-         hwps(is,ip) = hwps(is,ip) + gmatinv(is,ip,jp)*pwps(is,jp)
-       enddo
-       hwes(is,ip) = hwns(is,ip)
-    enddo
-    enddo
-!
-! conjugates of field perterbation capital PSI for each species
-!
-      do is=1,ns
-        do kp = 1, nphase
-          PSIpu1pe1(is,kp) = pwns(is,kp)
-          PSIpu2pe1(is,kp) = pwps(is,kp)
-          PSIpu3pe1(is,kp) = pwtpars(is,kp)
-          PSIpu1pe2(is,kp) = pwtpers(is,kp)
-!          write(*,*)is,kp,"  phipu2pe1j0 = ",PHIpu2pe1j0(is,kp)
-        enddo
-      enddo
-!
-      do is = 1,ns
-        do j=1,4
-          rwn(is,j) = 0.0
-          rwp(is,j) = 0.0
-          rwtpar(is,j) = 0.0
-          rwtper(is,j) = 0.0
-          fluxe(is,j) = 0.0
-        enddo
-        do kp=1,nphase
-        rwn(is,1) = rwn(is,1) + PSIpu1pe1(is,kp)*CONJG(hwns(is,kp))
-        rwtpar(is,1) = rwtpar(is,1) + PSIpu1pe1(is,kp)*CONJG(hwtpars(is,kp))
-        rwtper(is,1) = rwtper(is,1) + PSIpu1pe1(is,kp)*CONJG(hwtpers(is,kp))
-        rwp(is,1) = rwp(is,1) + PSIpu1pe1(is,kp)*CONJG(hwps(is,kp))
-        fluxe(is,1) = fluxe(is,1) + PSIpu1pe1(is,kp)*CONJG(hes(is,kp))
-        rwn(is,2) = rwn(is,2) + PSIpu3pe1(is,kp)*CONJG(hwns(is,kp))
-        rwtpar(is,2) = rwtpar(is,2) + PSIpu3pe1(is,kp)*CONJG(hwtpars(is,kp))
-        rwtper(is,2) = rwtper(is,2) + PSIpu3pe1(is,kp)*CONJG(hwtpers(is,kp))
-        rwp(is,2) = rwp(is,2) + PSIpu3pe1(is,kp)*CONJG(hwps(is,kp))
-        fluxe(is,2) = fluxe(is,2) + PSIpu3pe1(is,kp)*CONJG(hes(is,kp))
-        rwn(is,3) = rwn(is,3) + PSIpu1pe2(is,kp)*CONJG(hwns(is,kp))
-        rwtpar(is,3) = rwtpar(is,3) + PSIpu1pe2(is,kp)*CONJG(hwtpars(is,kp))
-        rwtper(is,3) = rwtper(is,3) + PSIpu1pe2(is,kp)*CONJG(hwtpers(is,kp))
-        rwp(is,3) = rwp(is,3) + PSIpu1pe2(is,kp)*CONJG(hwps(is,kp))
-        fluxe(is,3) = fluxe(is,3) + PSIpu1pe2(is,kp)*CONJG(hes(is,kp))
-        rwn(is,4) = rwn(is,4) + PSIpu2pe1(is,kp)*hwns(is,kp)
-        rwtpar(is,4) = rwtpar(is,4) + PSIpu2pe1(is,kp)*CONJG(hwtpars(is,kp))
-        rwtper(is,4) = rwtper(is,4) + PSIpu2pe1(is,kp)*CONJG(hwtpers(is,kp))
-        rwp(is,4) = rwp(is,4) + PSIpu2pe1(is,kp)*CONJG(hwps(is,kp))
-        fluxe(is,4) = fluxe(is,4) + PSIpu2pe1(is,kp)*CONJG(hes(is,kp))
-        enddo
-      enddo
-!
-      do is = 1,ns  ! species index
-      do j = 1,4    ! gradient drive index
-        diff_out(is,j,1) = -as(is)*REAL(xi*ky*rwn(is,j))/phi_norm
-        diff_out(is,j,2) = -as(is)*REAL(xi*ky*rwtpar(is,j))/phi_norm
-        diff_out(is,j,3) = -as(is)*REAL(xi*ky*rwtper(is,j))/phi_norm
-        diff_out(is,j,4) = -as(is)*REAL(xi*ky*rwp(is,j))/phi_norm
-        conv_out(is,j) = -as(is)*REAL(xi*ky*we*rwn(is,j))/phi_norm
-        flux_out(is,j) = -as(is)*REAL(xi*ky*fluxe(is,j)/phi_norm)
-      enddo
-        delta_out(is) = -zs(is)*as(is)*REAL(we)*REAL(xi*fluxe(is,1))
-!        flux_out(is,1) = flux_out(is,1)      &
-!        -damp_sig_in*ABS(zs(1)/zs(is))*rlts(1)*diff_out(1,2,1)/sqrt_two
-      enddo
-!
-! debug
-!      write(*,*)"fluxe(1) = ",fluxe(1,1),fluxe(2,1)
-!      do is=1,ns
-!        write(*,*)is,"diff"
-!      do i=1,4
-!        write(*,*)(diff_out(is,i,j),j=1,4)
-!      enddo
-!        write(*,*)is,"conv"
-!        write(*,*)(conv_out(is,j),j=1,4)
-!        write(*,*)is,"flux"
-!        write(*,*)(flux_out(is,j),j=1,4)
-!      enddo
-! check summ of coefficients
-!       do is=1,ns
-!       do j=1,1
-!         write(*,*)is,j,"particle  flux = ",   &
-!         diff_out(is,j,1)*ky*rlns(is),(diff_out(is,j,2)/sqrt_two+diff_out(is,j,3))*ky*rlts(is) &
-!         !,diff_out(is,j,4)*ky*vpar_shear_s(is)/sqrt_two,conv_out(is,j)*zs(is)/taus(is),flux_out(is,j)
-!       enddo
-!       enddo
-!
-      END SUBROUTINE get_QL_weights
-!
-!    
-!***********************
-! start of get_wavefunction
-      SUBROUTINE get_wavefunction
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_sgrid
-!
-      IMPLICIT NONE
-!
-      INTEGER :: n,i,j,k,np,npi,j0,imax
-      REAL :: dx,hp0
-      REAL :: hp(nb,max_plot)
-      REAL :: xp(max_plot)
-!
-! set up the theta-grid
-! npi is the number of pi intervals for the plot from -npi Pi to +npi Pi
-     npi=9  !npi <= 9 limited by max_plot = 2*npi*ms/8+1
-     np = ms/8   ! number of points per 1/2 period = 16 for ms=12
-     if(igeo.eq.0)then
-       dx = REAL(npi)*2.0*pi/REAL(max_plot-1)
-       do i=1,max_plot
-         xp(i) = -REAL(npi)*pi + REAL(i-1)*dx
-         plot_angle_out(i) = xp(i)        
-       enddo
-     else
-! general geometry case 0<y<Ly one loop counterclockwise 
-! y is the the straight field line coordinant of the Hermite basis
-! t_s is the mapping of the original theta coordinate 0 < t_s < -2Pi with t_s(0)=0, t_s(ms)=-2 Pi
-! this will be used for plotting, Note that t_s has the opposite sign to y.
-       dx = 2.0*pi/(y(ms)*width_in)
-       j0 = npi*np+1 ! the index of the midpoint
-       xp(j0) = 0.0
-       plot_angle_out(j0) = 0.0
-       j = 0  ! j is the local index for one circuit poloidally
-       k = 0  ! counts the number of 2 pi  intervals
-       imax=np*npi
-       do i=1,imax
-           j = j+1
-           if(j.gt.2*np)then
-             j = j - 2*np
-             k = k + 1
-           endif
-           xp(j0+i) = (REAL(k)*y(ms) + y(4*j))*dx  ! remember y is positive 0 <= y <= Ly
-           xp(j0-i) = -(REAL(k+1)*y(ms) - y(ms-4*j))*dx ! ok for up/down assymetric cases
-           plot_angle_out(j0+i) = -(REAL(k)*t_s(ms) + t_s(4*j))  ! remember t_s is negative  0 <= t_s <= -2 Pi
-           plot_angle_out(j0-i) = REAL(k+1)*t_s(ms) - t_s(ms-4*j)
-       enddo
-     endif
- !     write(*,*)"t_s = ",(t_s(i),i=0,ms)
- !   do i=1,imax
- !     write(*,*)i,"xp=",xp(i),"tp=",plot_angle_out(i)
- !   enddo
-! compute the hermite polynomials on the theta-grid using recursion
-      hp0 = sqrt_two/pi**0.25
-      do i=1,max_plot
-       hp(1,i) = hp0*EXP(-xp(i)*xp(i)/2.0)
-       hp(2,i) = xp(i)*sqrt_two*hp0*EXP(-xp(i)*xp(i)/2.0)
-       if(nbasis.gt.2)then
-         do j=3,nbasis
-          hp(j,i) = xp(i)*SQRT(2.0/REAL(j-1))*hp(j-1,i) &
-           - SQRT(REAL(j-2)/REAL(j-1))*hp(j-2,i)
-         enddo
-       endif
-      enddo
-!      compute the fields on the theta-grid
-      do n=1,nmodes_out
-       do k=1,3
-!        write(*,*)"field_weight_out=",(field_weight_out(n,k,j),j=1,nbasis)
-        do i=1,max_plot
-         plot_field_out(n,k,i) = 0.0
-         if((k.eq.1).or.(k.eq.2.and.use_bper_in).or.(k.eq.3.and.use_bpar_in))then
-          do j=1,nbasis
-           plot_field_out(n,k,i) = plot_field_out(n,k,i) &
-           + field_weight_out(n,k,j)*hp(j,i)
-          enddo
-         endif
-        enddo
-       enddo
-      enddo
-!
-      END SUBROUTINE get_wavefunction
-!
diff --git a/gftm/src/gftm_TM.f90 b/gftm/src/gftm_TM.f90
deleted file mode 100644
index 33131b7f9..000000000
--- a/gftm/src/gftm_TM.f90
+++ /dev/null
@@ -1,428 +0,0 @@
-!-----------------------------------------------------------------
-!
-      SUBROUTINE gftm_TM
-!
-!  Main transport model subroutine.
-!  Calls linear gftm over a spectrum of ky's and computes spectral integrals of
-!  field, intensity and fluxes.
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_kyspectrum
-      IMPLICIT NONE
-!
-      INTEGER :: i,j,is,imax, jmax_mix
-      LOGICAL :: save_iflux, save_find_width
-      REAL :: dky
-      REAL :: phi_bar0,phi_bar1
-      REAl :: v_bar0,v_bar1
-      REAL :: dky0,dky1,ky0,ky1
-      REAL :: pflux0(nsm),eflux0(nsm)
-      REAL :: stress_par0(nsm),stress_tor0(nsm)
-      REAL :: exch0(nsm)
-      REAL :: nsum0(nsm),tsum0(nsm)
-      REAL :: pflux1(nsm),eflux1(nsm)
-      REAL :: stress_par1(nsm),stress_tor1(nsm)
-      REAL :: exch1(nsm)
-      REAL :: nsum1(nsm),tsum1(nsm)
-      REAL :: save_vexb_shear
-!
-      CALL gftm_startup
-!
-! initialize fluxes
-!
-      do is=1,ns
-        particle_flux_out(is) = 0.0
-        energy_flux_out(is) = 0.0
-        stress_par_out(is) = 0.0
-        stress_tor_out(is) = 0.0
-        exchange_out(is) = 0.0
-        pflux0(is) = 0.0
-        eflux0(is) = 0.0
-        stress_par0(is) = 0.0
-        stress_tor0(is) = 0.0
-        exch0(is) = 0.0
-        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     
-      do i=1,nky
-        width_out(i) = width_in ! needed for spectral shift model double pass
-      enddo
-!
-! compute the flux spectrum
-!
-!    write(*,*)"vexb_shear = ",vexb_shear_s
-    if(alpha_quench_in .eq. 0.0 .and. vexb_shear_s .ne. 0.0)then
-!      write(*,*)"spectral shift"
-!  spectral shift model double pass
-       save_vexb_shear = vexb_shear_s
-       save_find_width = find_width_in
-       save_iflux = iflux_in
-       iflux_in=.FALSE.     ! do not compute eigenvectors on first pass
-       vexb_shear_s = 0.0  ! do not use spectral shift on first pass
-       jmax_out = 0         ! ID for first pass
-       CALL get_bilinear_spectrum
-       eigenvalue_first_pass(:,:,:) = eigenvalue_spectrum_out(:,:,:)
-       vexb_shear_s = save_vexb_shear
-       find_width_in = .FALSE.
-       iflux_in = save_iflux
-       if(sat_rule_in.eq.0)jmax_out = 1   ! flag for second pass
-       CALL get_bilinear_spectrum
-!  reset eigenvalues to the values with vexb_shear=0.
-!  note ql weights are with vexb_shear
-       eigenvalue_spectrum_out(:,:,:) = eigenvalue_first_pass(:,:,:)
-       find_width_in = save_find_width
-      else
-        jmax_out = 0
-        CALL get_bilinear_spectrum
-      endif
-!
-! sum over ky spectrum
-!
-      iflux_in=.TRUE. 
-      dky0=0.0
-      ky0=0.0 
-      do i=1,nky
-        ky_s = ky_spectrum(i)
-        dky = dky_spectrum(i)
-        ky1=ky_s
-        if(i.eq.1)then
-          dky1=ky1
-        elseif(kygrid_model_in.ne.0)then
-            dky = LOG(ky1/ky0)/(ky1-ky0)
-            dky1 = ky1*(1.0 - ky0*dky)
-            dky0 = ky0*(ky1*dky - 1.0)
-        endif
-! backward comatiblily for UNITS=GYRO
-!        if(units_in.eq.'GYRO')then
-! this is an error in the original integrator
-!           dky0 = dky0*SQRT(taus_in(1)*mass_in(2))
-!           dky1 = dky1*SQRT(taus_in(1)*mass_in(2))
-!       endif
-!
-! compute the field integrals
-!
-        v_bar1 = 0.0
-        phi_bar1 = 0.0
-        do imax = 1,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=ns0,ns
-          nsum1(is) = 0.0
-          tsum1(is) = 0.0
-          do imax = 1,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=ns0,ns
-            pflux1(is) = 0.0
-            eflux1(is) = 0.0
-            stress_tor1(is) = 0.0
-            stress_par1(is) = 0.0
-            exch1(is) = 0.0
-            do imax = 1,nmodes_in
-              pflux1(is) = pflux1(is) + flux_spectrum_out(1,is,i,imax)
-              eflux1(is) = eflux1(is) + flux_spectrum_out(2,is,i,imax)
-              stress_tor1(is) = stress_tor1(is) + &
-                 flux_spectrum_out(3,is,i,imax)
-              stress_par1(is) = stress_par1(is) + &
-                 flux_spectrum_out(4,is,i,imax)
-              exch1(is) = exch1(is) + flux_spectrum_out(5,is,i,imax)
-            enddo !imax
-            particle_flux_out(is) = particle_flux_out(is) &
-              + dky0*pflux0(is) + dky1*pflux1(is)
-            energy_flux_out(is) = energy_flux_out(is) &
-              + dky0*eflux0(is) + dky1*eflux1(is)
-            stress_tor_out(is) = stress_tor_out(is) &
-              + dky0*stress_tor0(is) + dky1*stress_tor1(is)
-            stress_par_out(is) = stress_par_out(is) &
-              + dky0*stress_par0(is) + dky1*stress_par1(is)
-            exchange_out(is) = exchange_out(is) &
-              + dky0*exch0(is) + dky1*exch1(is)
-!            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(*,*)"stress_tor_out=",stress_tor_out(is)
-             pflux0(is) = pflux1(is)
-             eflux0(is) = eflux1(is)
-             stress_par0(is) = stress_par1(is)
-             stress_tor0(is) = stress_tor1(is)
-             exch0(is) = exch1(is)
-           if(ky_s.le.1.0)then
-             q_low_out(is) = energy_flux_out(is)
-           endif
-         enddo  ! is 
-!
-        ky0 = ky1
-      enddo  ! i
-!
-      CALL gftm_shutdown
-!
-      END SUBROUTINE gftm_TM
-!
-!-----------------------------------------------------------------
-!
-      SUBROUTINE get_bilinear_spectrum
-!
-! computes the bilinear fluctuation moments 
-! and saves them in flux_spectrum_out, intensity_spectrum_out
-! and field_spectrum_out
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_kyspectrum
-      USE gftm_xgrid
-      IMPLICIT NONE
-!
-      LOGICAL :: unstable
-      INTEGER :: i,j,k,is,imax,t
-      REAL :: save_width
-      REAL :: gmax,fmax
-      REAL :: phi_bar
-      REAL :: gamma_cutoff,reduce,rexp
-      REAL :: gamma_net_1
-      REAL :: pflux1,eflux1
-      REAL :: stress_tor1,stress_par1
-      REAL :: exch1, gamma_max
-!
-!
-! setup the ky-spectrum
-!
-!      if(new_kyspectrum)CALL get_ky_spectrum
-      CALL get_ky_spectrum
-!
-! initialize output arrays
-!
-      do i=1,nky
-       spectral_shift_out(i) = 0.0
-       ave_p0_spectrum_out(i) = 0.0
-       do k=1,nmodes_in
-        do t = 1,2
-          eigenvalue_spectrum_out(t,i,k) = 0.0
-        enddo
-        do t = 1,4
-          field_spectrum_out(t,i,k) = 0.0
-        enddo
-        do is=ns0,ns
-          do t=1,4
-            intensity_spectrum_out(t,is,i,k) = 0.0
-          enddo
-          do t=1,5
-            flux_spectrum_out(t,is,i,k) = 0.0
-          enddo
-          nsts_phase_spectrum_out(is,i,k) = 0.0
-        enddo ! is
-        ne_te_phase_spectrum_out(i,k)=0.0
-       enddo  !k
-      enddo  !i
-!
-! loop over ky spectrum
-!
-! save maximum width
-      save_width = width_in
-      iflux_in=.TRUE. 
-      gmax = 0.0
-      fmax=0.0
-      do i=1,nky
-        ky_s = ky_spectrum(i)
-!
-        new_width=.TRUE.
-!
-        if(new_eikonal_in)then
-          if(jmax_out.eq.0)then   ! first pass
-            if(find_width_in)then
-              CALL gftm_max
-            else
-              nbasis = nbasis_max_in
-              new_width = .TRUE.
-              CALL gftm_LS
-              gamma_nb_min_out = gamma_out(1)
-            endif
-          else   ! second pass
-              gamma_reference_kx0(:) = eigenvalue_first_pass(1,i,:)
-              freq_reference_kx0(:) = eigenvalue_first_pass(2,i,:)
-              width_in = width_out(i)
-              nbasis = nbasis_max_in
-              new_width=.TRUE.
-              CALL gftm_LS
-              gamma_nb_min_out = gamma_out(1)
-          endif
-          mask_save(i) = 1
-          if(gamma_out(1).eq.0.0)mask_save(i)=0
-!          write(*,*)i,"ky=",ky_s,mask_save(i),gamma_out(1)
-          gamma_nb_min_save(i) = gamma_nb_min_out
-          width_save(i) = width_in
-          ft_save(i) = ft
-          R_unit_save(i) = R_unit
-          q_unit_save(i) = q_unit
-          do j=1,nx
-            wdx_save(i,j) = wdx(j)
-            b0x_save(i,j) = b0x(j)
-            b2x_save(i,j) = b2x(j)
-            cx_par_par_save(i,j) = cx_par_par(j)
-            cx_tor_par_save(i,j) = cx_tor_par(j)
-            cx_tor_per_save(i,j) = cx_tor_per(j)
-            kxx_save(i,j) = kxx(j)
-          enddo
-        else
-          gamma_nb_min_out = gamma_nb_min_save(i)
-          width_in = width_save(i)
-          ft = ft_save(i)
-          R_unit = R_unit_save(i)
-          q_unit = q_unit_save(i)
-          do j=1,nx
-             wdx(j) = wdx_save(i,j)
-             b0x(j) = b0x_save(i,j)
-             b2x(j) = b2x_save(i,j)
-             cx_par_par(j) = cx_par_par_save(i,j)
-             cx_tor_par(j) = cx_tor_par_save(i,j)
-             cx_tor_per(j) = cx_tor_per_save(i,j)
-             kxx(j) = kxx_save(i,j)
-          enddo
-          if(mask_save(i).eq.1)then
-            CALL gftm_LS
-          else
-            gamma_out(1)=0.0
-          endif
-        endif
-!        write(*,*)i,"ky=",ky_s,"width=",width_in
-!        write(*,*)"nbasis=",nbasis_max_in,nbasis_min_in
-!        write(*,*)"ft=",ft,"R=",R_unit,"q=",q_unit
-!        write(*,*)"wdx=",wdx(1),"b0x=",b0x(1)
-!
-        unstable=.TRUE.
-        gamma_max = MAX(gamma_out(1),gamma_out(2)) ! this covers ibranch=-1,0
-        if(gamma_max.eq.0.0.or.gamma_nb_min_out.eq.0.0)unstable=.FALSE.      
-        gamma_net_1 = gamma_nb_min_out 
-!       gamma_cutoff = (0.1*ky_s/R_unit)*SQRT(taus(1)*mass(2))  ! scaled like gamma
-        gamma_cutoff = 0.1*ky_s/R_unit
-        rexp = 1.0
-        reduce = 1.0
-        if(nbasis_max_in.ne.nbasis_min_in)then
-          if(gamma_net_1.lt.gamma_out(1) &
-             .and.gamma_net_1.lt.gamma_cutoff)then
-          reduce = (gamma_net_1/gamma_cutoff)**rexp
-!            write(*,*)"phi reduced",ky_s,gamma_nb_min_out,gamma_out(1)
-          endif
-        endif
-        if(sat_rule_in.ge.1)reduce=1.0
-!
-!        width_out(i) = width_save(i)
-        width_out(i) = width_in
-        if(unstable)then
-! save the spectral shift of the radial wavenumber due to VEXB_SHEAR
-         spectral_shift_out(i) = kx0_e
-         ave_p0_spectrum_out(i) = ave_p0_out
-! save field_spectrum_out and eigenvalue_spectrum_out
-         do imax=1,nmodes_out
-           QL_field_spectrum_out(1,i,imax) = v_QL_out(imax)
-           QL_field_spectrum_out(2,i,imax) = 1.0
-           QL_field_spectrum_out(3,i,imax) = a_par_QL_out(imax)
-           QL_field_spectrum_out(4,i,imax) = b_par_QL_out(imax)
-           field_spectrum_out(1,i,imax) = reduce*v_bar_out(imax)
-           field_spectrum_out(2,i,imax) = reduce*phi_bar_out(imax)
-           field_spectrum_out(3,i,imax) = reduce*a_par_bar_out(imax)
-           field_spectrum_out(4,i,imax) = reduce*b_par_bar_out(imax)
-           eigenvalue_spectrum_out(1,i,imax)=gamma_out(imax)
-           eigenvalue_spectrum_out(2,i,imax)=freq_out(imax)
-           if(ky_s.le.1.0.and.gamma_out(imax).gt.gmax)then
-             gmax=gamma_out(imax)
-             fmax=freq_out(imax)
-           endif
-!          write(*,*)ky_s,width_in
-!          write(*,*)"modes",imax,phi_QL_out(imax)
-!          write(*,*)gamma_out(imax),freq_out(imax)
-         enddo
-! save intensity_spectrum_out
-         do is=ns0,ns
-          do imax=1,nmodes_out
-            QL_intensity_spectrum_out(1,is,i,imax) = N_QL_out(imax,is)
-            QL_intensity_spectrum_out(2,is,i,imax) = T_QL_out(imax,is)
-            QL_intensity_spectrum_out(3,is,i,imax) = U_QL_out(imax,is)
-            QL_intensity_spectrum_out(4,is,i,imax) = Q_QL_out(imax,is)
-            intensity_spectrum_out(1,is,i,imax) = n_bar_out(imax,is)
-            intensity_spectrum_out(2,is,i,imax) = t_bar_out(imax,is)
-            intensity_spectrum_out(3,is,i,imax) = u_bar_out(imax,is)
-            intensity_spectrum_out(4,is,i,imax) = q_bar_out(imax,is)
-           enddo !imax
-         enddo  ! is
-! save flux_spectrum_out 
-         do is=ns0,ns
-            do imax=1,nmodes_out
-              phi_bar = reduce*phi_bar_out(imax)
-              pflux1 = particle_QL_out(imax,is)
-              eflux1 = energy_QL_out(imax,is)
-              stress_tor1 = stress_tor_QL_out(imax,is)
-              stress_par1 = stress_par_QL_out(imax,is)
-              exch1 = exchange_QL_out(imax,is)
-              QL_flux_spectrum_out(1,is,i,imax) = pflux1
-              QL_flux_spectrum_out(2,is,i,imax) = eflux1
-              QL_flux_spectrum_out(3,is,i,imax) = stress_tor1
-              QL_flux_spectrum_out(4,is,i,imax) = stress_par1
-              QL_flux_spectrum_out(5,is,i,imax) = exch1
-              flux_spectrum_out(1,is,i,imax) = phi_bar*pflux1
-              flux_spectrum_out(2,is,i,imax) = phi_bar*eflux1
-              flux_spectrum_out(3,is,i,imax) = phi_bar*stress_tor1
-              flux_spectrum_out(4,is,i,imax) = phi_bar*stress_par1
-              flux_spectrum_out(5,is,i,imax) = phi_bar*exch1
-           enddo !imax
-         enddo  ! is
-! save ne_te crossphase
-         do imax=1,nmodes_out
-           ne_te_phase_spectrum_out(i,imax) = ne_te_phase_out(imax)
-         enddo  !imax
-! save ns_ts crossphase
-         do is=1,ns_in
-           do imax=1,nmodes_out
-             nsts_phase_spectrum_out(is,i,imax) = Ns_Ts_phase_out(imax,is)
-           enddo  !imax
-          enddo    ! is
-        endif !unstable .T.
-!
-! reset width to maximum if used gftm_max
-        if(find_width_in)width_in=save_width
-!
-      enddo  ! i 
-!
-! recompute spectrum using non-local in ky multiscale model
-     if(sat_rule_in .ge. 1) call get_multiscale_spectrum
-!
-      if(new_eikonal_in)eikonal_unsaved=.FALSE.
-      gamma_out(1) = gmax
-      freq_out(1) = fmax
-      new_eikonal_in = .TRUE.  ! reset default for next call to gftm_TM
-      
-      END SUBROUTINE get_bilinear_spectrum
-!
-!-------------------------------------------------------------------------------
-!
diff --git a/gftm/src/gftm_TM_mpi.f90 b/gftm/src/gftm_TM_mpi.f90
deleted file mode 100644
index e8bcfc5d3..000000000
--- a/gftm/src/gftm_TM_mpi.f90
+++ /dev/null
@@ -1,531 +0,0 @@
-!-----------------------------------------------------------------
-!
-      SUBROUTINE gftm_TM_mpi
-!
-!  Main transport model subroutine.
-!  Calls linear gftm over a spectrum of ky's and computes spectral integrals of
-!  field, intensity and fluxes.
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_kyspectrum
-      IMPLICIT NONE
-!
-      INTEGER :: i,j,is,imax, jmax_mix
-      LOGICAL :: save_iflux, save_find_width
-      REAL :: dky
-      REAL :: phi_bar0,phi_bar1
-      REAl :: v_bar0,v_bar1
-      REAL :: dky0,dky1,ky0,ky1
-      REAL :: pflux0(nsm),eflux0(nsm)
-      REAL :: stress_par0(nsm),stress_tor0(nsm)
-      REAL :: exch0(nsm)
-      REAL :: nsum0(nsm),tsum0(nsm)
-      REAL :: pflux1(nsm),eflux1(nsm)
-      REAL :: stress_par1(nsm),stress_tor1(nsm)
-      REAL :: exch1(nsm)
-      REAL :: nsum1(nsm),tsum1(nsm)
-      REAL :: save_vexb_shear
-!
-      CALL gftm_startup
-!
-! initialize fluxes
-!
-      do is=1,ns
-          particle_flux_out(is) = 0.0
-          energy_flux_out(is) = 0.0
-          stress_par_out(is) = 0.0
-          stress_tor_out(is) = 0.0
-          exchange_out(is) = 0.0
-          pflux0(is) = 0.0
-          eflux0(is) = 0.0
-          stress_par0(is) = 0.0
-          stress_tor0(is) = 0.0
-          exch0(is) = 0.0
-        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
-      do i=1,nky
-       width_out(i) = width_in ! needed for spectral shift model double pass
-      enddo
-!
-! compute the flux spectrum
-!
-    if(alpha_quench_in .eq. 0.0 .and. vexb_shear_s .ne.0.0)then
-!  spectral shift model double pass
-       save_vexb_shear = vexb_shear_s
-       save_find_width = find_width_in
-       save_iflux = iflux_in
-       iflux_in=.FALSE.     ! do not compute eigenvectors on first pass
-       vexb_shear_s = 0.0  ! do not use spectral shift on first pass
-       jmax_out = 0         ! ID for first pass
-       CALL get_bilinear_spectrum_mpi
-       eigenvalue_first_pass(:,:,:) = eigenvalue_spectrum_out(:,:,:)
-       vexb_shear_s = save_vexb_shear
-       find_width_in = .FALSE.
-       iflux_in = save_iflux
-       if(sat_rule_in.eq.0)jmax_out = 1   ! flag for second pass
-       CALL get_bilinear_spectrum_mpi
-!  reset eigenvalues to the values with vexb_shear=0.
-!  note ql weights are with vexb_shear
-       eigenvalue_spectrum_out(:,:,:) = eigenvalue_first_pass(:,:,:)
-       find_width_in = save_find_width
-      else
-        ! only one pass for alpha_quench_in .ne. 0.0 or vexb_shear_s .eq. 0.0
-        jmax_out = 0
-        CALL get_bilinear_spectrum_mpi
-      endif
-!
-! sum over ky spectrum
-!
-      iflux_in=.TRUE. 
-      dky0=0.0
-      ky0=0.0 
-      do i=1,nky
-        ky_s = ky_spectrum(i)
-        dky = dky_spectrum(i)
-        ky1=ky_s
-        if(i.eq.1)then
-          dky1=ky1
-        elseif(kygrid_model_in.ne.0)then
-            dky = LOG(ky1/ky0)/(ky1-ky0)
-            dky1 = ky1*(1.0 - ky0*dky)
-            dky0 = ky0*(ky1*dky - 1.0)
-        endif
-! backward comatiblily for UNITS=GYRO
-!        if(units_in.eq.'GYRO')then
-! this is an error in the original integrator
-!           dky0 = dky0*SQRT(taus_in(1)*mass_in(2))
-!           dky1 = dky1*SQRT(taus_in(1)*mass_in(2))
-!        endif
-!
-! compute the field integrals
-!
-        v_bar1 = 0.0
-        phi_bar1 = 0.0
-        do imax = 1,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=ns0,ns
-          nsum1(is) = 0.0
-          tsum1(is) = 0.0
-          do imax = 1,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=ns0,ns
-            pflux1(is) = 0.0
-            eflux1(is) = 0.0
-            stress_tor1(is) = 0.0
-            stress_par1(is) = 0.0
-            exch1(is) = 0.0
-            do imax = 1,nmodes_in
-              pflux1(is) = pflux1(is) + flux_spectrum_out(1,is,i,imax)
-              eflux1(is) = eflux1(is) + flux_spectrum_out(2,is,i,imax)
-              stress_tor1(is) = stress_tor1(is) + &
-                 flux_spectrum_out(3,is,i,imax)
-              stress_par1(is) = stress_par1(is) + &
-                 flux_spectrum_out(4,is,i,imax)
-              exch1(is) = exch1(is) + flux_spectrum_out(5,is,i,imax)
-            enddo !imax
-            particle_flux_out(is) = particle_flux_out(is) &
-              + dky0*pflux0(is) + dky1*pflux1(is)
-            energy_flux_out(is) = energy_flux_out(is) &
-              + dky0*eflux0(is) + dky1*eflux1(is)
-            stress_tor_out(is) = stress_tor_out(is) &
-              + dky0*stress_tor0(is) + dky1*stress_tor1(is)
-            stress_par_out(is) = stress_par_out(is) &
-              + dky0*stress_par0(is) + dky1*stress_par1(is)
-            exchange_out(is) = exchange_out(is) &
-              + dky0*exch0(is) + dky1*exch1(is)
-!            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(*,*)"stress_tor_out=",stress_tor_out(is,1)
-             pflux0(is) = pflux1(is)
-             eflux0(is) = eflux1(is)
-             stress_par0(is) = stress_par1(is)
-             stress_tor0(is) = stress_tor1(is)
-             exch0(is) = exch1(is)
-           if(ky_s.le.1.0)then
-             q_low_out(is) = energy_flux_out(is)
-           endif
-         enddo  ! is 
-!
-        ky0 = ky1
-      enddo  ! i
-!
-      CALL gftm_shutdown
-!
-      END SUBROUTINE gftm_TM_mpi
-!
-!-----------------------------------------------------------------
-!
-      SUBROUTINE get_bilinear_spectrum_mpi
-!
-! computes the bilinear fluctuation moments 
-! and saves them in flux_spectrum_out, intensity_spectrum_out
-! and field_spectrum_out
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_mpi
-      USE gftm_species
-      USE gftm_kyspectrum
-      USE gftm_xgrid
-      IMPLICIT NONE
-!
-      LOGICAL :: unstable
-      INTEGER :: i,j,k,is,imax,t
-      REAL :: save_width
-      REAL :: gmax,fmax
-      REAL :: phi_bar
-      REAL :: gamma_cutoff,reduce,rexp
-      REAL :: gamma_net_1
-      REAL :: pflux1,eflux1
-      REAL :: stress_tor1,stress_par1
-      REAL :: exch1, gamma_max
-      ! mpi
-      REAL :: ne_te_phase_spectrum_save(nkym,maxmodes)
-      REAL :: nsts_phase_spectrum_save(nsm,nkym,maxmodes)
-      REAL :: eigenvalue_spectrum_save(2,nkym,maxmodes)
-      REAL :: field_spectrum_save(4,nkym,maxmodes)
-      REAL :: QL_field_spectrum_save(4,nkym,maxmodes)
-      REAL :: intensity_spectrum_save(4,nsm,nkym,maxmodes)
-      REAL :: QL_intensity_spectrum_save(4,nsm,nkym,maxmodes)
-      REAL :: flux_spectrum_save(5,nsm,nkym,maxmodes)
-      REAL :: QL_flux_spectrum_save(5,nsm,nkym,maxmodes)
-      REAL :: spectral_shift_save(nkym)
-      REAL :: ave_p0_spectrum_save(nkym)
-      REAL :: width_out_save(nkym)
-      INTEGER :: ierr
-!
-!
-! setup the ky-spectrum
-!
-      CALL get_ky_spectrum
-!
-! initialize mpi buffers for output arrays 
-!
-      do i=1,nky
-       spectral_shift_save(i) = 0.0
-       ave_p0_spectrum_save(i) = 0.0
-       width_out_save(i)=0.0
-       do k=1,nmodes_in
-        do t = 1,2
-          eigenvalue_spectrum_save(t,i,k) = 0.0
-        enddo
-        do t=1,4
-          field_spectrum_save(t,i,k) = 0.0
-          QL_field_spectrum_save(t,i,k) = 0.0
-        enddo
-        do is=ns0,ns
-          do t=1,4
-            intensity_spectrum_save(t,is,i,k) = 0.0
-            QL_intensity_spectrum_save(t,is,i,k) = 0.0
-          enddo
-            do t=1,5
-              flux_spectrum_save(t,is,i,k) = 0.0
-              QL_flux_spectrum_save(t,is,i,k) = 0.0
-            enddo
-          nsts_phase_spectrum_save(is,i,k)=0.0
-        enddo ! is
-        ne_te_phase_spectrum_save(i,k)=0.0
-       enddo  !k
-      enddo  !i
-!
-! loop over ky spectrum
-!
-! save maximum width
-      save_width = width_in
-      iflux_in=.TRUE.
-      gmax = 0.0
-      fmax = 0.0
-      do i=1+iProcgftm,nky,nProcgftm
-        ky_s = ky_spectrum(i)
-!
-        new_width=.TRUE.
-!
-        if(new_eikonal_in)then
-          if(jmax_out.eq.0)then   ! first pass
-            if(find_width_in)then
-              CALL gftm_max
-            else
-              nbasis = nbasis_max_in
-              new_width = .TRUE.
-              CALL gftm_LS
-              gamma_nb_min_out = gamma_out(1)
-            endif
-          else   ! second pass
-            gamma_reference_kx0(:) = eigenvalue_first_pass(1,i,:)
-            freq_reference_kx0(:) = eigenvalue_first_pass(2,i,:)
-            width_in = width_out(i)
-            nbasis = nbasis_max_in
-            new_width=.TRUE.
-            CALL gftm_LS
-            gamma_nb_min_out = gamma_out(1)
-          endif
-          mask_save(i) = 1
-          if(gamma_out(1).eq.0.0)mask_save(i)=0
-!          write(*,*)i,"ky=",ky_s,mask_save(i),gamma_out(1)
-          gamma_nb_min_save(i) = gamma_nb_min_out
-          width_save(i) = width_in
-          ft_save(i) = ft
-          R_unit_save(i) = R_unit
-          q_unit_save(i) = q_unit
-          do j=1,nx
-            wdx_save(i,j) = wdx(j)
-            b0x_save(i,j) = b0x(j)
-            cx_par_par_save(i,j) = cx_par_par(j)
-            cx_tor_par_save(i,j) = cx_tor_par(j)
-            cx_tor_per_save(i,j) = cx_tor_per(j)
-            kxx_save(i,j) = kxx(j)
-          enddo
-        else
-          gamma_nb_min_out = gamma_nb_min_save(i)
-          width_in = width_save(i)
-          ft = ft_save(i)
-          R_unit = R_unit_save(i)
-          q_unit = q_unit_save(i)
-          do j=1,nx
-             wdx(j) = wdx_save(i,j)
-             b0x(j) = b0x_save(i,j)
-             cx_par_par(j) = cx_par_par_save(i,j)
-             cx_tor_par(j) = cx_tor_par_save(i,j)
-             cx_tor_per(j) = cx_tor_per_save(i,j)
-             kxx(j) = kxx_save(i,j)
-          enddo
-          if(mask_save(i).eq.1)then
-            CALL gftm_LS
-          else
-            gamma_out(1)=0.0
-          endif
-        endif
-!        write(*,*)i,"ky=",ky_s,"width=",width_in
-!        write(*,*)"nbasis=",nbasis_max_in,nbasis_min_in
-!        write(*,*)"ft=",ft,"R=",R_unit,"q=",q_unit
-!        write(*,*)"wdx=",wdx(1),"b0x=",b0x(1)
-!
-        unstable=.TRUE.
-        gamma_max = MAX(gamma_out(1),gamma_out(2)) ! this covers ibranch=-1,0
-        if(gamma_max.eq.0.0.or.gamma_nb_min_out.eq.0.0)unstable=.FALSE.      
-        gamma_net_1 = gamma_nb_min_out 
-!       gamma_cutoff = (0.1*ky_s/R_unit)*SQRT(taus(1)*mass(2))  ! scaled like gamma
-        gamma_cutoff = 0.1*ky_s/R_unit
-        rexp = 1.0
-        reduce = 1.0
-        if(nbasis_max_in.ne.nbasis_min_in)then
-          if(gamma_net_1.lt.gamma_out(1) &
-             .and.gamma_net_1.lt.gamma_cutoff)then
-          reduce = (gamma_net_1/gamma_cutoff)**rexp
-!            write(*,*)"phi reduced",ky_s,gamma_nb_min_out,gamma_out(1)
-          endif
-       endif
-       if(sat_rule_in.ge.1)reduce=1.0
-!
-       width_out_save(i) = width_in
-!
-       if(unstable)then
-! save the spectral shift of the radial wavenumber due to VEXB_SHEAR
-         spectral_shift_save(i) = kx0_e
-         ave_p0_spectrum_save(i) = ave_p0_out
-! save field_spectrum_out and eigenvalue_spectrum_out
-         do imax=1,nmodes_out
-           QL_field_spectrum_save(1,i,imax) = v_QL_out(imax)
-           QL_field_spectrum_save(2,i,imax) = 1.0
-           QL_field_spectrum_save(3,i,imax) = a_par_QL_out(imax)
-           QL_field_spectrum_save(4,i,imax) = b_par_QL_out(imax)
-           field_spectrum_save(1,i,imax) = reduce*v_bar_out(imax)
-           field_spectrum_save(2,i,imax) = reduce*phi_bar_out(imax)
-           field_spectrum_save(3,i,imax) = reduce*a_par_bar_out(imax)
-           field_spectrum_save(4,i,imax) = reduce*b_par_bar_out(imax)
-           eigenvalue_spectrum_save(1,i,imax)=gamma_out(imax)
-           eigenvalue_spectrum_save(2,i,imax)=freq_out(imax)
-           if(ky_s.le.1.0.and.gamma_out(imax).gt.gmax)then
-             gmax=gamma_out(imax)
-             fmax=freq_out(imax)
-           endif
-!          write(*,*)ky_s,width_in
-!          write(*,*)"modes",imax,phi_QL_out(imax)
-!          write(*,*)gamma_out(imax),freq_out(imax)
-         enddo
-! save intensity_spectrum_out
-         do is=ns0,ns
-          do imax=1,nmodes_out
-            QL_intensity_spectrum_save(1,is,i,imax) = N_QL_out(imax,is)
-            QL_intensity_spectrum_save(2,is,i,imax) = T_QL_out(imax,is)
-            QL_intensity_spectrum_save(3,is,i,imax) = U_QL_out(imax,is)
-            QL_intensity_spectrum_save(4,is,i,imax) = Q_QL_out(imax,is)
-            intensity_spectrum_save(1,is,i,imax) = N_bar_out(imax,is)
-            intensity_spectrum_save(2,is,i,imax) = T_bar_out(imax,is)
-            intensity_spectrum_save(3,is,i,imax) = U_bar_out(imax,is)
-            intensity_spectrum_save(4,is,i,imax) = Q_bar_out(imax,is)
-           enddo !imax
-         enddo  ! is
-! save flux_spectrum_out 
-         do is=ns0,ns
-            do imax=1,nmodes_out
-              phi_bar = reduce*phi_bar_out(imax)
-              pflux1 = particle_QL_out(imax,is)
-              eflux1 = energy_QL_out(imax,is)
-              stress_tor1 = stress_tor_QL_out(imax,is)
-              stress_par1 = stress_par_QL_out(imax,is)
-              exch1 = exchange_QL_out(imax,is)
-              QL_flux_spectrum_save(1,is,i,imax) = pflux1
-              QL_flux_spectrum_save(2,is,i,imax) = eflux1
-              QL_flux_spectrum_save(3,is,i,imax) = stress_tor1
-              QL_flux_spectrum_save(4,is,i,imax) = stress_par1
-              QL_flux_spectrum_save(5,is,i,imax) = exch1
-              flux_spectrum_save(1,is,i,imax) = phi_bar*pflux1
-              flux_spectrum_save(2,is,i,imax) = phi_bar*eflux1
-              flux_spectrum_save(3,is,i,imax) = phi_bar*stress_tor1
-              flux_spectrum_save(4,is,i,imax) = phi_bar*stress_par1
-              flux_spectrum_save(5,is,i,imax) = phi_bar*exch1
-            enddo !imax
-         enddo  ! is
-! save ne_te crossphase
-         do imax=1,nmodes_out
-           ne_te_phase_spectrum_save(i,imax) = ne_te_phase_out(imax)
-         enddo  !imax
-! save ns_ts crossphase
-         do is=1,ns_in
-           do imax=1,nmodes_out
-             nsts_phase_spectrum_save(is,i,imax) = Ns_Ts_phase_out(imax,is)
-           enddo  !imax
-          enddo    ! is
-
-        endif !unstable .T.
-!
-! reset width to maximum if used gftm_max
-        if(find_width_in)width_in=save_width
-!
-      enddo  ! i 
-!
-! collect and broadcast the results 
-      call MPI_BARRIER(iCommgftm,ierr)
-
-      call MPI_ALLREDUCE(ne_te_phase_spectrum_save   &
-                        ,ne_te_phase_spectrum_out    &
-                        ,nkym*maxmodes               &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-       call MPI_ALLREDUCE(nsts_phase_spectrum_save   &
-                        ,nsts_phase_spectrum_out     &
-                        ,nsm*nkym*maxmodes           &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(eigenvalue_spectrum_save    &
-                        ,eigenvalue_spectrum_out     &
-                        ,2*nkym*maxmodes             &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(field_spectrum_save         &
-                        ,field_spectrum_out          &
-                        ,4*nkym*maxmodes             &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(QL_field_spectrum_save      &
-                        ,QL_field_spectrum_out       &
-                        ,4*nkym*maxmodes             &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(intensity_spectrum_save     &
-                        ,intensity_spectrum_out      &
-                        ,4*nsm*nkym*maxmodes         &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(QL_intensity_spectrum_save  &
-                        ,QL_intensity_spectrum_out   &
-                        ,4*nsm*nkym*maxmodes         &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(flux_spectrum_save          &
-                        ,flux_spectrum_out           &
-                        ,5*nsm*nkym*maxmodes       &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(QL_flux_spectrum_save       &
-                        ,QL_flux_spectrum_out        &
-                        ,5*nsm*nkym*maxmodes       &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(spectral_shift_save         &
-                        ,spectral_shift_out          &
-                        ,nkym                        &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-      call MPI_ALLREDUCE(ave_p0_spectrum_save         &
-                        ,ave_p0_spectrum_out          &
-                        ,nkym                        &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-     call MPI_ALLREDUCE(width_out_save               &
-                        ,width_out                   &
-                        ,nkym                        &
-                        ,MPI_DOUBLE_PRECISION        &
-                        ,MPI_SUM                     &
-                        ,iCommgftm                   &
-                        ,ierr)
-
-      ! recompute spectrum using non-local in ky multiscale model
-      
-      if(sat_rule_in.ge.1)call get_multiscale_spectrum
-      
-      !
-      if(new_eikonal_in)eikonal_unsaved=.FALSE.
-      gamma_out(1) = gmax
-      freq_out(1) = fmax
-      new_eikonal_in = .TRUE.  ! reset default for next call to gftm_TM
-      
-      END SUBROUTINE get_bilinear_spectrum_mpi
diff --git a/gftm/src/gftm_allocate.f90 b/gftm/src/gftm_allocate.f90
deleted file mode 100644
index 5dc09dd1f..000000000
--- a/gftm/src/gftm_allocate.f90
+++ /dev/null
@@ -1,150 +0,0 @@
-      SUBROUTINE gftm_allocate
-!
-! allocate internal modules
-!
-!-------------------------------------------------
-      USE gftm_dimensions
-      USE gftm_species
-      USE gftm_coeff
-      USE gftm_GFS
-      USE gftm_eigen
-      IMPLICIT NONE
-!
-!      write(*,*)"allocate",ns,nbasis,nx,nky
-!
-!     MODULE gftm_species
-! 
-! species parameters
-!
-      ALLOCATE(ei_exch(ns,ns))
-      ALLOCATE(resist(ns,ns))
-      ALLOCATE(zs(ns))
-      ALLOCATE(mass(ns))
-      ALLOCATE(vs(ns))
-      ALLOCATE(fts(ns))
-      ALLOCATE(rlts(ns))
-      ALLOCATE(rlns(ns))
-      ALLOCATE(vpar_shear_s(ns))
-      ALLOCATE(as(ns))
-      ALLOCATE(taus(ns))
-      ALLOCATE(vpar_s(ns))         
-!
-!
-!-------------------------------------------------
-!
-!      MODULE gftm_coeff
-!
-! store the hermite basis matrix coefficients
-!
-!  ave_theta
-      ALLOCATE(ave_kx(nbasis,nbasis))
-      ALLOCATE(ave_c_tor_par(nbasis,nbasis))
-      ALLOCATE(ave_c_tor_per(nbasis,nbasis))
-      ALLOCATE(ave_c_par_par(nbasis,nbasis))
-      ALLOCATE(ave_wdpar(nbasis,nbasis))
-      ALLOCATE(ave_wdper(nbasis,nbasis))
-      ALLOCATE(ave_wb(nbasis,nbasis))
-      ALLOCATE(ave_gradB(nbasis,nbasis))
-      ALLOCATE(ave_Binv(nbasis,nbasis))
-      ALLOCATE(ave_b0(nbasis,nbasis))
-      ALLOCATE(ave_b0inv(nbasis,nbasis))
-      ALLOCATE(ave_kpar(nbasis,nbasis))
-      ALLOCATE(ave_modkpar(nbasis,nbasis))
-      ALLOCATE(ave_p0(nbasis,nbasis))
-      ALLOCATE(ave_p0inv(nbasis,nbasis))
-      ALLOCATE(ave_bp(nbasis,nbasis))
-      ALLOCATE(ave_bpinv(nbasis,nbasis))
-!-------------------------------------------------
-!
-!      MODULE gftm_GFS
-!
-! allocate gftm_GFS
-      ALLOCATE(zomega(ntot))
-      ALLOCATE(matmirror(nune,nune))
-      ALLOCATE(matu(nu,nu))
-      ALLOCATE(matuc(nu,nu))
-      ALLOCATE(matdu(nu,nu))
-      ALLOCATE(matuu(nu,nu))
-      ALLOCATE(mate(ne,ne))
-      ALLOCATE(matde(ne,ne))
-      ALLOCATE(phib(nbasis,ntot))
-      ALLOCATE(psib(nbasis,ntot))
-      ALLOCATE(sigb(nbasis,ntot))
-      ALLOCATE(pe1j0phib(ns,ne,nbasis,ntot))
-      ALLOCATE(pe1j0psib(ns,ne,nbasis,ntot))
-      ALLOCATE(pe1j1sigb(ns,ne,nbasis,ntot))
-      ALLOCATE(pe2j0phib(ns,ne,nbasis,ntot))
-      ALLOCATE(pe2j0psib(ns,ne,nbasis,ntot))
-      ALLOCATE(pe2j1sigb(ns,ne,nbasis,ntot))
-      ALLOCATE(pe1j0phi(ns,ne,nbasis))
-      ALLOCATE(pe1j0psi(ns,ne,nbasis))
-      ALLOCATE(pe1j1sig(ns,ne,nbasis))
-      ALLOCATE(pe2j0phi(ns,ne,nbasis))
-      ALLOCATE(pe2j0psi(ns,ne,nbasis))
-      ALLOCATE(pe2j1sig(ns,ne,nbasis))
-      ALLOCATE(pu1pe1PSI(ntot,ntot))
-      ALLOCATE(pu1pe2PSI(ntot,ntot))
-      ALLOCATE(pu3pe1PSI(ntot,ntot))
-      ALLOCATE(pu2pe1PSI(ntot,ntot))
-      ALLOCATE(p0invpe1j0s(ns,ne,nbasis,nbasis))
-      ALLOCATE(b0invpe1j0s(ns,ne,nbasis,nbasis))
-      ALLOCATE(mateq(ntot,ntot))
-      ALLOCATE(mats(ntot,ntot))
-      ALLOCATE(matb(ntot,ntot))
-!
-!   gftm_LS local
-      ALLOCATE(di(ntot))
-      ALLOCATE(de(ntot))
-      ALLOCATE(ipive(nphase))
-      ALLOCATE(ipiv(ntot))
-      ALLOCATE(emat(ntot,ntot))
-      ALLOCATE(zmat(nphase,nphase))
-      ALLOCATE(gmat(nphase,nphase))
-      ALLOCATE(gmatinv(ns,nphase,nphase))
-!   gftm_eigen module
-      ALLOCATE(grow_index(ntot))
-      ALLOCATE(fv1(ntot))
-      ALLOCATE(fv2(ntot))
-      ALLOCATE(fv3(ntot))
-      ALLOCATE(rr(ntot))
-      ALLOCATE(ri(ntot))
-      ALLOCATE(ar(ntot,ntot))
-      ALLOCATE(ai(ntot,ntot))
-      ALLOCATE(vr(ntot,ntot))
-      ALLOCATE(vi(ntot,ntot))
-      ALLOCATE(amat(ntot,ntot))
-      ALLOCATE(bmat(ntot,ntot))
-      ALLOCATE(he(ntot))
-      ALLOCATE(hetot(ntot,ntot))
-      ALLOCATE(alpha(ntot))
-      ALLOCATE(beta(ntot))
-!
-      ALLOCATE(phi(nbasis))
-      ALLOCATE(psi(nbasis))
-      ALLOCATE(sig(nbasis))
-      ALLOCATE(pwns(ns,nphase))
-      ALLOCATE(pwps(ns,nphase))
-      ALLOCATE(pwtpars(ns,nphase))
-      ALLOCATE(pwtpers(ns,nphase))
-      ALLOCATE(pwes(ns,nphase))
-      ALLOCATE(hes(ns,ntot))
-      ALLOCATE(hwns(ns,ntot))
-      ALLOCATE(hwps(ns,ntot))
-      ALLOCATE(hwtpars(ns,ntot))
-      ALLOCATE(hwtpers(ns,ntot))
-      ALLOCATE(hwes(ns,ntot))
-      ALLOCATE(PSIpu1pe1(ns,nphase))
-      ALLOCATE(PSIpu2pe1(ns,nphase))
-      ALLOCATE(PSIpu3pe1(ns,nphase))
-      ALLOCATE(PSIpu1pe2(ns,nphase))
-!
-      ALLOCATE(rwn(ns,5))
-      ALLOCATE(rwp(ns,5))
-      ALLOCATE(rwtpar(ns,5))
-      ALLOCATE(rwtper(ns,5))
-      ALLOCATE(rwe(ns,5))
-      ALLOCATE(fluxe(ns,5))
-!
-      END SUBROUTINE gftm_allocate
-!-----------------------------------------------------
-!
diff --git a/gftm/src/gftm_collision1.f90 b/gftm/src/gftm_collision1.f90
deleted file mode 100644
index 7de636f4a..000000000
--- a/gftm/src/gftm_collision1.f90
+++ /dev/null
@@ -1,8481 +0,0 @@
-       REAL FUNCTION collision1(ie,iu,je,ju)
-!**********************************************************************
-!     Pitch-angle scatter collision coefficients computed and written by
-!     Mathematica notebook TGLF-2.0-u-ep-collisions_J0.nb
-!***********************************************************************
-       IMPLICIT NONE
-       INTEGER,INTENT(IN) :: ie,iu,je,ju
-       INTEGER,PARAMETER ::  mu=13, me=7, mue = 91
-       INTEGER ::  iue,jue
-       REAL,DIMENSION(mue,mue) :: coll1
-!
-       data coll1(1,1:mue)  / &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
-        0.,    &
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-       / 
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-       / 
-       data coll1(89,1:mue)  / &
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-       / 
-       data coll1(90,1:mue)  / &
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-       / 
-       data coll1(91,1:mue)  / &
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-        2.291502977226854     &
-       / 
-!
-       iue = iu + mu*(ie-1)
-       jue = ju + mu*(je-1)
-       collision1 = coll1(iue,jue)
-       RETURN
-!
-       END FUNCTION collision1
diff --git a/gftm/src/gftm_collision2.f90 b/gftm/src/gftm_collision2.f90
deleted file mode 100644
index 034387759..000000000
--- a/gftm/src/gftm_collision2.f90
+++ /dev/null
@@ -1,8481 +0,0 @@
-       REAL FUNCTION collision2(ie,iu,je,ju)
-!**********************************************************************
-!     Pitch-angle scatter collision coefficients computed and written by
-!     Mathematica notebook TGLF-2.0-u-ep-collisions_J0.nb
-!***********************************************************************
-       IMPLICIT NONE
-       INTEGER,INTENT(IN) :: ie,iu,je,ju
-       INTEGER,PARAMETER ::  mu=13, me=7, mue = 91
-       INTEGER ::  iue,jue
-       REAL,DIMENSION(mue,mue) :: coll2
-!
-       data coll2(1,1:mue)  / &
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-       / 
-       data coll2(2,1:mue)  / &
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-       / 
-       data coll2(3,1:mue)  / &
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-        0.17919355788035318,    &
-        0.,    &
-        -0.27780136128421873,    &
-        0.,    &
-        0.21608156664925662,    &
-        0.,    &
-        0.1820702818222344,    &
-        -0.06089028690439591,    &
-        0.,    &
-        0.02307425946537478,    &
-        0.,    &
-        0.04328610355150886,    &
-        0.,    &
-        -0.19752955302828923,    &
-        0.,    &
-        0.48907296010293067,    &
-        0.,    &
-        -0.7262828001676065,    &
-        0.,    &
-        -0.30083535332232714,    &
-        0.07787143978202948,    &
-        0.,    &
-        -0.05941425529999833,    &
-        0.,    &
-        0.031670901633333415,    &
-        0.,    &
-        0.08170627639628947,    &
-        0.,    &
-        -0.5256439661607146,    &
-        0.,    &
-        1.9460302378918755,    &
-        0.,    &
-        -0.4548911638557911     &
-       / 
-       data coll2(90,1:mue)  / &
-        0.,    &
-        -0.02559605260791109,    &
-        0.,    &
-        0.026282906200965073,    &
-        0.,    &
-        -0.020137161547893356,    &
-        0.,    &
-        0.008994880354293855,    &
-        0.,    &
-        0.0049864922802953515,    &
-        0.,    &
-        -0.019166945709002903,    &
-        0.,    &
-        0.,    &
-        0.0317980473080155,    &
-        0.,    &
-        -0.04189962592795382,    &
-        0.,    &
-        0.04309526362385441,    &
-        0.,    &
-        -0.032900280613830546,    &
-        0.,    &
-        0.011357688592283921,    &
-        0.,    &
-        0.016588697731195756,    &
-        0.,    &
-        0.,    &
-        -0.03307633475215255,    &
-        0.,    &
-        0.05526092844411323,    &
-        0.,    &
-        -0.07276895650829829,    &
-        0.,    &
-        0.07480036769629805,    &
-        0.,    &
-        -0.049920739969820715,    &
-        0.,    &
-        -0.0021734720655985917,    &
-        0.,    &
-        0.,    &
-        0.027907551037671396,    &
-        0.,    &
-        -0.06056394666120468,    &
-        0.,    &
-        0.10277069814037532,    &
-        0.,    &
-        -0.13894972806156147,    &
-        0.,    &
-        0.1340257014380768,    &
-        0.,    &
-        -0.049245614553895534,    &
-        0.,    &
-        0.,    &
-        -0.016058367621099023,    &
-        0.,    &
-        0.05116453497248585,    &
-        0.,    &
-        -0.11708472126338165,    &
-        0.,    &
-        0.2141917833359912,    &
-        0.,    &
-        -0.29472397337667644,    &
-        0.,    &
-        0.21577497578636984,    &
-        0.,    &
-        0.,    &
-        -0.0007684721877012635,    &
-        0.,    &
-        -0.0233690027234843,    &
-        0.,    &
-        0.09166724281385541,    &
-        0.,    &
-        -0.25457538093905896,    &
-        0.,    &
-        0.5295655615627766,    &
-        0.,    &
-        -0.7268333293956591,    &
-        0.,    &
-        0.,    &
-        0.019003327390237246,    &
-        0.,    &
-        -0.017849534197011963,    &
-        0.,    &
-        -0.014942579786293209,    &
-        0.,    &
-        0.1320639275945723,    &
-        0.,    &
-        -0.5316769201308489,    &
-        0.,    &
-        2.014873543718608,    &
-        0.     &
-       / 
-       data coll2(91,1:mue)  / &
-        0.,    &
-        0.,    &
-        -0.0069660587203692614,    &
-        0.,    &
-        0.006458523234030622,    &
-        0.,    &
-        -0.000391234459016232,    &
-        0.,    &
-        -0.009963170048649772,    &
-        0.,    &
-        0.022693885652188328,    &
-        0.,    &
-        -0.03545989586200449,    &
-        0.004925747369714628,    &
-        0.,    &
-        0.013191576400572558,    &
-        0.,    &
-        -0.022406560881790938,    &
-        0.,    &
-        0.02271756163736427,    &
-        0.,    &
-        -0.012207640815177001,    &
-        0.,    &
-        -0.00848910358035937,    &
-        0.,    &
-        0.03452836276904233,    &
-        -0.013282875220852475,    &
-        0.,    &
-        -0.015095360722625628,    &
-        0.,    &
-        0.03812717260916543,    &
-        0.,    &
-        -0.05411867373913992,    &
-        0.,    &
-        0.053600358485709876,    &
-        0.,    &
-        -0.027548479571123607,    &
-        0.,    &
-        -0.022660734117765875,    &
-        0.02461385921924375,    &
-        0.,    &
-        0.010006772675751563,    &
-        0.,    &
-        -0.0471807203211938,    &
-        0.,    &
-        0.08931114262668416,    &
-        0.,    &
-        -0.12126710778102279,    &
-        0.,    &
-        0.11077023902907968,    &
-        0.,    &
-        -0.024282255024745115,    &
-        -0.0379132304851737,    &
-        0.,    &
-        0.0035936229121489305,    &
-        0.,    &
-        0.04071824805578217,    &
-        0.,    &
-        -0.11173740774393082,    &
-        0.,    &
-        0.2070239771855995,    &
-        0.,    &
-        -0.27418277179822326,    &
-        0.,    &
-        0.18364840758701334,    &
-        0.051732649182667956,    &
-        0.,    &
-        -0.024617934670459363,    &
-        0.,    &
-        -0.012303127150516957,    &
-        0.,    &
-        0.09257531247567385,    &
-        0.,    &
-        -0.26049928506836295,    &
-        0.,    &
-        0.6066585155203938,    &
-        0.,    &
-        -0.6944399687924068,    &
-        -0.06448011117754504,    &
-        0.,    &
-        0.04904143211024348,    &
-        0.,    &
-        -0.03708014971925877,    &
-        0.,    &
-        -0.000024045119062066078,    &
-        0.,    &
-        0.1849843580275774,    &
-        0.,    &
-        -0.4548911638557911,    &
-        0.,    &
-        2.047786457283461     &
-       / 
-!
-       iue = iu + mu*(ie-1)
-       jue = ju + mu*(je-1)
-       collision2 = coll2(iue,jue)
-       RETURN
-!
-       END FUNCTION collision2
diff --git a/gftm/src/gftm_deallocate.f90 b/gftm/src/gftm_deallocate.f90
deleted file mode 100644
index c33f74d7c..000000000
--- a/gftm/src/gftm_deallocate.f90
+++ /dev/null
@@ -1,157 +0,0 @@
-      SUBROUTINE gftm_deallocate
-!
-! deallocate internal modules
-!
-!-------------------------------------------------
-      USE gftm_species
-      USE gftm_coeff
-      USE gftm_GFS
-      USE gftm_eigen
-      IMPLICIT NONE
-!
-!
-!     MODULE gftm_species
-! 
-! species parameters
-!
-      IF(ALLOCATED(ei_exch))DEALLOCATE(ei_exch)
-      IF(ALLOCATED(resist))DEALLOCATE(resist)
-      IF(ALLOCATED(zs))DEALLOCATE(zs)
-      IF(ALLOCATED(mass))DEALLOCATE(mass)
-      IF(ALLOCATED(vs))DEALLOCATE(vs)
-      IF(ALLOCATED(fts))DEALLOCATE(fts)
-      IF(ALLOCATED(rlts))DEALLOCATE(rlts)
-      IF(ALLOCATED(rlns))DEALLOCATE(rlns)
-      IF(ALLOCATED(vpar_shear_s))DEALLOCATE(vpar_shear_s)
-      IF(ALLOCATED(as))DEALLOCATE(as)
-      IF(ALLOCATED(taus))DEALLOCATE(taus)
-      IF(ALLOCATED(vpar_s))DEALLOCATE(vpar_s)
-
-!      write(*,*)"deallocated species"
-!
-!
-!-------------------------------------------------
-!
-!      MODULE gftm_coeff
-!
-!  ave_theta
-!
-      IF(ALLOCATED(ave_kx))DEALLOCATE(ave_kx)
-      IF(ALLOCATED(ave_c_tor_par))DEALLOCATE(ave_c_tor_par)
-      IF(ALLOCATED(ave_c_tor_per))DEALLOCATE(ave_c_tor_per)
-      IF(ALLOCATED(ave_c_par_par))DEALLOCATE(ave_c_par_par)
-      IF(ALLOCATED(ave_wdpar))DEALLOCATE(ave_wdpar)
-      IF(ALLOCATED(ave_wdper))DEALLOCATE(ave_wdper)
-      IF(ALLOCATED(ave_wb))DEALLOCATE(ave_wb)
-      IF(ALLOCATED(ave_gradB))DEALLOCATE(ave_gradB)
-      IF(ALLOCATED(ave_Binv))DEALLOCATE(ave_Binv)
-      IF(ALLOCATED(ave_b0))DEALLOCATE(ave_b0)
-      IF(ALLOCATED(ave_b0inv))DEALLOCATE(ave_b0inv)
-      IF(ALLOCATED(ave_kpar))DEALLOCATE(ave_kpar)
-      IF(ALLOCATED(ave_modkpar))DEALLOCATE(ave_modkpar)
-      IF(ALLOCATED(ave_p0))DEALLOCATE(ave_p0)
-      IF(ALLOCATED(ave_p0inv))DEALLOCATE(ave_p0inv)
-      IF(ALLOCATED(ave_bp))DEALLOCATE(ave_bp)
-      IF(ALLOCATED(ave_bpinv))DEALLOCATE(ave_bpinv)
-!      write(*,*)"deallocated ave_theta"
-!
-!
-!-------------------------------------------------
-!
-!      MODULE gftm_GFS
-!
-! allocate gftm_GFS
-      IF(ALLOCATED(zomega))DEALLOCATE(zomega)
-      IF(ALLOCATED(matmirror))DEALLOCATE(matmirror)
-      IF(ALLOCATED(matu))DEALLOCATE(matu)
-      IF(ALLOCATED(matuc))DEALLOCATE(matuc)
-      IF(ALLOCATED(matdu))DEALLOCATE(matdu)
-      IF(ALLOCATED(matuu))DEALLOCATE(matuu)
-      IF(ALLOCATED(mate))DEALLOCATE(mate)
-      IF(ALLOCATED(matde))DEALLOCATE(matde)
-      IF(ALLOCATED(phib))DEALLOCATE(phib)
-      IF(ALLOCATED(psib))DEALLOCATE(psib)
-      IF(ALLOCATED(sigb))DEALLOCATE(sigb)
-      IF(ALLOCATED(pe1j0phi))DEALLOCATE(pe1j0phi)
-      IF(ALLOCATED(pe1j0psi))DEALLOCATE(pe1j0psi)
-      IF(ALLOCATED(pe1j1sig))DEALLOCATE(pe1j1sig)
-      IF(ALLOCATED(pe2j0phi))DEALLOCATE(pe2j0phi)
-      IF(ALLOCATED(pe2j0psi))DEALLOCATE(pe2j0psi)
-      IF(ALLOCATED(pe2j1sig))DEALLOCATE(pe2j1sig)
-      IF(ALLOCATED(pe1j0phib))DEALLOCATE(pe1j0phib)
-      IF(ALLOCATED(pe1j0psib))DEALLOCATE(pe1j0psib)
-      IF(ALLOCATED(pe1j1sigb))DEALLOCATE(pe1j1sigb)
-      IF(ALLOCATED(pe2j0phib))DEALLOCATE(pe2j0phib)
-      IF(ALLOCATED(pe2j0psib))DEALLOCATE(pe2j0psib)
-      IF(ALLOCATED(pe2j1sigb))DEALLOCATE(pe2j1sigb)
-      IF(ALLOCATED(pu1pe1PSI))DEALLOCATE(pu1pe1PSI)
-      IF(ALLOCATED(pu1pe2PSI))DEALLOCATE(pu1pe2PSI)
-      IF(ALLOCATED(pu3pe1PSI))DEALLOCATE(pu3pe1PSI)
-      IF(ALLOCATED(pu2pe1PSI))DEALLOCATE(pu2pe1PSI)
-      IF(ALLOCATED(p0invpe1j0s))DEALLOCATE(p0invpe1j0s)
-      IF(ALLOCATED(b0invpe1j0s))DEALLOCATE(b0invpe1j0s)
-      IF(ALLOCATED(mateq))DEALLOCATE(mateq)
-      IF(ALLOCATED(mats))DEALLOCATE(mats)
-      IF(ALLOCATED(matb))DEALLOCATE(matb)
-!
-! dealocate eigenvalues, eigenvectors
-!
-!    write(*,*)"ready to deallocate gftm_LS"
-!  gftm_LS local
-      if(ALLOCATED(di))DEALLOCATE(di)
-      if(ALLOCATED(de))DEALLOCATE(de)
-      if(ALLOCATED(ipive))DEALLOCATE(ipive)
-      if(ALLOCATED(ipiv))DEALLOCATE(ipiv)
-      if(ALLOCATED(emat))DEALLOCATE(emat)
-      if(ALLOCATED(zmat))DEALLOCATE(zmat)
-      if(ALLOCATED(gmat))DEALLOCATE(gmat)
-      if(ALLOCATED(gmatinv))DEALLOCATE(gmatinv)
-!      write(*,*)"deallocated gftm_LS local"
-!  gftm_eigen module
-      if(ALLOCATED(grow_index))DEALLOCATE(grow_index)
-      if(ALLOCATED(fv1))DEALLOCATE(fv1)
-      if(ALLOCATED(fv2))DEALLOCATE(fv2)
-      if(ALLOCATED(fv3))DEALLOCATE(fv3)
-      if(ALLOCATED(rr))DEALLOCATE(rr)
-      if(ALLOCATED(ri))DEALLOCATE(ri)
-      if(ALLOCATED(ar))DEALLOCATE(ar)
-      if(ALLOCATED(ai))DEALLOCATE(ai)
-      if(ALLOCATED(vr))DEALLOCATE(vr)
-      if(ALLOCATED(vi))DEALLOCATE(vi)
-      if(ALLOCATED(amat))DEALLOCATE(amat)
-      if(ALLOCATED(bmat))DEALLOCATE(bmat)
-      if(ALLOCATED(he))DEALLOCATE(he)
-      if(ALLOCATED(hetot))DEALLOCATE(hetot)
-      if(ALLOCATED(alpha))DEALLOCATE(alpha)
-      if(ALLOCATED(beta))DEALLOCATE(beta)
-!
-      if(ALLOCATED(phi))DEALLOCATE(phi)
-      if(ALLOCATED(psi))DEALLOCATE(psi)
-      if(ALLOCATED(sig))DEALLOCATE(sig)
-      if(ALLOCATED(pwns))DEALLOCATE(pwns)
-      if(ALLOCATED(pwps))DEALLOCATE(pwps)
-      if(ALLOCATED(pwtpars))DEALLOCATE(pwtpars)
-      if(ALLOCATED(pwtpers))DEALLOCATE(pwtpers)
-      if(ALLOCATED(pwes))DEALLOCATE(pwes)
-      if(ALLOCATED(hes))DEALLOCATE(hes)
-      if(ALLOCATED(hwns))DEALLOCATE(hwns)
-      if(ALLOCATED(hwps))DEALLOCATE(hwps)
-      if(ALLOCATED(hwtpars))DEALLOCATE(hwtpars)
-      if(ALLOCATED(hwtpers))DEALLOCATE(hwtpers)
-      if(ALLOCATED(hwes))DEALLOCATE(hwes)
-      if(ALLOCATED(PSIpu1pe1))DEALLOCATE(PSIpu1pe1)
-      if(ALLOCATED(PSIpu2pe1))DEALLOCATE(PSIpu2pe1)
-      if(ALLOCATED(PSIpu3pe1))DEALLOCATE(PSIpu3pe1)
-      if(ALLOCATED(PSIpu1pe2))DEALLOCATE(PSIpu1pe2)
-      if(ALLOCATED(rwn))DEALLOCATE(rwn)
-      if(ALLOCATED(rwp))DEALLOCATE(rwp)
-      if(ALLOCATED(rwtpar))DEALLOCATE(rwtpar)
-      if(ALLOCATED(rwtper))DEALLOCATE(rwtper)
-      if(ALLOCATED(rwe))DEALLOCATE(rwe)
-      if(ALLOCATED(fluxe))DEALLOCATE(fluxe)
-!
-!      write(*,*)"deallocated eigen"
-!
-      END SUBROUTINE gftm_deallocate
-!-----------------------------------------------------
-!
diff --git a/gftm/src/gftm_eigensolver.f90 b/gftm/src/gftm_eigensolver.f90
deleted file mode 100644
index d456644f3..000000000
--- a/gftm/src/gftm_eigensolver.f90
+++ /dev/null
@@ -1,452 +0,0 @@
-      SUBROUTINE gftm_eigensolver
-!*********************************************
-!
-!*********************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_eigen
-      USE gftm_coeff
-      USE gftm_GFS
-      USE gftm_sgrid
-      USE gftm_velocity_matrix
-      USE gftm_gyro_average
-!
-      IMPLICIT NONE
-!
-      CHARACTER(1) :: rightvectors
-      INTEGER :: i,j,i1,j1,i2,j2
-      INTEGER :: is,js
-      INTEGER :: iu,ju,ku
-      INTEGER :: ie,je
-      INTEGER :: iue,jue
-      INTEGER :: itot,jtot
-      INTEGER :: ib,jb,kb
-      REAL :: one
-      REAL :: k_par0, k_par1, w_d0, betapsi, betasig
-      REAL :: ndamp, tdamp, pdamp
-      REAL :: beta2, max_freq
-      REAL,DIMENSION(nsm) :: vpar, vpar_shear
-      REAL :: collision1, collision2
-      REAL :: nuei1,nuei2
-      REAL :: Rmax, Rmin
-      REAL :: nus(nsm)
-! zggev
-      INTEGER :: lwork, info, ifail
-      REAL,ALLOCATABLE,DIMENSION(:) :: rwork
-      COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: at,bt
-      COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: vleft,vright
-      COMPLEX,ALLOCATABLE,DIMENSION(:) :: work
-!
-      REAL,ALLOCATABLE,DIMENSION(:) :: hN, hT
-!
-!       write(*,*)"nu = ",nu," ne = ", ne," ntot = ",ntot
-!       write(*,*)"nbasis = ",nbasis," ns0 = ",ns0,"  ns = ", ns
-       ifail = 0
-       lwork = 8*ntot
-!       write(*,*)" nu = ",nu," ne = ",ne," nbasis = ",nbasis
-!       write(*,*)" ntot = ",ntot," nune = ",nune," nphase = ",nphase
-       ALLOCATE(rwork(lwork))
-       ALLOCATE(at(ntot,ntot))
-       ALLOCATE(bt(ntot,ntot))
-       ALLOCATE(vleft(ntot,ntot))
-       ALLOCATE(vright(ntot,ntot))
-       lwork = 33*ntot
-       ALLOCATE(work(lwork))
-       ALLOCATE(hN(nu*ne))
-       ALLOCATE(hT(nu*ne))
-!
-!       ndamp = damp_psi_in*B_geo0_out**2
-!       tdamp = damp_sig_in/B_geo0_out**2
-!       write(*,*)"Rmaj_input = ",Rmaj_input," rmin_input = ",rmin_input
-!       Rmin = 1.0 - rmin_input/Rmaj_input
-!       Rmax = 1.0 + rmin_input/Rmaj_input
-!          ndamp = 0.035*(Rmin/Rmax)**2
-!          tdamp = 0.21*(Rmin/Rmax)**2
-!         ndamp = 0.031*(Rmin/Rmax)**2
-!         tdamp = 0.153*(Rmin/Rmax)**2
-!
-! this closure works for ne >= 3 and nu = 2 ne -1
-!
-        tdamp = 0.514
-        ndamp = 0.0028
-        tdamp = 0.510
-        ndamp = 0.0028
-        tdamp = 0.639
-        ndamp = 0.005*rmin_input/Rmaj_input
-        tdamp = 0.65
-! NUEE/2
-        ndamp = 0.0057
-        tdamp = 0.69
-        pdamp = 0.69
-! 35
-        ndamp = 0.0028
-        tdamp = 0.648
-        pdamp = 1.0
-
-! changed to dz=  ds B/Bp and added p_prime
-       ndamp = 0.0016
-       tdamp = 0.651
-
- !       write(*,*)"Bmin/Bmax = ",Bmin/Bmax
- !      ndamp = damp_psi_in
- !      tdamp = damp_sig_in
-!       pdamp = etg_factor_in*pi/2.0
-!       pdamp = 0.0
-!       nus(1)=1.0
-!       nus(2)=SQRT(mass(1)/mass(2))*(taus(1)/taus(2))**1.5
-!       nus(2)=0.0
-!       if(igeo.gt.0)then
-!        ndamp = ndamp*(grad_r0_out/kappa_loc)**2
-!       endif
-!
-!       gcut = 0.06  ! for nu=5, ne=3
-!
-      k_par0 = sqrt_two/(R_unit*q_unit*width_in)
-!       write(*,*)"R_unit = ",R_unit," q_unit = ",q_unit," width_in = ",width_in
-       w_d0 = ky/R_unit
-       betapsi = 0.0
-       betasig = 0.0
-       if(use_bper_in)betapsi = betae_in
-       if(use_bpar_in)betasig = betae_in
-!
-! load velocity subspace matricies
-!
-     call get_velocity_matrix
-!     call get_mat_uparc
-     do iu = 1,nu
-       do ju = 1,nu
-         matuc(iu,ju)= mat_upar(iu,ju)
-         matu(iu,ju) = mat_upar(iu,ju)
-         matdu(iu,ju) = mat_dupar(iu,ju)
-       enddo
-       do ie = 1,ne
-         iue = iu + nu*(ie-1)
-         hN(iue) = 0.0
-         hT(iue) = 0.0
- !        if(ie.eq.ne)hT(ie) = 1.0
-         if(iu.eq.nu)hN(iu) = 1.0
-!         if(ie.eq.1)then
- !          if(iu.eq.1)hN(iu) = 1.0
-!           if(iu.eq.3)hT(iue) = SQRT(2.0/3.0)
-!           if(iu.eq.3)hT(iue) = COS(pdamp)
- !        endif
- !        if(ie.eq.2)then
-!           if(iu.eq.1)hT(iue) = SQRT(1.0/3.0)
-!           if(iu.eq.1)hT(iue) = SIN(pdamp)
-!         endif
-        enddo
-     enddo
-     do ie = 1,ne
-     do je = 1,ne
-       mate(ie,je) = mat_eper(ie,je)
-       matde(ie,je) = mat_deper(ie,je)
-     enddo
-     enddo
-!
-! add the matu "closure"
-!
-     matuc(nu-1,nu) = (1.0 - tdamp)*matu(nu-1,nu)
-     matuc(nu,nu-1) = (1.0 - tdamp)*matu(nu,nu-1)
-     matdu(nu-1,nu) = (1.0 + tdamp)*matdu(nu-1,nu)
-     matdu(nu,nu-1) = (1.0 + tdamp)*matdu(nu,nu-1)
-     do iu = 1,nu
-     do ju = 1,nu
-       matuu(iu,ju) = 0.0
-       do ku = 1,nu
-        matuu(iu,ju) =  matuu(iu,ju) + matu(iu,ku)*matu(ku,ju)
-       enddo
-     enddo
-     enddo
-!
-!  load the mirror force matrix
-!
-     do ie = 1,ne
-     do je = 1,ne
-     do iu = 1,nu
-     do ju = 1,nu
-       iue = iu + nu*(ie-1)
-       jue = ju + nu*(je-1)
-       matmirror(iue,jue) = matuc(iu,ju)*matde(ie,je)-0.5*mate(ie,je)*matdu(iu,ju) 
-!       write(*,*)"matmirror",iue,jue,matmirror(iue,jue)
-     enddo
-     enddo
-     enddo
-     enddo
-!
-! copmute the field operator dot products projectors
-!
-     do is = ns0,ns
-     do ie = 1,ne
-     do iu = 1,nu
-     do ib = 1,nbasis
-     do jb = 1,nbasis
-       p0invpe1j0s(is,ie,jb,ib) = 0.0
-       b0invpe1j0s(is,ie,jb,ib) = 0.0
-       do kb = 1,nbasis
-       p0invpe1j0s(is,ie,jb,ib) = p0invpe1j0s(is,ie,jb,ib) + ave_p0inv(ib,kb)*mat_pe1j0s(is,ie,kb,jb)
-       b0invpe1j0s(is,ie,jb,ib) = b0invpe1j0s(is,ie,jb,ib) + ave_b0inv(ib,kb)*mat_pe1j0s(is,ie,kb,jb)
-       enddo
-     enddo
-     enddo
-     enddo
-     enddo
-     enddo
-
-!
-! copmute the Maxwell field projectors
-!
-     do is = ns0,ns
-     do ie = 1,ne
-     do iu = 1,nu
-     do ib = 1,nbasis
-     do jb = 1,nbasis
-       itot = ib+nbasis*(iu-1)+nbasis*nu*(ie-1)+nbasis*nu*ne*(is-ns0)
-       phib(jb,itot) = as(is)*zs(is)*one(1,iu)*p0invpe1j0s(is,ie,jb,ib)
-       psib(jb,itot) = betapsi*0.5*as(is)*zs(is)*vs(is)*one(2,iu)*b0invpe1j0s(is,ie,jb,ib)
-       sigb(jb,itot)= -betasig*as(is)*taus(is)*one(1,iu)*mat_pe1j1s(is,ie,jb,ib)
-     enddo
-     enddo
-     enddo
-     enddo
-     enddo
-!
-! debug
-     go to 10
-     do itot=1,ntot
-       do ib=1,nbasis
-         write(*,*)itot,ib,"phib = ",phib(ib,itot)
-       enddo
-     enddo
-     do is = ns0,ns
-     do ie = 1,ne
-     do ib = 1,nbasis
-     do jb = 1,nbasis
-       write(*,*)is,ie,jb,ib,"pe2j0s = ",mat_pe2j0s(is,ie,jb,ib)
-     enddo
-     enddo
-     enddo
-     enddo
-     do ib = 1,nbasis
-     do jb = 1,nbasis
-       write(*,*)ib,jb,"ave_wdpar = ",ave_wdpar(ib,jb)
-       write(*,*)ib,jb,"ave_wdper = ",ave_wdper(ib,jb)
-     enddo
-     enddo
-     do ib = 1,nbasis
-     do jb = 1,nbasis
-       write(*,*)ib,jb,"ave_kpar = ",ave_kpar(ib,jb)
-       write(*,*)ib,jb," ave_gradb = ",ave_gradb(ib,jb)
-     enddo
-     enddo
-10   continue
-!
-! copmute the gyro-average Maxwell field projectors
-!
-! first do the dot product on the subspace without nu for speed
-!
-     do is = 1,ns
-     do ie = 1,ne
-     do ib = 1,nbasis
-     do jtot = 1,ntot
-       pe1j0phib(is,ie,ib,jtot) = 0.0
-       pe1j0psib(is,ie,ib,jtot) = 0.0
-       pe1j1sigb(is,ie,ib,jtot) = 0.0
-       pe2j0phib(is,ie,ib,jtot) = 0.0
-       pe2j0psib(is,ie,ib,jtot) = 0.0
-       pe2j1sigb(is,ie,ib,jtot) = 0.0
-       do jb = 1,nbasis
-         pe1j0phib(is,ie,ib,jtot) = pe1j0phib(is,ie,ib,jtot) + mat_pe1j0s(is,ie,ib,jb)*phib(jb,jtot)
-         pe1j0psib(is,ie,ib,jtot) = pe1j0psib(is,ie,ib,jtot) + mat_pe1j0s(is,ie,ib,jb)*psib(jb,jtot)
-         pe1j1sigb(is,ie,ib,jtot) = pe1j1sigb(is,ie,ib,jtot) + mat_pe1j1s(is,ie,ib,jb)*sigb(jb,jtot)
-         pe2j0phib(is,ie,ib,jtot) = pe2j0phib(is,ie,ib,jtot) + mat_pe2j0s(is,ie,ib,jb)*phib(jb,jtot)
-         pe2j0psib(is,ie,ib,jtot) = pe2j0psib(is,ie,ib,jtot) + mat_pe2j0s(is,ie,ib,jb)*psib(jb,jtot)
-         pe2j1sigb(is,ie,ib,jtot) = pe2j1sigb(is,ie,ib,jtot) + mat_pe2j1s(is,ie,ib,jb)*sigb(jb,jtot)
-       enddo
-     enddo
-     enddo
-     enddo
-     enddo
-!
-! now summ the gyro-average Maxwell fields
-!
-     do is = 1,ns
-     do ie = 1,ne
-     do iu = 1,nu
-     do ib = 1,nbasis
-       itot = ib+nbasis*(iu-1)+nbasis*nu*(ie-1)+nbasis*nu*ne*(is-1)
-       do jtot = 1,ntot
-         pu1pe1PSI(itot,jtot) = one(1,iu)*pe1j0phib(is,ie,ib,jtot)                    &
-               - vs(is)*one(2,iu)*pe1j0psib(is,ie,ib,jtot)                            &
-               + 2.0*(taus(is)/zs(is))*one(1,iu)*pe1j1sigb(is,ie,ib,jtot)
-         pu1pe2PSI(itot,jtot) = one(1,iu)*pe2j0phib(is,ie,ib,jtot)                    &
-               - vs(is)*one(2,iu)*pe2j0psib(is,ie,ib,jtot)                            &
-               + 2.0*(taus(is)/zs(is))*one(1,iu)*pe2j1sigb(is,ie,ib,jtot)
-         pu3pe1PSI(itot,jtot) = one(3,iu)*pe1j0phib(is,ie,ib,jtot)                    &
-               - vs(is)*sqrt_two*matu(3,iu)*pe1j0psib(is,ie,ib,jtot)                  &
-               + 2.0*(taus(is)/zs(is))*one(3,iu)*pe1j1sigb(is,ie,ib,jtot)
-         pu2pe1PSI(itot,jtot) = one(2,iu)*pe1j0phib(is,ie,ib,jtot)                    &
-               - vs(is)*sqrt_two*matu(2,iu)*pe1j0psib(is,ie,ib,jtot)                  &
-               + 2.0*(taus(is)/zs(is))*one(2,iu)*pe1j1sigb(is,ie,ib,jtot)
-       enddo
-     enddo
-     enddo
-     enddo
-     enddo
-!
-! compute mateq:  the linear GK operator tensor product
-!
-      do is = ns0,ns
-      do js = ns0,ns
-      do ie = 1,ne
-      do je = 1,ne
-      do iu = 1,nu
-      do ju = 1,nu
-      do ib = 1,nbasis
-      do jb = 1,nbasis
-        itot = ib+nbasis*(iu-1)+nbasis*nu*(ie-1)+nbasis*nu*ne*(is-ns0)
-        jtot = jb+nbasis*(ju-1)+nbasis*nu*(je-1)+nbasis*nu*ne*(js-ns0)
-        iue = iu + nu*(ie-1)
-        jue = ju + nu*(je-1)
-        mateq(itot,jtot) = (-xi*vs(is)*k_par0*(ave_kpar(ib,jb)*matuc(iu,ju)      &
-        + ndamp*one(ib,jb)*one(iu,ju))*one(ie,je)                                &
-        - 2.0*w_d0*(taus(is)/zs(is))*ave_wdpar(ib,jb)*matuu(iu,ju)*one(ie,je)    &
-        - w_d0*(taus(is)/zs(is))*ave_wdper(ib,jb)*mate(ie,je)*one(iu,ju)         &
-        - xi*vs(is)*k_par0*ave_wb(ib,jb)*matmirror(iue,jue)                      &
-        - xi*one(ib,jb)*xnue_in*one(is,1)*(zeff_in*collision1(ie,iu,je,ju)       &
-        + collision2(ie,iu,je,ju)))*one(is,js)
-!        if((is.eq.1.and.js.eq.1).and.(ib.eq.1.and.jb.eq.1))then
-!        nuei1 = collision1(ie,iu,je,ju)
-!        write(*,*)"collision1",iue,jue,nuei1
-!        nuei2 = collision2(ie,iu,je,ju)
-!        write(*,*)"collision2",iue,jue,nuei2
-!        endif
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-!
-! compute matb and mats:  the time derivative and source matricies
-!
-      do is = ns0,ns
-      do js = ns0,ns
-      do ie = 1,ne
-      do je = 1,ne
-      do iu = 1,nu
-      do ju = 1,nu
-      do ib = 1,nbasis
-      do jb = 1,nbasis
-        itot = ib+nbasis*(iu-1)+nbasis*nu*(ie-1)+nbasis*nu*ne*(is-ns0)
-        jtot = jb+nbasis*(ju-1)+nbasis*nu*(je-1)+nbasis*nu*ne*(js-ns0)
-        mats(itot,jtot) = (ky*rlns(is))*pu1pe1PSI(itot,jtot)                          &
-        + (ky*rlts(is)/sqrt_two)*pu3pe1PSI(itot,jtot)                                 &
-        + (ky*rlts(is))*pu1pe2PSI(itot,jtot)                                          &
-        + (ky*vpar_shear_s(is)/vs(is))*pu2pe1PSI(itot,jtot)                           
- !
-        matb(itot,jtot) = one(itot,jtot) - (zs(is)/taus(is))*pu1pe1PSI(itot,jtot)
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-      enddo
-!
-!
-!..find the eigenvalues and eigenvectors
-!
-!
-      lwork=33*ntot
-      rightvectors="N"
-      if(iflux_in)rightvectors="V"
-!      write(*,*)"iflux = ",iflux_in
-      do i=1,ntot
-      do j=1,ntot
-        at(i,j) = mateq(i,j) + mats(i,j)
-        bt(i,j) = matb(i,j)
-        amat(i,j) = at(i,j)
-        bmat(i,j) = bt(i,j)
-!        write(*,*)i,j," mateq = ",mateq(i,j)
-!        write(*,*)" matb = ",bt(i,j)
-!        write(*,*)" mats = ",mats(i,j)
-      enddo
-      enddo
-!      call system_clock(cpucount1)
-      call zggev("N",rightvectors,ntot,at,ntot,bt,ntot,    &
-                  alpha,beta,vleft,ntot,vright,ntot,work,lwork,rwork,info)
-!      call system_clock(cpucount2,cpurate)
-!      write(*,*)"cputime for zggev =",REAL(cpucount2-cpucount1)/REAL(cpurate)
-!      write(*,*)"jmax = ",jmax,alpha(jmax)/beta(jmax)
-!      write(*,*)"work(1)",work(1)
-       if (info /= 0) then
-         call gftm_error(1,"ERROR: ZGGEV failed in gftm_eigensolver.f90")
-       endif
-      if(iflux_in) then
-          hetot(:,:) = vright(:,:)
-      endif
-!      cputime2=MPI_WTIME()
-      do j1=1,ntot
-        beta2=REAL(CONJG(beta(j1))*beta(j1))
-        if(beta2.ne.0.0)then  ! zomega = -xi*(frequency+xi*growthrate)
-!          zomega(j1)=alpha(j1)*CONJG(beta(j1))/beta2
-          zomega(j1)=alpha(j1)/beta(j1)
-        else
-          zomega(j1)=0.0
-        endif
-!        write(*,*)j1,"zomega=",zomega(j1)
-        rr(j1) = REAL(zomega(j1))
-        ri(j1) = AIMAG(zomega(j1))
-! filter out numerical instabilities that sometimes occur 
-! with high mode frequency
-!        if(filter_in.gt.0.0)then
- !         if(rr(j1).gt.0.0.and.ABS(ri(j1)).gt.max_freq)then
- !           rr(j1)=-rr(j1)
-!            write(*,*)"filtered mode ",j1,rr(j1),ri(j1)
-!            write(*,*)"beta = ",beta(j1),"alpha =",alpha(j1)
-!            write(*,*)(vright(j1,j2),j2=1,ntot)
-!          endif
-!        endif
-        do j2=1,ntot
-!          if(iflux_in)then
-!            vr(j1,j2) = REAL(vright(j1,j2))
-!            vi(j1,j2) = AIMAG(vright(j1,j2))
-!          else
-            vr(j1,j2) = 0.0
-            vi(j1,j2) = 0.0
-!          endif
-        enddo
-      enddo
-!
-      if(ALLOCATED(rwork))DEALLOCATE(rwork)
-      if(ALLOCATED(at))DEALLOCATE(at)
-      if(ALLOCATED(bt))DEALLOCATE(bt)
-      if(ALLOCATED(vleft))DEALLOCATE(vleft)
-      if(ALLOCATED(vright))DEALLOCATE(vright)
-      if(ALLOCATED(work))DEALLOCATE(work)
-      if(ALLOCATED(hN))DEALLOCATE(hN)
-      if(ALLOCATED(hT))DEALLOCATE(hT)
- !
-      END SUBROUTINE gftm_eigensolver
-! ___________________________________________
-!
-      REAL FUNCTION one(i,j)
-!
-!     Kroneker delta function
-!
-      IMPLICIT NONE
-      INTEGER,INTENT(IN) :: i,j
-!
-      if(i.eq.j)then
-        one = 1.0
-      else
-        one = 0.0
-      endif
-      RETURN
-!
-      END FUNCTION ONE
-
diff --git a/gftm/src/gftm_error.f90 b/gftm/src/gftm_error.f90
deleted file mode 100644
index 12e606e6d..000000000
--- a/gftm/src/gftm_error.f90
+++ /dev/null
@@ -1,19 +0,0 @@
-  SUBROUTINE gftm_error(itype,error_message)
-  
-  ! error handeling routine for gftm
-  ! simply writes the error or informatin message
-  ! if itype = 1 the error was fatal so gftm is shutdown
-  
-  implicit none
-  integer, intent(in):: itype
-  character(len=*), intent(in) :: error_message
- 
-  print *,'ERROR: (gftm) ',error_message
-
-  if (itype == 1) then
-     CALL gftm_shutdown
-     STOP
-  endif
- 
-  END SUBROUTINE gftm_error   
-      
diff --git a/gftm/src/gftm_geometry.f90 b/gftm/src/gftm_geometry.f90
deleted file mode 100644
index 7f93e5db4..000000000
--- a/gftm/src/gftm_geometry.f90
+++ /dev/null
@@ -1,1734 +0,0 @@
-SUBROUTINE get_xgrid_functions
-  !***********************************************************
-  !
-  !***********************************************************
-  USE gftm_global
-  !
-  new_width=.FALSE.
-  ! write(*,*)"get_xgrid_functions"
-  !
-  if(igeo.eq.0)call xgrid_functions_sa
-  if(igeo.ne.0)call xgrid_functions_geo
-  !
-END SUBROUTINE get_xgrid_functions
-!
-!
-SUBROUTINE xgrid_functions_sa
-  !***********************************************************
-  !
-  !***********************************************************
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_hermite
-  USE gftm_xgrid
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  INTEGER :: i
-  REAL :: thz(nx)
-  REAL :: thx,thx1,dthx,dthx1,dthx2
-  REAL :: sn,cn,eps,Rx,Rx1,Rx2
-  REAL :: kyi,wE,a0,vexb_shear_kx0
-  REAL :: zx, zx1, zx2
-  REAL,PARAMETER :: small=0.00000001
-  !
-  ! debug
-  ! write(*,*)"shat_sa=",shat_sa,"alpha_sa=",alpha_sa
-  ! write(*,*)"theta0_sa=",theta0_sa,"xwell_sa=",xwell_sa
-  ! write(*,*)"rmin_sa=",rmin_sa,"rmaj_sa=",rmaj_sa
-  ! write(*,*)"q_sa=",q_sa,"b_model_sa=",b_model_sa
-  ! debug
-  !
-  ! set the units used by the gftm equations
-  R_unit=rmaj_sa
-  q_unit=q_sa
-  !
-  ! set global input values
-  !
-  rmin_input = rmin_sa
-  Rmaj_input = rmaj_sa
-  betae_s = betae_in
-  debye_s = debye_in
-  !
-  ! fill the x-grid eikonal function arrays wdx and b0x
-  eps = rmin_sa/rmaj_sa
-  !
-  ! generalized quench rule kx0 shift
-  !
-  !EPS2011 midplane_shear = shat_sa - alpha_sa
-  !EPS2011 sign_kx0=1.0
-  kx0 = 0.0
-  kx0_e = 0.0
-  if(alpha_quench_in.eq.0.0.and.gamma_reference_kx0(1).ne.0.0)then
-     vexb_shear_kx0 = alpha_e_in*vexb_shear_s
-     kyi = ky*vs(2)*mass(2)/ABS(zs(2))
-     if(units_in.eq.'GYRO')then
-       wE = MIN(kyi/0.3,1.0)*vexb_shear_kx0/gamma_reference_kx0(1)
-     ! write(*,*)"wE=",wE
-     else
-       wE=0.0
-     endif
-     kx0_e = -(0.36*vexb_shear_kx0/gamma_reference_kx0(1) + 0.38*wE*TANH((0.69*wE)**6))
-     if(sat_rule_in.ge.1)kx0_e = -(0.53*vexb_shear_kx0/gamma_reference_kx0(1) + 0.25*wE*TANH((0.69*wE)**6))
-     if(sat_rule_in.eq.2)then
-       if(ABS(kymax_out*vzf_out*vexb_shear_kx0).gt.small)then
-         kx0_e = -0.32*((ky/kymax_out)**0.3)*vexb_shear_kx0/(ky*vzf_out)
-       else
-         kx0_e = 0.0
-      endif
-!      write(*,*)"kx0_e = ",kx0_e,kymax_out,vzf_out
-endif
-
-     a0 = 1.3
-     if(sat_rule_in.eq.1)a0=1.45
-     if(sat_rule_in.eq.2)a0=1.6
-     if(ABS(kx0_e).gt.a0)kx0_e = a0*kx0_e/ABS(kx0_e)
-!     a0 = alpha_e_in*2.0
-!     if(alpha_e_in.ne.0.0)then
-!        kx0_e = a0*TANH(kx0_e/a0)
-!     else
-!        kx0_e = 0.0
-!     endif
-     !
-     ! EPS2011 kx0 = alpha_kx_e_in*0.19*TANH(vexb_shear_s*rmaj_sa/vs(2))*kyi*kyi/(kyi*kyi+0.001)/ky
-     ! EPS2011 kx0 = kx0 -alpha_kx_p_in*sign_Bt_in*TANH((0.26/3.0)*vpar_shear_in(2)*rmaj_sa/vs(2)) &
-     ! EPS2011 *(0.06*kyi*kyi/(kyi*kyi+0.001)+0.25*TANH((1.9*kyi)**3))/ky
-     ! EPS2011 if(midplane_shear.gt.0.0)then
-     ! EPS2011 kx0 = kx0 -alpha_kx_p_in*sign_Bt_in*TANH((0.26/3.0)*vpar_shear_in(2)*Rmaj_sa/vs(2)) &
-     ! EPS2011 *midplane_shear*(1.215*EXP(-(5.4*kyi)**3)+1.274**TANH((1.7*kyi)**2))/(1.0 + kyi**2)
-     ! EPS2011 else
-     ! EPS2011 kx0 = kx0 -alpha_kx_p_in*sign_Bt_in*TANH((0.26/3.0)*vpar_shear_in(2)*Rmaj_sa/vs(2)) &
-     ! EPS2011 *midplane_shear*(1.132**TANH((1.4*kyi)**2))/(1.0 + kyi**2)
-     ! EPS2011 endif
-     ! EPS2011 kx0 = kx0 + alpha_kx_n_in*0.19*TANH(vns_shear_in(2)*rmaj_sa/vs(2))*kyi*kyi/(kyi*kyi+0.001)/ky
-     ! EPS2011 kx0 = kx0 - alpha_kx_t_in*0.19*TANH(vts_shear_in(2)*rmaj_sa/vs(2))*kyi*kyi/(kyi*kyi+0.001)/ky
-     ! EPS2011 if(kx0.lt.0.0)sign_kx0=-1.0
-     kx0 = sign_Bt_in*kx0_e ! this is here to cancel the sign_Bt_in factor in kxx below
-  endif
-!
-! map to zx
-!
-  dthx1 = pi/32.0
-  dthx2 = pi/1024.0
-  thx = 0.0
-  zx2 = 0.0
-  thz(nxgrid_in) = 0.0
-  do i=nxgrid_in+1,nx
-     zx = width_in*x(i)
-     zx1 = zx2
-     do while(zx2 .le. zx)  ! find crossing with course grid
-      thx = thx + dthx1
-      zx2 = thx + eps*sin(thx)
-     enddo
-     thx = thx-dthx1        ! go back one grid
-     zx1 = thx + eps*sin(thx)
-     zx2 = zx1
-     do while(zx2 .le. zx)  ! refine crossing with fine grid
-       thx = thx + dthx2
-       zx2 = thx + eps*sin(thx)
-     enddo
-     thx1 = thx-dthx2
-     zx1 = thx1 + eps*sin(thx1)
-!     write(*,*)i," zx1 = ",zx1," zx = ",zx,"  zx2 = ",zx2
-     thz(i) = thx1 + dthx2*(zx2-zx)/(zx2-zx1)  ! interpolate to final crossing point
-     thz(2*nxgrid_in-i) = -thz(i)
-   enddo
-   do i=1,nx
-!     write(*,*)"map",i,width_in*x(i),thz(i)
-     thx = thz(i)
-     sn = sin(thx)
-     cn = cos(thx)
-     Rx = 1.0 + eps*cn
-     Bx(i) = 1.0/Rx
-     kxx(i) = -shat_sa*(thx-theta0_sa) + alpha_sa*sn - kx0
-     kxx(i) = sign_Bt_in*kxx(i)
-     ! wdx(i) = -xwell_sa*MIN(1.0,alpha_sa)+ &
-     ! cn+sn*(shat_sa*(thx-theta0_sa) - alpha_sa*sn)
-     ! wdx(i) = -xwell_sa*MIN(1.0,alpha_sa)+ cn - sn*kxx(i)
-     wdx(i) = cn - sn*kxx(i)
-     wbx(i) = width_in*eps*sn/Rx
-     ! b0x(i) = 1.0+(shat_sa*(thx-theta0_sa) - alpha_sa*sn)**2
-     b0x(i) = 1.0+(kxx(i))**2
-     b2x(i) = 1.0
-     wdpx(i) = 0.0   ! not used for s-alpha
-     if(b_model_sa.eq.1)then
-        ! put B dependence into k_per**2
-        b2x(i) = Bx(i)**2
-     endif
-     if(b_model_sa.eq.2)then
-        ! put 1/R(theta) factor into wd
-        wdx(i) = wdx(i)/Rx
-        ! put B dependence into k_per**2
-        b2x(i) = Bx(i)**2
-     endif
-     ! debug
-     ! write(*,*)i," b2x = ",b2x(i)
-     !
-     ! momentum equation stress projection coefficients
-     !
-     cx_tor_par(i) = rmaj_sa*Rx*sign_Bt_in
-     cx_tor_per(i) = -rmin_sa/q_sa
-     cx_par_par(i) = Bx(i)
-  enddo
-  ! compute the flux surface averages
-  !
-  B2_ave_out = 0.0
-  R2_ave_out = 0.0
-  RBt_ave_out = rmaj_sa
-  B_ave_out = 0.0
-  Bt_ave_out = 0.0
-  dthx = pi_2/REAL(2*nx)
-  thx = 0.0
-  do i=1,2*nx
-     Rx1 = 1.0 + eps*COS(thx)
-     thx = thx + dthx
-     Rx2 = 1.0 + eps*COS(thx)
-     R2_ave_out = R2_ave_out + dthx*(Rx1**2 + Rx2**2)/2.0
-     B2_ave_out = B2_ave_out + dthx*(0.5/Rx1**2 + 0.5/Rx2**2)
-     B_ave_out = B_ave_out + dthx*(0.5/Rx1 +0.5/Rx2)
-     Bt_ave_out = Bt_ave_out + dthx*(0.5*Rx1 + 0.5*Rx2)
-  enddo
-  R2_ave_out = (R2_ave_out*rmaj_sa**2)/pi_2
-  B2_ave_out = B2_ave_out/pi_2
-  B_ave_out = B_ave_out/pi_2
-  Bt_ave_out = Bt_ave_out/pi_2
-  Grad_r_ave_out = 1.0
-  kx_geo0_out = 1.0
-  SAT_geo0_out = 1.0
-  SAT_geo1_out = 1.0
-  SAT_geo2_out = 1.0
-  grad_r0_out = 1.0
-  !
-  ! poloidal magnetic field at outboard midplane
-  !
-  Bp0_out = rmin_sa/(q_sa*(rmaj_sa+rmin_sa))
-  Bt0_out = 1.0/Rmaj_input
-  B_geo0_out = Bt0_out
-  !
-END SUBROUTINE xgrid_functions_sa
-!
-SUBROUTINE xgrid_functions_geo
-  !******************************************************************************!************************
-  !
-  ! PURPOSE: compute the geometric coefficients on the x-grid
-  !
-  !
-  !******************************************************************************!************************
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_hermite
-  USE gftm_xgrid
-  USE gftm_sgrid
-  IMPLICIT NONE
-  !
-  INTEGER :: i,m
-  INTEGER :: m1,m2
-  REAL :: y_x
-  REAL :: Ly
-  REAL :: thx
-  REAL :: sign_theta,loops
-  REAL :: dkxky1,dkxky2
-  REAL :: wd1,wd2,wdp1,wdp2,wb1,wb2
-  REAL :: b1,b2
-  REAL :: y1,y2
-  REAL :: kxx1,kxx2
-  REAL :: cxtorper1,cxtorper2
-  REAL :: B2x1,B2x2,R2x1,R2x2,norm_ave,dlp
-  REAL :: kyi
-  REAL :: wE,wd0,a0,vexb_shear_kx0
-  REAL :: kykx_geo_ave
-  REAL,PARAMETER :: small=0.00000001
-  !
-  !
-  ! find length along magnetic field y
-  !
-  y(0)=0.0
-  ! pk_geo = Bp/B = ds/dy
-  do m=1,ms
-     y(m) = y(m-1)+s_p(m)*ds*2.0/(pk_geo(m)+pk_geo(m-1))
-  enddo
-  ! set the global units
-  Ly=y(ms)
-  ! R_unit = Rmaj_s*b_geo(0)/(qrat_geo(0)*(costheta_geo(0)+costheta_p_geo(0)))
-!  R_unit = Rmaj_s*b_geo(0)/(qrat_geo(0)*costheta_geo(0))
-  R_unit = Rmaj_s
-  q_unit = Ly/(pi_2*R_unit)
-  ! midplane effective shear: reduces to s-alpha in shifted circle
-  ! note: S_prime(0)=0.0, S_prime(ms)=-2 pi q_prime, y(0)=0.0, y(ms)=Ly
-  ! midplane shear is average of left and right y-derivatives at midplane for general geometry
-  midplane_shear = -(Ly/pi_2)*((rmin_s/q_s)**2) &
-       *0.5*(S_prime(1)/y(1)+(S_prime(ms)-S_prime(ms-1))/(y(ms)-y(ms-1)))
-  ! write(*,*)"midplane_shear = ",midplane_shear
-  midplane_shear = midplane_shear + 0.11
-  ! save f for output
-  RBt_ave_out = f/B_unit
-  !
-  ! write(*,*)"qrat_geo(0)=",qrat_geo(0),"b_geo(0)=",b_geo(0)
-  ! write(*,*)"costheta_geo(0)=",costheta_geo(0)
-  ! write(*,*)"sintheta_geo(0)=",sintheta_geo(0)
-  ! write(*,*)"Ly = ",Ly,"R_unit = ",R_unit,"Rmaj_s =",Rmaj_s
-  ! write(*,*)"q_unit=",q_unit
-  ! open(2,file='y_s.dat')
-  ! do m=0,ms
-  ! write(2,*)m,pi_2*y(m)/Ly
-  ! enddo
-  ! close(2)
-  !
-  ! generalized quench rule kx0 shift
-  !
-  kx0 = kx0_loc/ky ! note that kx0 is kx/ky
-  kx0_e=0.0
-  kx0_p=0.0
-  !EPS2011 sign_kx0=1.0
-  if(alpha_quench_in.eq.0.0.and.gamma_reference_kx0(1).ne.0.0)then
-     vexb_shear_kx0 = alpha_e_in*vexb_shear_s
-     kyi = ky*vs(2)*mass(2)/ABS(zs(2))
-     wE=0.0
-     wd0 = ABS(ky/Rmaj_s)
-     if(units_in.eq.'GYRO')then
-       kx0_factor = ABS(b_geo(0)/qrat_geo(0)**2)
-       kx0_factor = 1.0+0.40*(kx0_factor-1.0)**2
-     ! write(*,*)"kx0_factor=",kx0_factor
-       wE = kx0_factor*MIN(kyi/0.3,1.0)*vexb_shear_kx0/gamma_reference_kx0(1)
-     ! write(*,*)"wE=",wE
-     else
-       kx0_factor = 1.0
-       wE = 0.0
-     endif
-     grad_r0_out = B_geo(0)/qrat_geo(0)
-     B_geo0_out = b_geo(0)
-     kx_geo0_out= 1.0/qrat_geo(0)
-!write(*,*)"kx_geo0_out = ",kx_geo0_out
-!write(*,*)"grad_r0_out = ",grad_r0_out
-     kx0_e = -(0.36*vexb_shear_kx0/gamma_reference_kx0(1) + 0.38*wE*TANH((0.69*wE)**6))
-     if(sat_rule_in.eq.1)kx0_e = -(0.53*vexb_shear_kx0/gamma_reference_kx0(1) + 0.25*wE*TANH((0.69*wE)**6))
-     if(sat_rule_in.eq.2)then
-       if(ABS(kymax_out*vzf_out*vexb_shear_kx0).gt.small)then
-         kx0_e = -0.32*((ky/kymax_out)**0.3)*vexb_shear_kx0/(ky*vzf_out)
-       else
-         kx0_e = 0.0
-       endif
-!       write(*,*)"kx0_e = ",kx0_e,kymax_out,vzf_out
-     endif
-!     a0 = alpha_e_in*2.0
-!     if(alpha_e_in.ne.0.0)then
-!        kx0_e = a0*TANH(kx0_e/a0)
-!     else
-!        kx0_e = 0.0
-!     endif
-     a0 = 1.3
-     if(sat_rule_in.eq.1)a0=1.45
-     if(sat_rule_in.eq.2)a0=1.6
-     if(ABS(kx0_e).gt.a0)kx0_e = a0*kx0_e/ABS(kx0_e)
-     if(units_in.eq.'GYRO')then
-        kx0 = sign_Bt_in*kx0_e ! cancel the sign_Bt_in factor in kxx below
-     else
-       if(sat_rule_in.eq.1)kx0 = sign_Bt_in*kx0_e/(2.1)  ! goes with xnu_model=2
-       if(sat_rule_in.eq.2)kx0 = sign_Bt_in*kx0_e*0.7/grad_r0_out**2     ! goes with xnu_model=3, the factor 0.7/grad_r0_out**2 is needed for stress_tor
-       ! note kx0 = alpha_e*gamma_ExB_HB/gamma Hahm - Burrell form of gamma_ExB
-       ! The 2.1 effectively increases ay0 & ax0 and reduces toroidal stress to agree with CGYRO
-     endif
-     !
-     !APS2010 kx0 = alpha_kx_e_in*0.19*TANH(vexb_shear_s*Rmaj_s/vs(2))*kyi*kyi/(kyi*kyi+0.001)/ky
-     !EPS2011 kx0 = kx0 -alpha_kx_p_in*sign_Bt_in*TANH((0.26/3.0)*vpar_shear_in(2)*Rmaj_s/vs(2)) &
-     !EPS2011 *(0.06*kyi*kyi/(kyi*kyi+0.001)+0.25*TANH((1.9*kyi)**3))/ky
-     !EPS2011 if(midplane_shear.gt.0.0)then
-     !EPS2011 kx0_p = -alpha_kx_p_in*sign_Bt_in*TANH((0.26/3.0)*vpar_shear_in(2)*Rmaj_s/vs(2)) &
-     !EPS2011 *midplane_shear*(1.43*EXP(-(5.4*kyi)**3)+1.50*TANH((1.7*kyi)**2))/(1.0 + kyi**2)
-     !EPS2011 else
-     !EPS2011 kx0_p = -alpha_kx_p_in*sign_Bt_in*TANH((0.26/3.0)*vpar_shear_in(2)*Rmaj_s/vs(2)) &
-     !EPS2011 *midplane_shear*(2.13*TANH((1.4*kyi)**2))/(1.0 + kyi**2)
-     !EPS2011 endif
-     ! kx0 = kx0 + alpha_kx_n_in*0.19*TANH(vns_shear_in(2)*Rmaj_s/vs(2))*kyi*kyi/(kyi*kyi+0.001)/ky
-     ! kx0 = kx0 - alpha_kx_t_in*0.19*TANH(vts_shear_in(2)*Rmaj_s/vs(2))*kyi*kyi/(kyi*kyi+0.001)/ky
-     !
-     !ESP2011 if(kx0.lt.0.0)sign_kx0=-1.0
-     !EPS2011 kx0 = kx0_e + kx0_p
-     ! write(*,*)ky,"kx0_e",kx0_e,"kx0_p=",kx0_p,"kx0=",kx0
-  endif
-  !
-  !*************************************************************
-  ! begin calculation of wdx and b0x
-  !*************************************************************
-  ! compute drift wdx and pependicular wavenumber squared b0x
-  ! at the Hermite nodes x(i)
-  ! thx is the ballooning angle = 2 pi y/Ly
-  ! x is the argument of the Hermite basis functions = thx/width_in
-  !
-  do i=1,nx
-     thx = width_in*x(i)
-     sign_theta=1.0
-     if(thx.lt.0.0) sign_theta=-1.0
-     !
-     ! use quasi-periodic property of S_prime to evaluate it when thx > 2pi
-     ! S_prime(0)=0
-     ! S_prime(t+2pi*m) = m*S_prime(2pi) + S_prime(t)
-     !
-     loops = REAL(INT(ABS(thx/pi_2)))
-     y_x = Ly*(ABS(thx) - loops*pi_2)/pi_2
-     if(thx.lt.0.0)then
-        !
-        ! not always up/down symmetric so can't just use symmetry
-        ! for negative theta = -(t+m*2pi) use
-        ! S_prime(-t-m*2pi) = -(m+1)*S_prime(2pi)+S_prime(2pi-t)
-        !
-        y_x=Ly-y_x
-        loops=loops+1.0
-     endif
-     do m=1,ms
-        if(y(m).ge.y_x) exit
-     enddo
-!     write(*,*)"exit at",m,ms,y_x,y(ms)
-     if(m.gt.ms)m=ms
-     m1=m-1
-     m2=m
-     !
-     ! dkxky is the offset for S_prime due to the number of loops
-     !
-     dkxky1 = sign_theta*loops*S_prime(ms)
-     y1=y(m1)
-     dkxky2 = sign_theta*loops*S_prime(ms)
-     y2=y(m2)
-     ! write(*,*)"check interpolation",m1,m2
-     ! write(*,*)"y=",y1,y2
-     ! write(*,*)S_prime(m1)+dkxky1,S_prime(m2)+dkxky2
-     !
-     ! note that costheta_geo and sintheta_geo are periodic so
-     ! we can use f(-t-m*2pi) = f(2pi-t) if f(0)=f(2pi) and 0<t<2pi
-     !
-     ! intepolate kxx
-     kxx1 = (kx_factor(m1)*(S_prime(m1)+dkxky1)-kx0*b_geo(m1)/qrat_geo(m1)**2)*qrat_geo(m1)/b_geo(m1)
-     kxx2 = (kx_factor(m2)*(S_prime(m2)+dkxky2)-kx0*b_geo(m2)/qrat_geo(m2)**2)*qrat_geo(m2)/b_geo(m2)
-     kxx(i) = kxx1 +(kxx2-kxx1)*(y_x-y1)/(y2-y1)
-     kxx(i) = sign_Bt_in*kxx(i)
-     ! interpolate wdx
-     wd1 = (qrat_geo(m1)/b_geo(m1))*(costheta_geo(m1) &
-          +(kx_factor(m1)*(S_prime(m1)+dkxky1)-kx0*b_geo(m1)/qrat_geo(m1)**2)*sintheta_geo(m1))
-     wd2 = (qrat_geo(m2)/b_geo(m2))*(costheta_geo(m2) &
-          +(kx_factor(m2)*(S_prime(m2)+dkxky2)-kx0*b_geo(m2)/qrat_geo(m2)**2)*sintheta_geo(m2))
-     ! write(*,*)"wd1,,wd2=",wd1,wd2
-     wdx(i) = wd1 +(wd2-wd1)*(y_x-y1)/(y2-y1)
-!     wdx(i) = (R_unit/Rmaj_s)*wdx(i)
-     ! write(*,*)i,"wdx = ",wdx(i),y_x,x(i),y1,y2
-     ! interpolate wdpx
-     wdp1 = (qrat_geo(m1)/b_geo(m1))*costheta_p_geo(m1)
-     wdp2 = (qrat_geo(m2)/b_geo(m2))*costheta_p_geo(m2)
-     wdpx(i) = wdp1 + (wdp2-wdp1)*(y_x-y1)/(y2-y1)
-!     wdpx(i) = (R_unit/Rmaj_s)*wdpx(i)
-     ! interpolate wbx
-     wb1 = -(width_in*Ly/pi_2)*pk_geo(m1)*sintheta_geo(m1)*b_geo(m1)/(Rmaj_s*f/R(m1))
-     wb2 = -(width_in*Ly/pi_2)*pk_geo(m2)*sintheta_geo(m2)*b_geo(m2)/(Rmaj_s*f/R(m2))
-     wbx(i) = wb1 + (wb2-wb1)*(y_x-y1)/(y2-y1)
-!     write(*,*)i, thx, "wbx = ",wbx(i)
-     ! interpolate b2x = b_geo**2
-     b1 = b_geo(m1)**2
-     b2 = b_geo(m2)**2
-     b2x(i) =  b1 +(b2-b1)*(y_x-y1)/(y2-y1)
-     ! interpolate b0x
-     b1 = (1.0+(kx_factor(m1)*(S_prime(m1)+dkxky1)-kx0*b_geo(m1)/qrat_geo(m1)**2)**2) &
-          *qrat_geo(m1)**2
-     b2 = (1.0+(kx_factor(m2)*(S_prime(m2)+dkxky2)-kx0*b_geo(m2)/qrat_geo(m2)**2)**2) &
-          *qrat_geo(m2)**2
-     ! write(*,*)"b1,b2,b3,b4=",b1,b2,b3,b4
-     b0x(i) =  b1 +(b2-b1)*(y_x-y1)/(y2-y1)
-     if(b0x(i).lt.0.0)then
-        write(*,*)"interpolation error b0x < 0",i,b0x(i),b1,b2
-        b0x(i)=(b1+b2)/2.0
-     endif
-     ! factor needed for k_par matrix
-     b1 = b_geo(m1)
-     b2 = b_geo(m2)
-     Bx(i) = b1 +(b2-b1)*(y_x-y1)/(y2-y1)
-     !
-     ! interpolate viscous stress projection coefficients
-     !
-     cxtorper1 = -R(m1)*Bp(m1)/b_geo(m1)
-     cxtorper2 = -R(m2)*Bp(m2)/b_geo(m2)
-     cx_tor_par(i) = f/b_geo(m1) + (f/b_geo(m2)-f/b_geo(m1))*(y_x-y1)/(y2-y1)
-     cx_tor_par(i) = sign_Bt_in*cx_tor_par(i)
-     cx_tor_per(i) = cxtorper1 + (cxtorper2-cxtorper1)*(y_x-y1)/(y2-y1)
-     cx_par_par(i) = b_geo(m1) + (b_geo(m2)-b_geo(m1))*(y_x-y1)/(y2-y1)
-     !
-     ! debug
-     ! write(*,*)"b0x = ",b0x(i)
-     ! write(*,*)" y_x =",y_x," m = ",m
-     ! write(*,*)i," loops = ",loops
-  enddo
-  ! write(*,*)"ave_shear =",ave_shear,midplane_shear
-  !
-  ! compute flux surface averages
-  !
-  B2_ave_out = 0.0
-  R2_ave_out = 0.0
-  B_ave_out = 0.0
-  Bt_ave_out = 0.0
-  Grad_r_ave_out = 0.0
-  kykx_geo_ave=0.0
-  norm_ave=0.0
-  SAT_geo1_out = 0.0
-  SAT_geo2_out = 0.0
-  do i=1,ms
-     dlp = s_p(i)*ds*(0.5/Bp(i)+0.5/Bp(i-1))
-     norm_ave = norm_ave + dlp
-     B2x1 = b_geo(i-1)**2
-     B2x2 = b_geo(i)**2
-     B2_ave_out = B2_ave_out + dlp*(B2x1+B2x2)/2.0
-     R2x1 = R(i-1)**2
-     R2x2 = R(i)**2
-     R2_ave_out = R2_ave_out + dlp*(R2x1+R2x2)/2.0
-     B_ave_out = B_ave_out + dlp*(b_geo(i-1)+b_geo(i))/2.0
-     Bt_ave_out = Bt_ave_out + dlp*(f/b_geo(i-1)+f/b_geo(i))/(2.0*Rmaj_s)
-     Grad_r_ave_out = Grad_r_ave_out + dlp*0.5*((R(i-1)*Bp(i-1))**2+(R(i)*Bp(i))**2)*(q_s/rmin_s)**2
-     kykx_geo_ave = kykx_geo_ave + dlp*0.5*(B_geo(i-1)**2/qrat_geo(i-1)**4+B_geo(i)**2/qrat_geo(i)**4)
-     SAT_geo1_out = SAT_geo1_out +dlp*((b_geo(0)/b_geo(i-1))**4 +(b_geo(0)/b_geo(i))**4)/2.0
-     SAT_geo2_out = SAT_geo2_out +dlp*((qrat_geo(0)/qrat_geo(i-1))**4 +(qrat_geo(0)/qrat_geo(i))**4)/2.0
- enddo
-  R2_ave_out = R2_ave_out/norm_ave
-  B2_ave_out = B2_ave_out/norm_ave
-  B2_ave_out = B2_ave_out/B_unit**2
-  B_ave_out = B_ave_out/norm_ave
-  Bt_ave_out = Bt_ave_out/norm_ave
-  Grad_r_ave_out = Grad_r_ave_out/norm_ave
-  kykx_geo_ave = kykx_geo_ave/norm_ave
-  SAT_geo1_out = SAT_geo1_out/norm_ave
-  SAT_geo2_out = SAT_geo2_out/norm_ave
-  !
-  ! poloidal magnetic field on outboard midplane
-  !
-  Bp0_out = Bp(0)/B_unit
-   if(units_in.eq.'GYRO') then
-    SAT_geo0_out = 1.0
-    SAT_geo1_out = 1.0
-    SAT_geo2_out = 1.0
-  else
- ! Nov 2019     SAT_geo0_out = 0.946/qrat_geo(0) ! normed to GASTD with CGYRO
-    SAT_geo0_out = 0.946/qrat_geo(0)          ! normed to GASTD with CGYRO
-    if(sat_rule_in.eq.2)SAT_geo0_out = 1.0
-!    write(*,*)"SAT_geo0_out = ",SAT_geo0_out
-    grad_r0_out = B_geo(0)/qrat_geo(0)
-    B_geo0_out = b_geo(0)
-!    write(*,*)"B_geo0 = ",b_geo(0)
-    kx_geo0_out= 1.0/qrat_geo(0)
-  endif
-! for GENE units need to multiply intensity by (Bref/Bunit)**2
-  if(units_in.eq.'GENE')then
-     SAT_geo0_out = SAT_geo0_out*(Bref_out)**2
-  endif
-  !
-  ! write(*,*)"R2_ave_out=",R2_ave_out
-  ! write(*,*)"B2_ave_out=",B2_ave_out
-  ! write(*,*)"B_ave_out=",B_ave_out
-  ! write(*,*)"Bt_ave_out=",Bt_ave_out
-  ! write(*,*)"Grad_r_ave_out =",Grad_r_ave_out
-  ! write(*,*)"kykx_geo_ave = ",kykx_geo_ave
-  ! write(*,*)"SAT_geo0_out=",SAT_geo0_out
-  ! write(*,*)"grad_r0= ",grad_r0_out
-  ! write(*,*)"ky_over_kx_geo = ",B_geo(0)/qrat_geo(0)**2
-  ! write(*,*)"B_geo0 = ",B_geo(0)
-  !
-  ! do m=0,ms
-  ! write(*,*)m,s_prime(ms-m),s_prime(ms)-s_prime(m)
-  ! enddo
-  !*************************************************************
-  ! end of calculation of wdx and b0x
-  !*************************************************************
-  !
-  !
-END SUBROUTINE xgrid_functions_geo
-!
-!*************************************************************
-!
-!---------------------------------------------------------------
-! mercier_luc.f [various callers]
-!
-! PURPOSE: Compute ballooning mode eikonal form of poloidally varying terms
-! in the gftm equations using the mercier-luc local equilibrium expansion
-!
-! DEFINITIONS:
-! Length is in units of rmin at the last closed
-! flux surface (a_unit).
-! NOTES:
-! To follow what's going on in this routine, it is
-! necessary to have the following papers at hand:
-!
-! (1) R.L. Miller, M.S. Chu, J.M. Greene, Y.R. Lin-liu
-! and R.E. Waltz, 'Noncircular, finite aspect ratio,
-! local equilibrium model', Phys. Plasmas 5 (1998) 973.
-!
-! (2) R.E. Waltz and R.L. Miller, 'Ion temperature gradient
-! turbulence simulations and plasma flux surface shape',
-! Phys. Plasmas 6 (1999) 4265.
-!
-! **See MILLER_inputs for control variables**
-!
-! REVISIONS:
-! 13 Aug 02: jc
-! Documentation after MILLER de-spaghetti.
-! 18 Nov 03: jc
-! Removed reset of s_delta and s_kappa when they
-! are input as zero.
-! 24 Nov 03: jc
-! Entire code has been rewritten for greater
-! efficiency and clarity. Documentation greatly
-! improved as well.
-! 13 Jan 10: gms
-! added vprime and vpp and interchange stability calculation
-!---------------------------------------------------------------
-
-SUBROUTINE mercier_luc
-
-  !-------------------------------------------
-  ! the following must be defined from a previous call to one of the
-  ! geometry routines miller_geo, fourier_geo,ELITE_geo and stored in gftm_sgrid:
-  ! ms ! the number of points in the s-grid (flux surface contour)
-  ! ds ! the arc length differential on a flux surface
-  ! R(ms) ! the major radius on the s-grid
-  ! Z(ms) ! the vertical coordinate on the s-grid
-  ! Bp(ms) ! the poloidal magnetic field on the s-grid normalized to B_unit
-  ! q_s = local flux surface safety factor
-  ! q_prime_s = dq/dpsi
-  ! p_prime_s = dp/dpsi
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  INTEGER :: m,m1,m2,m3,m4
-  !
-  REAL :: sin_u(0:ms),r_curv(0:ms)
-  REAL :: psi_x(0:ms)
-  REAL :: Bt(0:ms),B(0:ms)
-  REAL :: d_0(0:ms),d_p(0:ms),d_ffp(0:ms)
-  REAL :: delta_s, ds2
-  !
-  REAL :: R_s, Z_s
-  REAL :: R_ss, Z_ss
-  REAL :: error_check
-  REAL :: dq1,dq2
-  REAL :: d0_s1,d0_s2
-  REAL :: dp_s1,dp_s2
-  REAL :: dffp_s1,dffp_s2
-  REAL :: vprime, vpp, dvpp1,dvpp2
-  REAL :: ave_M1,ave_M2,ave_M3,ave_M4
-  REAL :: p_prime_M,q_prime_M,H  !
-  !-----------------------
-  !
-  ! compute the first and second derivatives of R,Z on the s-grid
-  ! and the local radius of curvature.
-  ! Note that for the Mercier-Luc coordinate dR/ds = cos(u), dZ/ds = -sin(u)
-  ! so (dR/ds)**2+(dZ/ds)**2 = 1, error_check compute the error in this relation
-  ! to make sure that the input flux surface coordinates R(s), Z(s) are ok.
-  !
-  delta_s = 12.0*ds
-  ds2 = 12.0*ds**2
-  ! write(*,*)"ms = ",ms," ds = ",ds
-  ! do m=0,ms
-  ! write(*,*)m,"R = ",R(m)," Z = ",Z(m)
-  ! enddo
-  ! note that the point 0 and ms are the same so m+1->1 and m-1->ms-1 at m=0
-  error_check=0.0
-  do m=0,ms
-     m1 = MOD(ms+m-2,ms)
-     m2 = MOD(ms+m-1,ms)
-     m3 = MOD(m+1,ms)
-     m4 = MOD(m+2,ms)
-     R_s = (R(m1)-8.0*R(m2)+8.0*R(m3)-R(m4))/delta_s
-     Z_s = (Z(m1)-8.0*Z(m2)+8.0*Z(m3)-Z(m4))/delta_s
-     s_p(m) = sqrt(R_s**2 + Z_s**2)
-     R_ss = (-R(m1)+16.0*R(m2)-30.0*R(m)+16.0*R(m3)-R(m4))/ds2
-     Z_ss = (-Z(m1)+16.0*Z(m2)-30.0*Z(m)+16.0*Z(m3)-Z(m4))/ds2
-     r_curv(m) = (s_p(m)**3)/(R_s*Z_ss - Z_s*R_ss)
-     sin_u(m) = -Z_s/s_p(m)
-     ! write(*,*)m,m1,m2,m3,m4
-     ! write(*,*)m," r_curv =",r_curv(m),"sin_u =",sin_u(m)
-     ! write(*,*)"error=",m,ABS(s_p(m) -1.0)
-     ! error_check = error_check + (s_p(m)**2 -1.0)**2
-  enddo
-  ! open(3,file='curv.dat',status='replace')
-  ! do m=0,ms
-  ! write(3,*)r_curv(m),sin_u(m),s_p(m)
-  ! enddo
-  ! close(3)
-  !
-  error_check = SQRT(error_check/real(ms))
-  if(error_check .gt. 1.00) &
-       write(*,*)"error in s-grid derivative = ",error_check
-  !---------------------------------------------------------------
-  ! Compute f=R*Bt such that the eikonal S which solves
-  ! B*Grad(S)=0 has the correct quasi-periodicity S(s+Ls)=S(s)-2*pi*q_s
-  !
-  ! Ls
-  ! / ds
-  ! 1/f = | ---------------
-  ! / R**2 Bp 2pi q
-  ! 0
-  !
-  ! f -> R for a circular flux-surface
-  !
-  ! Define psi_x
-  do m=0,ms
-     psi_x(m)=R(m)*Bp(m)
-  enddo
-  !
-  ! First compute 2 pi q/f:
-  !
-  f = 0.0
-  do m=1,ms
-     f = f &
-          +0.5*ds*(s_p(m-1)/(R(m-1)*psi_x(m-1)) + s_p(m)/(R(m)*psi_x(m)))
-     ! fixed error that changes results slightly for gftm_1.93 compared to previous.
-     ! +ds*s_p(m)*2.0/(R(m-1)*psi_x(m-1)+R(m)*psi_x(m))
-  enddo
-  !
-  f = pi_2*q_s/f
-  ! write(*,*)"f = ",f,q_s
-  ! write(*,*)"ds=",ds
-  Bt0_out = f/Rmaj_input
-  Bref_out = 1.0
-  betae_s = betae_in
-  debye_s = debye_in
-  if(units_in .eq. 'GENE')then
-! convert inputs from GENE reference magnetic field to Bunit
-    Bref_out = f/Rmaj_input ! Bref/Bunit
-    ! write(*,*)"Bref/Bunit = ",Bref_out
-    betae_s = betae_in*Bref_out**2
-    p_prime_s = p_prime_loc*Bref_out**2
-    debye_s = debye_in/Bref_out
-  endif
-  !
-  !-----------------------------------------------------------
-  !-----------------------------------------------------------
-  ! Compute toroidal and total fields:
-  !
-  ! 2 2 2
-  ! B = B + B
-  ! p t
-  !
-  ! B = f/R
-  ! t
-  !
-  do m=0,ms
-     Bt(m) = f/R(m)
-     B(m) = SQRT(Bt(m)**2 + Bp(m)**2)
-     ! write(*,*)m,"Bt =",Bt(m)," B =",B(m)
-  enddo
-  !----------------------------------------------------------
-  !---------------------------------------------------------------
-  ! Compute Miller's D , D and D needed for kx.
-  ! 0 p ff'
-  !
-  d_0(0) = 0.0
-  d_p(0) = 0.0
-  d_ffp(0) = 0.0
-  !
-  dq1 = ds*s_p(0)*f/(R(0)*psi_x(0)**2)
-  d0_s1 = -dq1*(2.0/r_curv(0)+2.0*sin_u(0)/R(0))
-  dp_s1 = dq1*4.0*pi*R(0)/Bp(0)
-  dffp_s1 = dq1*(R(0)/Bp(0))*(B(0)/f)**2
-  !
-  do m=1,ms
-     dq2 = ds*s_p(m)*f/(R(m)*psi_x(m)**2)
-     d0_s2 = -dq2*(2.0/r_curv(m)+2.0*sin_u(m)/R(m))
-     dp_s2 = dq2*4.0*pi*R(m)/Bp(m)
-     dffp_s2 = dq2*(R(m)/Bp(m))*(B(m)/f)**2
-     !
-     d_0(m) = d_0(m-1)+0.5*(d0_s1+d0_s2)
-     d_p(m) = d_p(m-1)+0.5*(dp_s1+dp_s2)
-     d_ffp(m) = d_ffp(m-1)+0.5*(dffp_s1+dffp_s2)
-     !
-     d0_s1 = d0_s2
-     dp_s1 = dp_s2
-     dffp_s1 = dffp_s2
-     !
-  enddo
-  !
-  ! d_p(0)=0.0
-  ! do m=1,ms
-  ! d_p(m)=d_p(m-1)+d_0(ms-(m-1))-d_0(ms-m)
-  ! write(*,*)t_s(m),d_0(m),d_p(m),d_ffp(m)
-  ! write(*,*)m,d_p(m),d_0(ms-m)-d_0(ms),d_0(m)
-  ! enddo
-  !
-  !---------------------------------------------------------------
-
-
-  !---------------------------------------------------------------
-  ! Begin computing geometric quantities required for solution
-  ! of gyrokinetic equation:
-  !
-  ! - b_geo replaces bmaj(j)=b_theta(j)/b_unit
-  !
-  ! - pk_geo is close to pk = rmin/(rmaj*q), the coefficient
-  ! of d/dtheta
-  !
-  ! - qrat_geo -> 1 in a circle
-  !
-  ! Note that for the physical quantity
-  !
-  ! k_theta = nq/r
-  !
-  ! we use
-  !
-  ! kyrhos_s = n*q_s/rmin_s*rhos_unit_s
-  !
-  ! which is exactly the same as for the circle.
-  !
-  ! Also, "omega_star" remains unchanged from circle with
-  ! logarithmic density gradients along minor axis.
-  !
-  ! - "ky*rhos" in Bessel function is kyrhos_s*qrat_geo(j)/b_geo(j)
-  !
-  ! - "kx*rhos" is kxoky_geo(j)*ky*rhos
-  !
-  do m=0,ms
-     b_geo(m) = B(m)
-     pk_geo(m) = Bp(m)/B(m)
-     qrat_geo(m) = (rmin_s/R(m))*(B(m)/Bp(m))/q_s
-  enddo
-  !---------------------------------------------------------------
-  !
-  ! Determine ff_prime from:
-  !
-  ! 2 pi q_prime = d_0(ms)
-  ! +d_p(ms)*p_prime
-  ! +d_ffp(ms)*ff_prime
-  !
-  ff_prime = (pi_2*q_prime_s-d_0(ms)-d_p(ms)*p_prime_s) &
-       /d_ffp(ms)
-  ! write(*,*)"ff_prime=",ff_prime,"f=",f
-  ! write(*,*)"d_0,d_p,d_ffp",d_0(ms),d_p(ms),d_ffp(ms)
-  !---------------------------------------------------------------
-
-  !--------------------------------------------------------------
-  ! Compute [[kx/ky]] (herein, kxoky_geo) from Waltz-Miller [2]
-  ! paper.
-  ! 2
-  ! (R B_p) S1
-  ! kxoky_geo = ---------- ------
-  ! B R B_p
-  !
-  ! S1
-  ! ------ = -(d_0(theta)+d_p(theta)*p_prime+d_ffp(theta)*ff_prime)
-  ! R B_p
-  !
-  do m=0,ms
-
-     S_prime(m) = -(d_0(m)+d_p(m)*p_prime_s+d_ffp(m)*ff_prime)
-     kx_factor(m) = (psi_x(m)**2)/B(m)
-     kxoky_geo(m) = S_prime(m)*kx_factor(m)
-     ! write(*,*)"check s_prime",S_prime(m)
-
-  enddo
-  !---------------------------------------------------------------
-  !---------------------------------------------------------------
-  ! Compute drift coefficients:
-  !
-  !
-  ! p_prime_zero forces grad-B-curvature to zero to compensates
-  ! for b_par =0
-  !
-  p_prime_zero_s = 1.0
-  if(use_mhd_rule_in)p_prime_zero_s = 0.0
-  !
-  ! write(*,*)"debug p_prime_zero",p_prime_zero_s
-
-  do m=0,ms
-
-     epsl_geo(m) = 2.0/rmaj_s*qrat_geo(m)/b_geo(m)
-
-     ! Waltz/Miller [[cos_p]] 
-
-     costheta_p_geo(m) = p_prime_zero_s*rmaj_s*(Bp(m)/B(m)**2)*(4.0*pi*R(m)*p_prime_s)
-
-     ! Waltz/Miller [[cos]] without the p_prime term 
-
-     costheta_geo(m) = &
-          -rmaj_s*(Bp(m)/B(m)**2)*(Bp(m)/r_curv(m) &
-          -(f**2/(Bp(m)*R(m)**3))*sin_u(m)) 
-
-  enddo
-
-  !----------------------------------------------------------
-  ! Functions which require theta-derivatives:
-  !
-  do m=0,ms
-
-     ! Waltz/Miller [[sin]]
-     m1=MOD(ms+m-2,ms)
-     m2=MOD(ms+m-1,ms)
-     m3=MOD(m+1,ms)
-     m4=MOD(m+2,ms)
-     sintheta_geo(m) = -rmaj_s*(f/(R(m)*B(m)**2))* &
-          (B(m1)-8.0*B(m2)+8.0*B(m3)-B(m4))/(delta_s*s_p(m))
-     ! write(*,*)m,m1,m2,m3,m4,"sintheta_geo=",sintheta_geo(m)
-
-  enddo
-  !
-  ! compute vprime and vpp
-  !
-  vprime = 0.0
-  vpp = 0.0
-  dvpp1 = (s_p(0)*R(0)/psi_x(0)**3) &
-       *(4.0*pi*p_prime_s*R(0)**2 + ff_prime - 2.0*psi_x(0)/r_curv(0))
-  do m=1,ms
-     dvpp2 = (s_p(m)*R(m)/psi_x(m)**3) &
-          *(4.0*pi*p_prime_s*R(m)**2 + ff_prime - 2.0*psi_x(m)/r_curv(m))
-     vprime = vprime + 0.5*ds*(s_p(m-1)/Bp(m-1) + s_p(m)/Bp(m))
-     vpp = vpp + 0.5*ds*(dvpp1 + dvpp2)
-     dvpp1 = dvpp2
-  enddo
-  vprime = pi_2*vprime
-  vpp = pi_2*vpp
-  ! write(*,*)"vprime = ",vprime,"vpp = ",vpp
-  !
-  ave_M1 = 0.0
-  ave_M2 = 0.0
-  ave_M3 = 0.0
-  ave_M4 = 0.0
-  do m=1,ms
-     ave_M1 = ave_M1 + 0.5*ds*(s_p(m-1)/Bp(m-1)**3 + s_p(m)/Bp(m)**3)
-     ave_M2 = ave_M2 + 0.5*ds*(s_p(m-1)*R(m-1)/psi_x(m-1)**3 + s_p(m)*R(m)/psi_x(m)**3)
-     ave_M3 = ave_M3 + 0.5*ds*(s_p(m-1)*(B(m-1)/psi_x(m-1))**2/Bp(m-1) + s_p(m)*(B(m)/psi_x(m))**2/Bp(m))
-     ave_M4 = ave_M4 + 0.5*ds*(s_p(m-1)*B(m-1)**2/Bp(m-1) + s_p(m)*B(m)**2/Bp(m))
-  enddo
-  ! write(*,*)"M1=",ave_M1,"M2=",ave_M2,"M3=",ave_M3,"M4=",ave_M4
-  p_prime_M = 4.0*pi*p_prime_s
-  q_prime_M = pi_2*q_prime_s
-  DM_out = 0.25 + (p_prime_M/MAX(q_prime_M**2,1e-12))*((vpp/pi_2 - p_prime_M*ave_M1)*ave_M3 &
-       + (f**2*p_prime_M*ave_M2 - q_prime_M*f)*ave_M2)
-  H = (f*p_prime_M*q_prime_M/MAX(q_prime_M**2,1e-12))*ave_M3*(ave_M2/ave_M3 - vprime/(pi_2*ave_M4))
-  ! write(*,*)"H = ",H
-  DR_out = DM_out - (0.5 - H)**2
-  !
-  !
-  !--------------------------------------------------------------------
-  !--------------------------------------------------------------------
-  !
-  ! call mercier_write
-  ! open(2,file='functions_geo.dat',status='replace')
-  ! do m=ms/2,0,-1
-  ! write(2,*)t_s(m),costheta_geo(m),sintheta_geo(m),kxoky_geo(m)
-  ! enddo
-  ! do m=ms-1,ms/2,-1
-  ! write(2,*)t_s(m)+pi_2,costheta_geo(m),sintheta_geo(m) &
-  ! ,kx_factor(m)*(S_prime(m)-S_prime(ms))
-  ! enddo
-  close(2)
-  !
-END SUBROUTINE mercier_luc
-!
-!
-!---------------------------------------------------------------
-! mercier_write.f
-!
-! PURPOSE:
-! Output of some internal MILLER variables, as well
-! as selected values of required external variables
-! like costheta, etc.
-!
-! REVISIONS:
-! 30 june 2005: gms
-! Based on MILLER_write.f90 from GYRO
-!---------------------------------------------------------------
-
-SUBROUTINE mercier_write
-  !
-  USE gftm_global
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  INTEGER :: j,jj
-  character(len=7) ang(0:4)
-  character(len=11) names(0:12)
-  REAL :: theta_write(0:4)
-  !---------------------------------------------------
-
-  open(unit=3,file='mercier.out',status='replace')
-  write(3,10) 'rmin',rmin_loc
-  write(3,10) 'rmaj0',rmaj_loc
-  write(3,10) 'kappa',kappa_loc
-  write(3,10) 's_kappa',s_kappa_loc
-  write(3,10) 'delta',delta_loc
-  write(3,10) 's_delta',s_delta_loc
-  write(3,10) 'drmindx',drmindx_loc
-  write(3,10) 'drmajdx',drmajdx_loc
-  write(3,10) 'q',q_loc
-  write(3,10) 'f',f
-  write(3,10) 'ff_prime',ff_prime
-  write(3,10) 'q_prime',q_prime_s
-  write(3,10) 'p_prime',p_prime_s
-
-  ang(0) = '0.00*pi'
-  ang(1) = '0.50*pi'
-  ang(2) = '1.00*pi'
-  ang(3) = '1.50*pi'
-  ang(4) = '2.00*pi'
-  names(0) = 'theta '
-  names(1) = 't_s '
-  names(2) = 'b_geo '
-  names(3) = 'grad_r '
-  names(4) = 'R '
-  names(5) = 'Z '
-  names(6) = 'pk_geo '
-  names(7) = 'qrat_geo '
-  names(8) = 'cos '
-  names(9) = 'cos_p '
-  names(10) = 'sin '
-  names(11) = 'epsl '
-  names(12) = 'kxoky_geo '
-  !
-
-  theta_write(0) = 0.0
-  theta_write(1) = 0.5*pi
-  theta_write(2) = 1.0*pi
-  theta_write(3) = 1.5*pi
-  theta_write(4) = 2.0*pi
-  write(3,*)
-  write(3,30)names(0),names(1),(names(j),j=2,7)
-  write(3,*)
-  !
-  do jj=0,4
-     do j=ms,2,-1
-        if(t_s(j).gt.theta_write(jj)-pi_2)exit
-     enddo
-     if(ABS(t_s(j-1)+pi_2-theta_write(jj)) &
-          .lt.ABS(t_s(j)+pi_2-theta_write(jj)))j=j-1
-     !
-     write(3,20)ang(jj),t_s(j),b_geo(j),q_s*R(j)*Bp(j)/rmin_loc, &
-          R(j),Z(j),pk_geo(j),qrat_geo(j)
-     !
-  enddo
-  !
-  write(3,*)
-  write(3,30)names(0),names(1),(names(j),j=8,12)
-  write(3,*)
-  !
-  do jj=0,4
-     do j=ms,2,-1
-        if(t_s(j).gt.theta_write(jj)-pi_2)exit
-     enddo
-     if(ABS(t_s(j-1)+pi_2-theta_write(jj)) &
-          .lt.ABS(t_s(j)+pi_2-theta_write(jj)))j=j-1
-     !
-     write(3,20) ang(jj),t_s(j),costheta_geo(j),costheta_p_geo(j), &
-          sintheta_geo(j),epsl_geo(j),kxoky_geo(j), &
-          (S_prime(j)-S_prime(ms))*kx_factor(j)
-     !
-  enddo
-  close(3)
-
-10 format(t2,a,':',t20,f10.6)
-20 format(t2,a,1x,10(es10.3,1x))
-30 format(t2,10a)
-  !
-END SUBROUTINE mercier_write
-!
-!
-!---------------------------------------------------------------
-! miller_geo.f [various callers]
-!
-! PURPOSE:
-! Core routine for calculation of MILLER shaped flux surface
-! quantities R(theta), Z(theta), grad_r(theta)
-!
-! DEFINITIONS:
-! Length is in units of rmin at the last closed
-! flux surface (a_unit).
-!
-! R(r,theta) = R0(r) + r cos[theta + x_delta*sin(theta)]
-! Z(r,theta) = kappa r sin(theta)
-!
-!
-! NOTES:
-! To follow what's going on in this routine, it is
-! necessary to have the following papers at hand:
-!
-! (1) R.L. Miller, M.S. Chu, J.M. Greene, Y.R. Lin-liu
-! and R.E. Waltz, 'Noncircular, finite aspect ratio,
-! local equilibrium model', Phys. Plasmas 5 (1998) 973.
-!
-! (2) R.E. Waltz and R.L. Miller, 'Ion temperature gradient
-! turbulence simulations and plasma flux surface shape',
-! Phys. Plasmas 6 (1999) 4265.
-!
-! **See MILLER_inputs for control variables**
-!
-! REVISIONS:
-! 13 Aug 02: jc
-! Documentation after MILLER de-spaghetti.
-! 18 Nov 03: jc
-! Removed reset of s_delta and s_kappa when they
-! are input as zero.
-! 24 Nov 03: jc
-! Entire code has been rewritten for greater
-! efficiency and clarity. Documentation greatly
-! improved as well.
-! 24 June 05: gms
-! produced this version which only computes R,Z,Bp for input
-! into mercier_luc.f which completes the calculation of the Waltz-Miller
-! functions [[sin]],[[cos]], etc.
-! 15 June 2010: updated to GYRO conventions with squarness (zeta_loc) and
-! squarness shear s_zeta_loc = rmin*d(zeta)/dx. Included elevation Zmaj_loc.
-! Also changed definition of s_delta = rmin*d(delta)/dx from Waltz-Miller convention to GYRO's.
-! July 26, 2021 set elevation Zmaj_loc =0.0 and DZMAJDX_LOC=0.0 since these break the up/down symmetry of Miller by contributing to Grad_r
-!---------------------------------------------------------------
-
-SUBROUTINE miller_geo
-  !
-  USE gftm_global
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  !
-  !-------------------------------------------
-  !
-  INTEGER,PARAMETER :: mts=5
-  INTEGER :: m
-  !-----------------------------------------------
-  !
-  REAL :: theta, x_delta
-  REAL :: dtheta
-  REAL :: arg_r,darg_r,arg_z,darg_z
-  REAL :: R_t,Z_t
-  REAL :: R_r, Z_r
-  REAL :: l_t, grad_r, det
-  REAL :: scale_max, l_t1, arclength
-  !
-  !-------------------------------------------
-  ! set global input values
-  !
-  rmin_input = rmin_loc
-  Rmaj_input = rmaj_loc
-  ! set elevation to zero
-  zmaj_loc = 0.0
-  dzmajdx_loc=0.0
-  ! write(*,*)"miller_geo"
-  x_delta = ASIN(delta_loc)
-  ! write(*,*)"pi = ",pi," x_delta = ",x_delta
-  !
-  ! set the flux surface constants needed for mercier-luc
-  !
-  Rmaj_s = rmaj_loc
-  Zmaj_s = zmaj_loc
-  q_s = q_loc
-  if(rmin_loc.lt.0.00001)rmin_loc=0.00001
-  rmin_s = rmin_loc
-  p_prime_s = p_prime_loc
-  q_prime_s = q_prime_loc
-  !
-  !--------------------------------------------------------------
-  !
-  ! compute the arclength around the flux surface
-  !
-  theta = 0.0
-  arg_r = theta+x_delta*sin(theta)
-  darg_r = 1.0+x_delta*cos(theta)
-  arg_z = theta + zeta_loc*sin(2.0*theta)
-  darg_z = 1.0 + zeta_loc*2.0*cos(2.0*theta)
-  r_t = -rmin_loc*sin(arg_r)*darg_r
-  z_t = kappa_loc*rmin_loc*cos(arg_z)*darg_z
-  l_t = SQRT(r_t**2+z_t**2)
-  ! scale dtheta by l_t to keep mts points in each ds interval of size pi_2/ms
-  dtheta = pi_2/(REAL(mts*ms)*l_t)
-  !
-  l_t1 = l_t
-  scale_max=l_t
-  arclength = 0.0
-  do while(theta.lt.pi_2)
-     theta = theta + dtheta
-     if(theta.gt.pi_2)then
-        theta=theta-dtheta
-        dtheta=pi_2-theta
-        theta = pi_2
-     endif
-     ! write(*,*)"theta = ",theta,"dtheta=",dtheta
-     arg_r = theta+x_delta*sin(theta)
-     ! d(arg_r)/dtheta
-     darg_r = 1.0+x_delta*cos(theta)
-     ! dR/dtheta
-     r_t = -rmin_loc*sin(arg_r)*darg_r
-     !
-     arg_z = theta + zeta_loc*sin(2.0*theta)
-     ! d(arg_z)/dtheta
-     darg_z = 1.0 + zeta_loc*2.0*cos(2.0*theta)
-     ! dZ/dtheta
-     z_t = kappa_loc*rmin_loc*cos(arg_z)*darg_z
-     ! dl/dtheta
-     l_t = SQRT(r_t**2+z_t**2)
-     ! arclength along flux surface in poloidal direction
-     arclength = arclength + 0.50*(l_t + l_t1)*dtheta
-     ! save maximum expansion scale for later
-     if(l_t.gt.scale_max) scale_max = l_t
-     l_t1 = l_t
-  enddo
-  Ls = arclength
-  !
-  ! debug
-  ! write(*,*)"arclength = ", arclength
-  ! write(*,*)"scale_max =",scale_max
-  !
-  ! Find the theta points which map to an equally spaced s-grid of ms points along the arclength
-  ! going clockwise from the outboard midplane around the flux surface
-  ! by searching for the theta where dR**2 + dZ**2 >= ds**2 for a centered difference df=f(m+1)-f(m-1).
-  ! This keeps the finite difference error of dR/ds, dZ/ds on the s-grid small
-  !
-  ds = arclength/REAL(ms)
-  ! write(*,*)"ds=",ds
-  t_s(0)=0.0
-  t_s(ms)=-pi_2
-  ! make a first guess based on theta=0.0
-  theta=0.0
-  arg_r = theta+x_delta*sin(theta)
-  darg_r = 1.0+x_delta*cos(theta)
-  arg_z = theta + zeta_loc*sin(2.0*theta)
-  darg_z = 1.0 + zeta_loc*2.0*cos(2.0*theta)
-  r_t = -rmin_loc*sin(arg_r)*darg_r
-  z_t = kappa_loc*rmin_loc*cos(arg_z)*darg_z
-  l_t = SQRT(r_t**2+z_t**2)
-  dtheta = -ds/l_t
-  theta=dtheta
-  l_t1=l_t
-  !
-  do m=1,ms/2
-     arg_r = theta+x_delta*sin(theta)
-     darg_r = 1.0+x_delta*cos(theta)
-     arg_z = theta + zeta_loc*sin(2.0*theta)
-     darg_z = 1.0 + zeta_loc*2.0*cos(2.0*theta)
-     r_t = -rmin_loc*sin(arg_r)*darg_r
-     z_t = kappa_loc*rmin_loc*cos(arg_z)*darg_z
-     l_t = SQRT(r_t**2+z_t**2)
-     dtheta = -ds/(0.5*(l_t+l_t1))
-     t_s(m)=t_s(m-1)+dtheta
-     theta = t_s(m) +dtheta
-     l_t1=l_t
-  enddo
-  ! distribute endpoint error over interior points
-  dtheta = (t_s(ms/2)-(-pi))/REAL(ms/2)
-  ! write(*,*)"enpoint error =",dtheta
-  ! dtheta=0.0
-  ! t_s(ms/2)=-pi
-  do m=1,ms/2
-     t_s(m) = t_s(m)-REAL(m)*dtheta
-     t_s(ms-m)=-pi_2 - t_s(m)
-  enddo
-  ! write(*,*)"t_s(ms/2)+pi=",t_s(ms/2)+pi
-  !
-  ! open(2,file='t_s.dat',status='replace')
-  ! do m=0,ms
-  ! write(2,*)m,t_s(m)
-  ! enddo
-  ! close(2)
-  !
-  !--------------------------------------------------------------
-  !
-  !
-  !---------------------------------------------------------------
-  ! all equilibrium functions satisfy
-  !
-  ! f(0) = f(l_theta)
-  !
-  ! Loop to compute most geometrical quantities needed for Mercie-Luc expansion
-  ! R, Z, R*Bp on flux surface s-grid
-  !
-  ! NOTES:
-  ! If grad_r_theta diverges because denominator goes
-  ! through zero, magnetic field lines are intersecting
-  ! and the magnetic surfaces are not nested.
-  !
-  do m=0,ms
-
-     theta = t_s(m)
-     arg_r = theta + x_delta*sin(theta)
-     darg_r = 1.0 + x_delta*cos(theta)
-     arg_z = theta + zeta_loc*sin(2.0*theta)
-     darg_z = 1.0 + zeta_loc*2.0*cos(2.0*theta)
-
-     ! R(theta)
-     ! Z(theta)
-
-     R(m) = rmaj_loc + rmin_loc*cos(arg_r)
-     Z(m) = Zmaj_loc + kappa_loc*rmin_loc*sin(arg_z)
-
-     ! dR/dtheta
-     ! dZ/dtheta
-
-     R_t = -rmin_loc*sin(arg_r)*darg_r
-     Z_t = kappa_loc*rmin_loc*cos(arg_z)*darg_z
-
-     ! dl/dtheta
-
-     l_t = SQRT(R_t**2+Z_t**2)
-     ! dR/dr
-     ! dZ/dr
-     R_r = drmajdx_loc + drmindx_loc*cos(arg_r) &
-          -sin(arg_r)*s_delta_loc*sin(theta)/sqrt(1.0 - delta_loc**2)
-     Z_r = dzmajdx_loc + kappa_loc*sin(arg_z)*(drmindx_loc +s_kappa_loc) &
-          +kappa_loc*cos(arg_z)*s_zeta_loc*sin(2.0*theta)
-     ! Jacobian
-     det = R_r*z_t - R_t*Z_r
-     ! grad_r
-     grad_r = ABS(l_t/det)
-
-     if(m.eq.0)then
-        B_unit = 1.0/grad_r ! B_unit choosen to make b0x(0)=ky**2 i.e. qrat_geo(0)/b_geo(0)=1.0
-        if(drmindx_loc.eq.1.0)B_unit=1.0 ! Waltz-Miller convention
-        ! write(*,*)"B_unit = ",B_unit
-     endif
-     ! Bp = (r/q) B_unit*Abs(grad_r)/R
-
-
-     Bp(m) = (rmin_s/(q_s*R(m)))*grad_r*B_unit
-     !
-  enddo
-  !
-  !
-  ! write(*,*)"rmin=",rmin_loc,"rmaj=",rmaj_loc,"q_loc=",q_loc
-  ! write(*,*)shift_loc,kappa_loc,delta_loc,s_kappa_loc,s_delta_loc
-  ! open(3,file='Bp.dat',status='replace')
-  ! open(2,file='RZ.dat',status='replace')
-  ! do m=0,ms
-  ! write(3,*)m,Bp(m)
-  ! write(2,*)m,R(m),Z(m)
-  ! enddo
-  ! close(3)
-  ! close(2)
-  !
-  ! Note the definitions:
-  !
-  ! q_prime -> dq/dpsi = dq/dr dr/dpsi
-  ! p_prime -> dp/dpsi = dp/dr dr/dpsi
-  !
-  ! R B_p
-  ! and dpsi/dr = -------- = b_unit (r/q)
-  ! |grad r|
-  !
-  ! So, we can write:
-  ! 2
-  ! q_prime = (q/r) s/b_unit
-  ! p_prime = (q/r) (1/b_unit) dp/dr
-  ! = (q/r) (1/b_unit) p * dlnpdr
-  ! rescale p_prime and q_prime to keep normalized eikonal invariant
-  p_prime_s = p_prime_loc*B_unit ! B_unit**2/B_unit
-  q_prime_s = q_prime_loc/B_unit !
-  ! write(*,*)"p_prime_s =",p_prime_s,"q_prime_s =",q_prime_s
-  !
-END SUBROUTINE miller_geo
-!
-!---------------------------------------------------------------
-!
-SUBROUTINE fourier_geo
-  ! maps the fourier representation of R,Z onto the contour s-grid
-  ! and computes Bp,t_s, Ls used by mercier-luc
-  !
-  USE gftm_global
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  !
-  !-------------------------------------------
-  !
-  INTEGER,PARAMETER :: mts=5
-  INTEGER :: n, m
-  !-----------------------------------------------
-  !
-  REAL :: theta, nr
-  REAL :: dtheta
-  REAL :: arg
-  REAL :: R_t,Z_t
-  REAL :: R_r, Z_r
-  REAL :: l_t, grad_r, det
-  REAL :: scale_max, l_t1, arclength
-  !
-  !--------------------------------------------------------------
-  !
-  ! set the flux surface constants needed for mercier-luc
-  !
-  Rmaj_s = fourier_in(1,0)/2.0
-  Zmaj_s = fourier_in(3,0)/2.0
-  q_s = q_fourier_in
-  rmin_s = fourier_in(1,1)
-  ! write(*,*)"Rmaj_s=",Rmaj_s,"Zmaj_s=",Zmaj_s,"q_s=",q_s,"rmin_s=",rmin_s
-  rmin_s=MAX(rmin_s,0.00001)
-  p_prime_s = p_prime_fourier_in
-  q_prime_s = q_prime_fourier_in
-  !
-  ! set global input values
-  !
-  rmin_input = rmin_s
-  Rmaj_input = Rmaj_s
-  !
-  ! compute the arclength around the flux surface
-  !
-  theta = 0.0
-  R_t = 0.0
-  Z_t = 0.0
-  ! write(*,*)"nfourier_in=",nfourier_in
-  do n=1,nfourier_in
-     nr = REAL(n)
-     arg = nr*theta
-     R_t = R_t -nr*fourier_in(1,n)*SIN(arg) + nr*fourier_in(2,n)*COS(arg)
-     Z_t = Z_t -nr*fourier_in(3,n)*SIN(arg) + nr*fourier_in(4,n)*COS(arg)
-  enddo
-  l_t = SQRT(r_t**2+z_t**2)
-  ! scale dtheta by l_t to keep mts points in each ds interval of size pi_2/ms
-  dtheta = pi_2/(REAL(mts*ms)*l_t)
-  !
-  l_t1 = l_t
-  scale_max=l_t
-  arclength = 0.0
-  do while(theta.lt.pi_2)
-     theta = theta + dtheta
-     if(theta.gt.pi_2)then
-        theta=theta-dtheta
-        dtheta=pi_2-theta
-        theta = pi_2
-     endif
-     R_t = 0.0
-     Z_t = 0.0
-     do n=1,nfourier_in
-        nr = REAL(n)
-        arg = nr*theta
-        R_t = R_t -nr*fourier_in(1,n)*SIN(arg) + nr*fourier_in(2,n)*COS(arg)
-        Z_t = Z_t -nr*fourier_in(3,n)*SIN(arg) + nr*fourier_in(4,n)*COS(arg)
-     enddo
-     ! dl/dtheta
-     l_t = SQRT(r_t**2+z_t**2)
-     ! arclength along flux surface in poloidal direction
-     arclength = arclength + 0.50*(l_t + l_t1)*dtheta
-     ! save maximum expansion scale for later
-     if(l_t.gt.scale_max) scale_max = l_t
-     l_t1 = l_t
-  enddo
-  Ls = arclength
-  !
-  ! debug
-  ! write(*,*)"arclength = ", arclength
-  ! write(*,*)"scale_max =",scale_max
-  !
-  ! Find the theta points which map to an equally spaced s-grid of ms points along the arclength
-  ! going clockwise from the outboard midplane around the flux surface
-  ! by searching for the theta where dR**2 + dZ**2 >= ds**2 for a centered difference df=f(m+1)-f(m-1).
-  ! This keeps the finite difference error of dR/ds, dZ/ds on the s-grid small
-  !
-  ds = arclength/REAL(ms)
-  ! write(*,*)"ds=",ds
-  t_s(0)=0.0
-  t_s(ms)=-pi_2
-  ! make a first guess based on theta=0.0
-  theta=0.0
-  R_t = 0.0
-  Z_t = 0.0
-  do n=1,nfourier_in
-     nr = REAL(n)
-     arg = nr*theta
-     R_t = R_t -nr*fourier_in(1,n)*SIN(arg) + nr*fourier_in(2,n)*COS(arg)
-     Z_t = Z_t -nr*fourier_in(3,n)*SIN(arg) + nr*fourier_in(4,n)*COS(arg)
-  enddo
-  l_t = SQRT(r_t**2+z_t**2)
-  dtheta = -ds/l_t
-  theta=dtheta
-  l_t1=l_t
-  !
-  do m=1,ms/2
-     R_t = 0.0
-     Z_t = 0.0
-     do n=1,nfourier_in
-        nr = REAL(n)
-        arg = nr*theta
-        R_t = R_t -nr*fourier_in(1,n)*SIN(arg) + nr*fourier_in(2,n)*COS(arg)
-        Z_t = Z_t -nr*fourier_in(3,n)*SIN(arg) + nr*fourier_in(4,n)*COS(arg)
-     enddo
-     l_t = SQRT(r_t**2+z_t**2)
-     dtheta = -ds/(0.5*(l_t+l_t1))
-     t_s(m)=t_s(m-1)+dtheta
-     theta = t_s(m) +dtheta
-     l_t1=l_t
-  enddo
-  ! distribute endpoint error over interior points
-  dtheta = (t_s(ms/2)-(-pi))/REAL(ms/2)
-  ! write(*,*)"enpoint error =",dtheta
-  ! dtheta=0.0
-  ! t_s(ms/2)=-pi
-  do m=1,ms/2
-     t_s(m) = t_s(m)-REAL(m)*dtheta
-     t_s(ms-m)=-pi_2 - t_s(m)
-  enddo
-  ! write(*,*)"t_s(ms/2)+pi=",t_s(ms/2)+pi
-  !
-  ! open(2,file='t_s.dat',status='replace')
-  ! do m=0,ms
-  ! write(2,*)m,t_s(m)
-  ! enddo
-  ! close(2)
-  !
-  !---------------------------------------------------------------
-  ! all equilibrium functions satisfy
-  !
-  ! f(0) = f(l_theta)
-  !
-  ! Loop to compute most geometrical quantities needed for Mercie-Luc expansion
-  ! R, Z, R*Bp on flux surface s-grid
-  !
-  ! NOTES:
-  ! If grad_r_theta diverges because denominator goes
-  ! through zero, magnetic field lines are intersecting
-  ! and the magnetic surfaces are not nested.
-  !
-  !--------------------------------------------------------------
-  !
-  ! compute R,Z,BP on the arc-length s-grid
-  !
-  do m=0,ms
-     theta = t_s(m)
-     R(m) = fourier_in(1,0)/2.0
-     Z(m) = fourier_in(3,0)/2.0
-     R_t = 0.0
-     Z_t = 0.0
-     R_r = fourier_in(5,0)/2.0
-     Z_r = fourier_in(7,0)/2.0
-     do n=1,nfourier_in
-        ! R(theta)
-        ! Z(theta)
-        nr=REAL(n)
-        arg = theta*nr
-        R(m) = R(m) + fourier_in(1,n)*COS(arg) + fourier_in(2,n)*SIN(arg)
-        Z(m) = Z(m) + fourier_in(3,n)*COS(arg) + fourier_in(4,n)*SIN(arg)
-
-        ! dR/dtheta
-        ! dZ/dtheta
-        ! note these are derivatives wrt the fourier theta variable
-        ! the factors dtheta/ds needed to take s-derivatives drop out of the grad_r calculation
-
-        R_t = R_t -nr*fourier_in(1,n)*SIN(arg) + nr*fourier_in(2,n)*COS(arg)
-        Z_t = Z_t -nr*fourier_in(3,n)*SIN(arg) + nr*fourier_in(4,n)*COS(arg)
-
-        ! dR/dr
-        ! dZ/dr
-        R_r = R_r + fourier_in(5,n)*COS(arg) + fourier_in(6,n)*SIN(arg)
-        Z_r = Z_r + fourier_in(7,n)*COS(arg) + fourier_in(8,n)*SIN(arg)
-     enddo
-     ! dl/dtheta
-
-     l_t = SQRT(R_t**2+Z_t**2)
-     ! Jacobian
-     det = R_r*z_t - R_t*Z_r
-     ! grad_r
-     grad_r = ABS(l_t/det)
-     !
-     B_unit = 1.0
-     ! if(m.eq.0)then
-     ! B_unit = 1.0/grad_r ! B_unit choosen to make bx(0)=ky**2 i.e. qrat_geo(0)/b_geo(0)=1.0
-     ! if(drmindx_loc.eq.1.0)B_unit=1.0 ! Waltz-Miller convention
-     ! write(*,*)"B_unit = ",B_unit
-     ! endif
-     ! Bp = (r/q) B_unit*Abs(grad_r)/R
-
-
-     Bp(m) = (rmin_s/(q_s*R(m)))*grad_r*B_unit
-     !
-  enddo
-
-  !
-  ! open(3,file='Bp.dat',status='replace')
-  ! open(2,file='RZ.dat',status='replace')
-  ! do m=0,ms
-  ! write(3,*)m,Bp(m)
-  ! write(2,*)m,R(m),Z(m)
-  ! enddo
-  ! close(3)
-  ! close(2)
-  !
-  ! Note the definitions:
-  !
-  ! q_prime -> dq/dpsi = dq/dr dr/dpsi
-  ! p_prime -> dp/dpsi = dp/dr dr/dpsi
-  !
-  ! R B_p
-  ! and dpsi/dr = -------- = b_unit (r/q)
-  ! |grad r|
-  !
-  ! So, we can write:
-  ! 2
-  ! q_prime = (q/r) s/b_unit
-  ! p_prime = (q/r) (1/b_unit) dp/dr
-  ! = (q/r) (1/b_unit) p * dlnpdr
-  ! rescale p_prime and q_prime to keep normalized eikonal invariant
-  p_prime_s = p_prime_fourier_in*B_unit ! B_unit**2/B_unit
-  q_prime_s = q_prime_fourier_in/B_unit !
-  ! write(*,*)"p_prime_s =",p_prime_s,"q_prime_s =",q_prime_s
-  !
-END SUBROUTINE fourier_geo
-!
-!--------------------------------------------------------------------
-!
-SUBROUTINE ELITE_geo
-  !
-  ! interpolates the input R_ELITE,Z_ELITE,Bp_ELITE onto the s-grid
-  ! used by mercier_luc and sets the arclength Ls and differential ds
-  !
-  USE gftm_global
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  !
-  INTEGER :: i,j,k,imax,im,ip
-  REAL :: arclength,drde,dzde,de
-  REAL :: Rmax,Zmax,Bpmax,emax,Zmin,Rmin
-  REAL :: e_length,s_length
-  REAL :: da
-  REAL :: a,b,c
-  REAL :: area,R0,Z0
-  !
-  ! compute the arclength, area and centroid cooridinates of the flux surface
-  !
-  Rmax = R_ELITE(0)
-  Rmin = R_ELITE(0)
-  Zmax = Z_ELITE(0)
-  Zmin = Z_ELITE(0)
-  imax=0
-  drde = (R_ELITE(1)-R_ELITE(n_ELITE))/2.0
-  dzde = (Z_ELITE(1)-Z_ELITE(n_ELITE))/2.0
-  da = SQRT(drde**2 + dzde**2)
-  arclength = da
-  area = ABS(drde)*ABS(Z_ELITE(0))
-  ! integral from 0.0 to ABS(Z_ELITE(i)) at each R_ELITE assuming Z=0 is inside of the flux surface
-  ! this makes it unecessary to find the Z reflected across Z=0 a the same R
-  Z0 = ABS(drde)*ABS(Z_ELITE(0))*Z_ELITE(0)/2.0
-  R0 = ABS(drde)*ABS(Z_ELITE(0))*(R_ELITE(1)+R_ELITE(n_ELITE))/2.0
-  do i=1,n_ELITE-1
-     if(Z_ELITE(i).gt.Zmax)Zmax = Z_ELITE(i)
-     if(Z_ELITE(i).lt.Zmin)Zmin = Z_ELITE(i)
-     if(R_ELITE(i).lt.Rmin)Rmin = R_ELITE(i)
-     if(R_ELITE(i).gt.Rmax)then
-        Rmax = R_ELITE(i)
-        imax = i
-     endif
-     drde = (R_ELITE(i+1)-R_ELITE(i-1))/2.0
-     dzde = (Z_ELITE(i+1)-Z_ELITE(i-1))/2.0
-     da = SQRT(drde**2 + dzde**2)
-     arclength = arclength + da
-     area = area + ABS(drde)*ABS(Z_ELITE(i))
-     Z0 = Z0 + ABS(drde)*ABS(Z_ELITE(i))*Z_ELITE(i)/2.0
-     R0 = R0 + ABS(drde)*ABS(Z_ELITE(i))*(R_ELITE(i+1)+R_ELITE(i-1))/2.0
-  enddo
-  write(*,*)"imax = ",imax,"Rmax = ",Rmax,"Rmin = ",Rmin
-  write(*,*)"Zmax = ",Zmax,"Zmin = ",Zmin
-  de = arclength/REAL(n_ELITE)
-  ds = arclength/REAL(ms)
-  Z0 = Z0/area
-  R0 = R0/area
-  write(*,*)"area = ",area,"volume = ",pi_2*R0*area
-  write(*,*)"Z0 = ",Z0,"R0 = ",R0
-  write(*,*)"arclength = ",arclength
-  !
-  ! set global input values
-  !
-  rmin_input = (Rmax-Rmin)/2.0
-  Rmaj_input = (Rmax+Rmin)/2.0
-
-  !
-  ! find the major and minor radius at Z0
-  !
-  ! signdZ=1.0
-  ! if(Z_ELITE(0).lt.Z)signZ=-1.0
-  !
-  ! i1 = 0
-  ! do i=0,n_ELITE
-  ! if(Z_ELITE
-  !
-  ! enddo
-  !
-  ! find maximum of quardratic fit through R(e): R(e) = a + b e + c e^2
-  !
-  im = imax-1
-  if(im.lt.0)im=n_ELITE-1
-  ip = imax + 1
-  a = R_ELITE(im)
-  b = (2.0*R_ELITE(imax)-0.5*R_ELITE(ip)-1.5*R_ELITE(im))/de
-  c = (0.5*R_ELITE(ip)+0.5*R_ELITE(im)-R_ELITE(imax))/de**2
-  ! dR/de=0 at emax=-b/(2 c)
-  emax= -b/(2.0*c)
-  write(*,*)"emax/de=",emax/de
-  Rmax = a + b*emax + c*emax**2
-  ! interpolate Z,Bp onto the point emax
-  a = Z_ELITE(im)
-  b = (2.0*Z_ELITE(imax)-0.5*Z_ELITE(ip)-1.5*Z_ELITE(im))/de
-  c = (0.5*Z_ELITE(ip)+0.5*Z_ELITE(im)-Z_ELITE(imax))/de**2
-  Zmax = a + b*emax + c*emax**2
-  a = Bp_ELITE(im)
-  b = (2.0*Bp_ELITE(imax)-0.5*Bp_ELITE(ip)-1.5*Bp_ELITE(im))/de
-  c = (0.5*Bp_ELITE(ip)+0.5*Bp_ELITE(im)-Bp_ELITE(imax))/de**2
-  Bpmax = a + b*emax + c*emax**2
-  !
-  ! compute B_unit = d psi/dr *(q/r)
-  !
-  rmin_s = arclength/pi_2
-  B_unit = Rmax*Bpmax*q_ELITE/rmin_s ! this choice makes bx(0) = ky^2 i.e. qrat_geo(0)/b_geo(0)=1.0
-  B_unit = 1.0
-  !
-  ! interpolate R,Z,Bp onto the s-grid
-  !
-  if(emax/de.lt.1.0)then
-     imax=im
-  else
-     emax = emax - de
-  endif
-  e_length = -emax
-  s_length = ds
-  R(0) = Rmax
-  Z(0) = 0.0
-  Bp(0) = Bpmax/B_unit
-  k = 0
-  do i=1,n_ELITE-1
-     j = imax + i
-     if(j .gt. n_ELITE)then
-        ! wrap around the flux surface
-        j = imax + i - n_ELITE
-     endif
-     e_length = e_length + de
-     if(e_length.gt.s_length)then
-        k = k+1
-        R(k) = R_ELITE(j-1)+(R_ELITE(j)-R_ELITE(j-1))*(e_length-s_length)/de
-        Z(k) = Z_ELITE(j-1)+(Z_ELITE(j)-Z_ELITE(j-1))*(e_length-s_length)/de - Zmax
-        Bp(k) = (Bp_ELITE(j-1)+(Bp_ELITE(j)-Bp_ELITE(j-1))*(e_length-s_length)/de)/B_unit
-        s_length = s_length + ds
-     endif
-  enddo
-  R(ms) = R(0)
-  Z(ms) = Z(0)
-  Bp(ms) = Bp(0)
- ! write(*,*)"k = ",k
-  !
-  ! set remaining variables for gftm_sgrid input
-  !
-  Ls = arclength
-  Rmaj_s = Rmax
-  p_prime_s = p_prime_ELITE
-  q_s = q_ELITE
-  q_prime_s = q_prime_ELITE
-  ! debug
- ! write(*,*)"Rmax = ",Rmax
- ! write(*,*)"Zmax = ",Zmax
- ! write(*,*)"Bpmax = ",Bpmax
- ! write(*,*)"B_unit = ",B_unit
- ! write(*,*)"Ls = ",Ls
- ! write(*,*)"ds = ",ds
- ! write(*,*)"Rmaj_s =",Rmaj_s
- ! write(*,*)"rmin_s = ",rmin_s
- ! write(*,*)"p_prime_s = ",p_prime_s
- ! write(*,*)"q_s = ",q_s
- ! write(*,*)"q_prime_s = ",q_prime_s
-  ! open(3,file='Bp.dat',status='replace')
-  ! open(2,file='RZ.dat',status='replace')
-  ! do i=0,ms
-  ! write(3,*)i,Bp(i)
-  ! write(2,*)i,R(i),Z(i)
-  ! enddo
-  ! close(3)
-  ! close(2)
-  !
-END SUBROUTINE ELITE_geo
diff --git a/gftm/src/gftm_hermite.f90 b/gftm/src/gftm_hermite.f90
deleted file mode 100644
index fedb79102..000000000
--- a/gftm/src/gftm_hermite.f90
+++ /dev/null
@@ -1,163 +0,0 @@
-!
-!***********************
-! start of gauher
-!
-      SUBROUTINE gauher
-!
-!     computes abscisca's and weights for Gauss- Hermite integration
-!     adapted from Numerical Recipes in Fortran Pg.147
-!     reversed order of roots so that x(m) is largest and x(1) is smallest
-!     only the positive roots are found and stored
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_hermite
-!
-      IMPLICIT NONE
-      REAL,PARAMETER :: eps=3.0E-14
-      INTEGER,PARAMETER:: maxit=100
-      INTEGER :: n
-      INTEGER :: i,its,j,m
-      REAL :: h0
-      REAL :: y(nxm),wy(nxm)    
-      REAL :: p1,p2,p3,pp,z,z1
-!
-      gauher_uncalled = .FALSE.
-!
-      nx = 2*nxgrid_in -1
-!      write(*,*)"gauher",nx
-      h0 = 1.0/pi**0.25
-!
-! set up the hermite basis x-grid
-!
-      m = (nx+1)/2
-!
-      n = 2*m-1
-      do i=m,1,-1
-!       choose initial guess z
-        if(i.eq.m)then
-         z = SQRT(REAL(2*n+1))-1.85575*REAL(2*n+1)**(-0.16667)
-        elseif(i.eq.m-1)then
-         z = z - 1.14*n**.426/z
-        elseif(i.eq.m-2)then
-         z = 1.86*z - 0.86*y(m)
-        elseif(i.eq.m-3)then
-         z=1.91*z - 0.91*y(m-1)
-        else
-         z = 2.0*z - y(i+2)
-        endif
-        do its = 1,maxit
-          p1 = h0
-          p2 = 0.0
-          do j=1,n
-            p3 = p2
-            p2 = p1
-            p1 = z*SQRT(2.0/REAL(j))*p2 - SQRT(REAL(j-1)/REAL(j))*p3
-          enddo
-          pp = SQRT(2.0*REAL(n))*p2
-          z1 = z
-          z = z1 - p1/pp
-          if(ABS(z-z1).le.eps)exit
-         enddo
-!         write(*,*)i,"its = ",its
-         y(i) = z
-         wy(i) = 2.0/(pp*pp)
-      enddo
-         wy(1) = wy(1)/2.0
-!
-!      write(*,*)"*** check x,wx ***"
-!      do i=1,nx
-!       write(*,*)x(i),wx(i)
-!      enddo
-      do i=1,m
-        x(m+i-1) = y(i)
-        x(i) = - y(m+1-i)
-        wx(m+i-1) = wy(i)/2.0
-        wx(i) = wy(m+1-i)/2.0
-      enddo
-      x(m)=0.0
-      wx(m) = 2.0*wx(m)
-!      write(*,*)"  check weights "
-!      do i=1,nx
-!       write(*,*)x(i),wx(i)
-!      enddo
-      END SUBROUTINE gauher
-!    
-!***********************
-! start of gauss_hermite
-!
-      SUBROUTINE gauss_hermite
-!
-!     initializes the hermite basis functions and
-!     ten point Gauss-Hermite integration with absissas x
-!     and weights w.
-!
-!     The hermite basis functions of the wave function are
-!       H(1,i) = 1.0
-!       H(2,i) = 2.0*x(i)
-!       for j>= 3
-!       H(j,i) = 2.0*x(i)*H(j-1,i)-2.0*(j-2)*H(j-2,i)
-!
-!       H(3,i) = 4.0*x(i)**2 -2.0
-!       H(4,i) = 8.0*x(i)**3 -12.0*x(i)
-!       H(5,i) = 16.0*x(i)**4 -48.0*x(i)**2 + 12.0
-!       H(6,i) = 32.0*x(i)**5 -160.0*x(i)**3 + 120.0*x(i)
-!       H(7,i) = 64.0*x(i)**6 -480.0*x(i)**4 +720.0*x(i)**2 -120.0
-!       H(8,i) = 128.0*x(i)**7 -1344.0*x(i)**5 +3360.0*x(i)**3 -1680.0*x(i)
-!       H(9,i) = 256.0*x(i)**8 -3584.0*x(i)**6 +13440.0*x(i)**4 -13440.0*x(i)**2 +1680.0
-!       H(10,i)= 512.0*x(i)**9 -9216.0*x(i)**7 +48384.0*x(i)**5 -80640.0*x(i)**3 +30240.0*x(i)
-!       H(11,i)= 1024.0*x(i)**10 -23040.0*x(i)**8 +161280.0*x(i)**6 -403200.0*x(i)**4 +302400.0*x(i)**2 -30240.0
-!     The normalized hermite polynomial are
-!       h(j+1,i) = H(j,i)/SQRT(sum(w*H(j)**2))
-!     These have been pre-evaluated for speed.
-!     They are orthonormal with error of 1.0E-8.
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_hermite
-!
-      IMPLICIT NONE
-      INTEGER :: i,j
-      REAL :: h0
-!
-      gauss_hermite_uncalled = .FALSE.
-!      write(*,*)"hermite",nbasis
-      h0 = sqrt_two/pi**0.25
-      do i=1,nx
-       h(1,i) = h0
-       h(2,i) = x(i)*sqrt_two*h0
-       if(nbasis.gt.2)then
-         do j=3,nbasis+1
-          h(j,i) = x(i)*SQRT(2.0/REAL(j-1))*h(j-1,i) &
-           - SQRT(REAL(j-2)/REAL(j-1))*h(j-2,i)
-         enddo
-       endif
-      enddo
-!      write(*,*)"hemite",nbasis,nx
-!      do j=1,nx
-!       write(*,*)(h(i,j),i=1,nbasis)
-!      enddo
-!      do i=1,nbasis
-!        h2(i,i)=0.0
-!        do k=1,nx
-!         h2(i,i) = h2(i,i) + wx(k)*h(i,k)*h(i,k)
-!        enddo
-!      enddo
-!      do i=1,nbasis
-!      do k=1,nx
-!        h(i,k) = h(i,k)/SQRT(h2(i,i))
-!      enddo
-!      enddo
-!       write(*,*)"***** Hermite ***"
-!      do i=1,nbasis
-!      do j=i,nbasis
-!       h2(i,j)=0.0
-!      do k=1,nx
-!         h2(i,j) = h2(i,j) + wx(k)*h(i,k)*h(j,k)
-!      enddo
-!        write(*,*)i,j,h2(i,j)
-!      enddo
-!      enddo
-!
-      END SUBROUTINE gauss_hermite
-
diff --git a/gftm/src/gftm_init_mpi.f90 b/gftm/src/gftm_init_mpi.f90
deleted file mode 100644
index 200b3719f..000000000
--- a/gftm/src/gftm_init_mpi.f90
+++ /dev/null
@@ -1,60 +0,0 @@
-!\
-! module for MPI version of gftm
-!/
-
-      MODULE gftm_mpi
-
-        use mpi
-
-        IMPLICIT NONE
-
-        ! local communicator
-        integer :: iCommgftm    = -1
-        integer :: iProcgftm    = -1
-        integer :: nProcgftm    = -1
-        integer :: iProc0gftm   = 0
-        integer :: iGroupIDgftm = 1
-
-      END MODULE gftm_mpi
-!
-!______________________________________________________
-!
-!--------------------------------------------------------------
-! gftm_init.f90
-!
-! PURPOSE:
-!  Initialize external gftm interface.
-!---------------------------------------------------------------
-
-subroutine gftm_init(path_in,mpi_comm_in)
-
-  use gftm_interface
-  use gftm_mpi
-
-  implicit none
-
-  ! Input parameters (IN) - REQUIRED
-  character(len=*), intent(in) :: path_in
-  integer,          intent(in) :: mpi_comm_in
-  integer :: ierr
-
-  ! Local variable
-  logical :: inputdat_flag
-
-  gftm_path_in = path_in
-  iCommgftm    = mpi_comm_in
-
-  call MPI_COMM_RANK(iCommgftm,iProcgftm,ierr)
-  call MPI_COMM_SIZE(iCommgftm,nProcgftm,ierr)
-
-  inquire(file=trim(path_in)//'input.gftm.gen',exist=inputdat_flag)
-
-  if (inputdat_flag .eqv. .true.) then
-     if (gftm_quiet_flag_in .eqv. .false.) then
-        print '(a,a,a)', 'INFO: (gftm) gftm_init reading ',trim(path_in),'input.gftm.gen'
-     endif
-     call gftm_read_input
-  endif
-
-end subroutine gftm_init
-
diff --git a/gftm/src/gftm_inout.f90 b/gftm/src/gftm_inout.f90
deleted file mode 100644
index 4065a97d3..000000000
--- a/gftm/src/gftm_inout.f90
+++ /dev/null
@@ -1,2137 +0,0 @@
-!-----------------------------------------------------------------
-!  input routines
-!-----------------------------------------------------------------
-SUBROUTINE put_units(units)
-!
-USE gftm_global
-!
-IMPLICIT NONE
-CHARACTER (len=*) :: units
-
-if(units .eq. 'GYRO' .or. units .eq. 'CGYRO' .or. units .eq. 'GENE')then
-   units_in = units
-else
-   call gftm_error(1,"Invalid units selected")
-endif
-!
-END SUBROUTINE put_units
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_species(nsp,zsp,msp)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN):: nsp
-  REAL,INTENT(IN) :: zsp(nsm),msp(nsm)
-  INTEGER :: is
-  !
-  use_default_species=.FALSE.
-! check for valid input
-  if(nsp.lt.2.or.nsp.gt.nsm)call gftm_error(1,"input number of species invlaid")
-  do is=1,nsp
-    if(gftm_isnan(zsp(is)))call gftm_error(1,"input zs_in is NAN")
-    if(gftm_isinf(zsp(is)))call gftm_error(1,"input zs_in is INF")
-    if(gftm_isnan(msp(is)))call gftm_error(1,"input mass_in is NAN")
-    if(gftm_isinf(msp(is)))call gftm_error(1,"input mass_in is INF")
-    if(ABS(zsp(is)).lt.1.0)call gftm_error(1,"input ABS(zs_in) is < 1")
-    if(msp(is).le.0.0)call gftm_error(1,"input mass_in is <= 0")
-  enddo
-  ! transfer values
-  ns_in = nsp
-  do is=1,nsp
-      zs_in(is)=zsp(is)
-      mass_in(is)=msp(is)
-  enddo
-  new_matrix = .TRUE.
-  !
-END SUBROUTINE put_species
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_kys(kys)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: kys
-
-  if(gftm_isnan(kys))call gftm_error(1,"input ky_in is NAN")
-  if(gftm_isinf(kys))call gftm_error(1,"input ky_in is INF")
-  if(kys.le.0)call gftm_error(1,"input kys is <= 0")
-  !
-  ! transfer values
-  !
-  ky_in = kys
-  !
-END SUBROUTINE put_kys
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_signs(sign_Bt,sign_It)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: sign_Bt,sign_It
-
-  if(gftm_isnan(sign_Bt))call gftm_error(1,"input sign_Bt_in is NAN")
-  if(gftm_isnan(sign_It))call gftm_error(1,"input sign_It_in is NAN")
-  !
-  ! transfer values
-  !
-  sign_Bt_in = sign_Bt
-  sign_It_in = sign_It
-  !
-END SUBROUTINE put_signs
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_gaussian_width(width,width_min,nwidth,find_width)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  LOGICAL,INTENT(IN) :: find_width
-  INTEGER,INTENT(IN) :: nwidth
-  REAL,INTENT(IN) :: width,width_min
-
-  if(gftm_isnan(width))call gftm_error(1,"input width_in is NAN")
-  if(gftm_isinf(width))call gftm_error(1,"input width_in is INF")
-  if(gftm_isnan(width_min))call gftm_error(1,"input width_min_in is NAN")
-  if(gftm_isinf(width_min))call gftm_error(1,"input width_min_in is INF")
-  if(nwidth.le.0)call gftm_error(1,"input nwidth_in <= 0")
-
-  !
-  ! update flow controls
-  ! 
-  new_width = .TRUE.
-  !
-  ! transfer values
-  !
-  width_in = width
-  width_min_in=width_min
-  find_width_in = find_width
-  width_in = 1.74
-  width_min_in = width_in
-  find_width_in = .false.
-  nwidth_in=MIN(nwidth,nt0)
-  !
-END SUBROUTINE put_gaussian_width
-!
-!
-SUBROUTINE put_eikonal(new_eikonal)
-  !*********************************************
-  !
-  !*********************************************
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  LOGICAL,INTENT(IN) :: new_eikonal
-  !
-  !  set flow control switch
-  !
-  new_eikonal_in = new_eikonal
-  ! check consistency
-  if(new_eikonal_in)then
-     eikonal_unsaved=.TRUE.
-  else
-     if(eikonal_unsaved)then
-        write(*,*)"warning put_eikonal:"
-        write(*,*)"new_eikonal = .FALSE.attempted before call with new_eikonal=.TRUE."
-        new_eikonal_in = .TRUE.
-     endif
-  endif
-  !
-END SUBROUTINE put_eikonal
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_gradients(rln,rlt,vpar_shear,vexb_shear)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: rln(nsm),rlt(nsm),vpar_shear(nsm)
-  REAL,INTENT(IN) :: vexb_shear
-  INTEGER :: is
-
-  do is=1,nsm
-   if(gftm_isnan(rln(is)))call gftm_error(1,"input rlns_in is NAN")
-   if(gftm_isinf(rln(is)))call gftm_error(1,"input rlns_in is INF")
-   if(gftm_isnan(rlt(is)))call gftm_error(1,"input rlts_in is NAN")
-   if(gftm_isnan(rlt(is)))call gftm_error(1,"input rlts_in is INF")
-   if(gftm_isnan(vpar_shear(is)))call gftm_error(1,"input vpar_shear_in is NAN")
-   if(gftm_isnan(vpar_shear(is)))call gftm_error(1,"input vpar_shear_in is INF")
-  enddo
-  if(gftm_isnan(vexb_shear))call gftm_error(1,"input vexb_shear_in is NAN")
-  if(gftm_isinf(vexb_shear))call gftm_error(1,"input vexb_shear_in is INF")
-
-  !
-  ! transfer values
-  !
-  do is=1,nsm
-     rlns_in(is) = rln(is)
-     rlts_in(is) = rlt(is)
-     vpar_shear_in(is) = vpar_shear(is)
-  enddo
-  vexb_shear_in = vexb_shear
-  !    
-END SUBROUTINE put_gradients
-!
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_profile_shear(vns_shear,vts_shear)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: vns_shear(nsm),vts_shear(nsm)
-  INTEGER :: is
-  !
-  ! transfer values
-  !
-  do is=1,nsm
-     vns_shear_in(is) = vns_shear(is)
-     vts_shear_in(is) = vts_shear(is)
-  enddo
-  !    
-END SUBROUTINE put_profile_shear
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_averages(tsp,asp,vpar,vexb,betae,xnue,zeff,debye)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: tsp(nsm),asp(nsm),vpar(nsm)
-  REAL,INTENT(IN) :: vexb,betae,xnue,zeff,debye
-  INTEGER :: is, count
-
-  do is=1,nsm
-    if(gftm_isnan(tsp(is)))call gftm_error(1,"input taus_in is NAN")
-    if(gftm_isinf(tsp(is)))call gftm_error(1,"input taus_in is INF")
-    if(tsp(is).lt.0.0)call gftm_error(1,"input taus_in is < 0")
-    if(gftm_isnan(asp(is)))call gftm_error(1,"input as_in is NAN")
-    if(gftm_isinf(asp(is)))call gftm_error(1,"input as_in is INF")
-    if(asp(is).lt.0.0)call gftm_error(1,"input as_in is < 0")
-    if(gftm_isnan(vpar(is)))call gftm_error(1,"input vpar_in is NAN")
-    if(gftm_isinf(vpar(is)))call gftm_error(1,"input vpar_in is INF")
-  enddo
-    if(gftm_isnan(vexb))call gftm_error(1,"input vexb_in is NAN")
-    if(gftm_isinf(vexb))call gftm_error(1,"input vexb_in is INF")
-    if(gftm_isnan(betae))call gftm_error(1,"input betae_in is NAN")
-    if(gftm_isinf(betae))call gftm_error(1,"input betae_in is INF")
-    if(betae.lt.0.0)call gftm_error(1,"input betae_in is < 0")
-    if(gftm_isnan(xnue))call gftm_error(1,"input xnue_in is NAN")
-    if(gftm_isinf(xnue))call gftm_error(1,"input xnue_in is INF")
-    if(xnue.lt.0.0)call gftm_error(1,"input xnue_in is < 0")
-    if(gftm_isnan(zeff))call gftm_error(1,"input zeff_in is NAN")
-    if(gftm_isinf(zeff))call gftm_error(1,"input zeff_in is INF")
-    if(zeff.lt.0.0)call gftm_error(1,"input zeff_in is < 0")
-    if(gftm_isnan(debye))call gftm_error(1,"input debye_in is NAN")
-    if(gftm_isinf(debye))call gftm_error(1,"input debye_in is INF")
-    if(debye.lt.0.0)call gftm_error(1,"input debye_in is < 0")
-  !
-  ! set flow control switch
-  new_matrix = .TRUE.
-  ! transfer values
-  count = 0
-  do is=1,nsm
-     taus_in(is) = tsp(is)
-     as_in(is) = asp(is)
-     vpar_in(is) = vpar(is)
-      if(as_in(is) .gt. 0.0) count = count +1
-  enddo
-  nstotal_in = count
-  if(as_in(1) .le. 0.0 .or. as_in(2) .le. 0.0)then
-     write(*,*)"error: electron or ion density <= zero. Setting them both to 1.0"
-      as_in(1) = 1.0
-      as_in(2) = 1.0
-  endif
-  if(taus_in(1) .le. 0.0 .or. taus_in(2) .le. 0.0)then
-     write(*,*)"error: electron or ion temperature <= zero. Setting them both to 1.0"
-      taus_in(1) = 1.0
-      taus_in(2) = 1.0
-  endif
-  vexb_in = vexb
-  betae_in = betae
-  xnue_in = xnue
-  zeff_in = zeff
-  debye_in = debye
-  !      
-END SUBROUTINE put_averages
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_switches(iflux,use_bper,use_bpar,use_mhd_rule,use_bisection, &
-     use_inboard_detrapped,ibranch,nmodes,nb_max,nb_min,nxgrid,nkys,use_ave_ion_grid)
-  !
-  USE gftm_global
-  USE gftm_dimensions
-  !
-  IMPLICIT NONE
-  LOGICAL :: iflux,use_bper,use_bpar,use_mhd_rule,use_bisection
-  LOGICAL :: use_inboard_detrapped, use_ave_ion_grid
-  INTEGER :: ibranch,nmodes,nb_max,nb_min
-  INTEGER :: nxgrid,nkys
-  !
-  ! validaty checks
-  ! reset to defaults if invlaid
-  !
-  if(nb_max.lt.2.or.nb_max.gt.nb)nb_max=nbasis_max_in
-  if(nb_min.lt.2.or.nb_min.gt.nb)nb_min=nbasis_min_in
-  if(nb_max.lt.nb_min)nb_max=nb_min
-!  if(2*(nb_max/2).ne.nb_max)nb_max = 2*(nb_max/2)  ! must be even
-!  if(2*(nb_min/2).ne.nb_min)nb_min = 2*(nb_min/2)  ! must be even
-  if(ibranch.lt.-1.or.ibranch.gt.0)ibranch=ibranch_in
-  if(nxgrid.lt.1.or.2*nxgrid-1.gt.nxm)nxgrid=MIN((nxm+1)/2,nxgrid_in)
-  if(nmodes.lt.1.or.nmodes.gt.maxmodes)nmodes=nmodes_in
-  if(nkys.lt.2.or.nkys.gt.nkym)nkys=nky_in
-  !      write(*,*)nb_max,nb_min,ibranch,nxgrid,nmodes,nkys
-  !
-  ! check for changes and update flow controls
-  !
-  !      if(nxgrid.ne.nxgrid_in)new_start = .TRUE.
-  !      if(nb_max.ne.nbasis_max_in)new_start = .TRUE.
-  !
-  ! transfer values
-  !
-  iflux_in = iflux
-  use_bper_in = use_bper
-  use_bpar_in = use_bpar
-  use_mhd_rule_in = use_mhd_rule
-  use_bisection_in = use_bisection
-  ibranch_in = ibranch
-  nmodes_in = nmodes
-  if(ibranch_in.eq.0)nmodes_in=2
-  nbasis_max_in = nb_max
-  nbasis_min_in = nb_min
-!  nbasis_max_in = 6
-!  nbasis_min_in = 6
-  nxgrid_in = nxgrid
-  nky_in = nkys
-  use_inboard_detrapped_in = use_inboard_detrapped
-  use_ave_ion_grid_in = use_ave_ion_grid
-  !
-END SUBROUTINE put_switches
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_rare_switches(rtheta_trap,rwdia_trap,rpark,rghat,rgchat, &
-     rwd_zero,rLinsker,rgradB,rfilter,rdamp_psi,rdamp_sig)
-  !
-  USE gftm_global
-  USE gftm_dimensions
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: rtheta_trap,rwdia_trap,rpark,rghat,rgchat,rwd_zero
-  REAL,INTENT(IN) :: rLinsker,rgradB,rfilter
-  REAL,INTENT(IN) :: rdamp_psi,rdamp_sig
-  !
-  ! transfer values
-  !
-  theta_trapped_in = rtheta_trap
-  wdia_trapped_in = rwdia_trap
-  park_in = rpark
-  ghat_in = rghat
-  gchat_in = rgchat
-  wd_zero_in = rwd_zero
-  Linsker_factor_in = rLinsker
-  gradB_factor_in = rgradB
-  filter_in = rfilter
-  damp_psi_in = rdamp_psi
-  damp_sig_in = rdamp_sig
-  !
-END SUBROUTINE put_rare_switches
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_model_parameters(adi_elec,alpha_e,alpha_p,alpha_mach,  &
-     alpha_quench,alpha_zf,xnu_fac,debye_fac,etg_fac,rlnp_cut,        &
-     sat_rule,kygrid_model,xnu_model,vpar_model,vpar_shear_model)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  LOGICAL,INTENT(IN) :: adi_elec
-  INTEGER :: sat_rule,xnu_model,kygrid_model
-  INTEGER :: vpar_model,vpar_shear_model
-  REAL,INTENT(IN) :: alpha_e,alpha_p,alpha_mach,alpha_zf
-  REAL,INTENT(IN) :: alpha_quench,xnu_fac,debye_fac,etg_fac,rlnp_cut
-  !
-  ! check for changes and update flow controls
-  !
-  if(adi_elec .NEQV. adiabatic_elec_in)new_matrix = .TRUE.
-  if(kygrid_model.lt.0.or.kygrid_model.gt.5)kygrid_model = kygrid_model_in
-  if(xnu_model.lt.0.or.xnu_model.gt.3)xnu_model = xnu_model_in
-  if(sat_rule.lt.0.or.sat_rule.gt.2)sat_rule=sat_rule_in
-  !if(vpar_model.lt.-1.or.vpar_model.gt.1)vpar_model=vpar_model_in
-  if(vpar_shear_model.lt.0.or.vpar_shear_model.gt.1)vpar_shear_model=vpar_shear_model_in
-  !
-  ! transfer values
-  !
-  adiabatic_elec_in = adi_elec
-  alpha_mach_in = alpha_mach
-  alpha_p_in = alpha_p
-  alpha_e_in = alpha_e
-  alpha_quench_in = alpha_quench
-  alpha_zf_in = alpha_zf
-  xnu_factor_in = xnu_fac
-  debye_factor_in = debye_fac
-  etg_factor_in = etg_fac
-  rlnp_cutoff_in = rlnp_cut
-  sat_rule_in = sat_rule
-  xnu_model_in = xnu_model
-  kygrid_model_in = kygrid_model
-  !vpar_model_in = vpar_model      depreciated input switch
-  vpar_shear_model_in = vpar_shear_model
-  !
-  if(alpha_quench_in .ne.0.0)then
-     ! turn off spectral shift and model and only use Waltz quench rule
-     alpha_e_in = 0.0
-  endif
-  !
-END SUBROUTINE put_model_parameters
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_s_alpha_geometry(rmin,rmaj,q,shat,alpha,xwell, &
-     theta0,b_model,ft_model)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER:: b_model,ft_model
-  REAL,INTENT(IN) :: rmin,rmaj,q,shat,alpha,theta0,xwell
-
-  if(gftm_isnan(rmin))call gftm_error(1,"input rmin_sa is NAN")
-  if(gftm_isinf(rmin))call gftm_error(1,"input rmin_sa is INF")
-  if(gftm_isnan(rmaj))call gftm_error(1,"input rmaj_sa is NAN")
-  if(gftm_isinf(rmaj))call gftm_error(1,"input rmaj_sa is INF")
-  if(gftm_isnan(q))call gftm_error(1,"input q_sa is NAN")
-  if(gftm_isinf(q))call gftm_error(1,"input q_sa is INF")
-  if(gftm_isnan(shat))call gftm_error(1,"input shat_sa is NAN")
-  if(gftm_isinf(shat))call gftm_error(1,"input shat_sa is INF")
-  if(gftm_isnan(alpha))call gftm_error(1,"input alpha_sa is NAN")
-  if(gftm_isinf(alpha))call gftm_error(1,"input alpha_sa is INF")
-  if(gftm_isnan(xwell))call gftm_error(1,"input xwell_sa is NAN")
-  if(gftm_isinf(xwell))call gftm_error(1,"input xwell_sa is INF")
-  if(gftm_isnan(theta0))call gftm_error(1,"input theta0_sa is NAN")
-  if(gftm_isinf(theta0))call gftm_error(1,"input theta0_sa is INF")
-  !
-  ! set geometry type flag for shifted circle
-  igeo = 0
-  ! set flow control switch
-  new_geometry = .TRUE.
-  !
-  ! transfer values
-  !
-  rmin_sa = rmin
-  rmaj_sa = rmaj
-  q_sa = ABS(q)
-  q_in = q_sa   ! needed for kygrid_model_in = 3
-  shat_sa = shat
-  alpha_sa = alpha
-  xwell_sa = xwell
-  theta0_sa = theta0
-  b_model_sa = b_model
-  ft_model_sa = ft_model
-  !
-  ! validatiy checks
-  !
-  if(rmin_sa.ge.rmaj_sa)rmin_sa=0.999*rmaj_sa   
-  if(ft_model_sa.lt.0.or.ft_model_sa.gt.3)then
-     write(*,*)"******* ERROR ft_model_sa invalid *******"  
-     ft_model_sa = 1
-  endif
-  !
-END SUBROUTINE put_s_alpha_geometry
-!
-!-----------------------------------------------------------------
-!
-
-SUBROUTINE put_Miller_geometry(rmin,rmaj,zmaj,drmindx,drmajdx,dzmajdx, &
-     kappa,s_kappa,delta,s_delta,zeta,s_zeta,q,q_prime,p_prime,kx0_m)
-  !
-  ! This routine eliminates the need for subroutine miller_init 
-  ! and the miller.dat input file.
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  REAL,INTENT(IN) :: rmin,rmaj,zmaj,q,q_prime,p_prime,kx0_m
-  REAL,INTENT(IN) :: drmindx,drmajdx,dzmajdx
-  REAL,INTENT(IN) :: kappa,s_kappa,delta,s_delta,zeta,s_zeta
-
-  if(gftm_isnan(rmin))call gftm_error(1,"input rmin_loc is NAN")
-  if(gftm_isinf(rmin))call gftm_error(1,"input rmin_loc is INF")
-  if(gftm_isnan(rmaj))call gftm_error(1,"input rmaj_loc is NAN")
-  if(gftm_isinf(rmaj))call gftm_error(1,"input rmaj_loc is INF")
-  if(gftm_isnan(drmindx))call gftm_error(1,"input drmindx_loc is NAN")
-  if(gftm_isinf(drmindx))call gftm_error(1,"input drmindx_loc is INF")
-  if(gftm_isnan(drmajdx))call gftm_error(1,"input drmajdx_loc is NAN")
-  if(gftm_isinf(drmajdx))call gftm_error(1,"input drmajdx_loc is INF")
-  if(gftm_isnan(dzmajdx))call gftm_error(1,"input dzmajdx_loc is NAN")
-  if(gftm_isinf(dzmajdx))call gftm_error(1,"input dzmajdx_loc is INF")
-  if(gftm_isnan(kappa))call gftm_error(1,"input kappa_loc is NAN")
-  if(gftm_isinf(kappa))call gftm_error(1,"input kappa_loc is INF")
-  if(gftm_isnan(s_kappa))call gftm_error(1,"input s_kappa_loc is NAN")
-  if(gftm_isinf(s_kappa))call gftm_error(1,"input s_kappa_loc is INF")
-  if(gftm_isnan(delta))call gftm_error(1,"input delta_loc is NAN")
-  if(gftm_isinf(delta))call gftm_error(1,"input delta_loc is INF")
-  if(gftm_isnan(s_delta))call gftm_error(1,"input s_delta_loc is NAN")
-  if(gftm_isinf(s_delta))call gftm_error(1,"input s_delta_loc is INF")
-  if(gftm_isnan(zeta))call gftm_error(1,"input zeta_loc is NAN")
-  if(gftm_isinf(zeta))call gftm_error(1,"input zeta_loc is INF")
-  if(gftm_isnan(s_zeta))call gftm_error(1,"input s_zeta_loc is NAN")
-  if(gftm_isinf(s_zeta))call gftm_error(1,"input s_zeta_loc is INF")
-  if(gftm_isnan(q))call gftm_error(1,"input q_loc is NAN")
-  if(gftm_isinf(q))call gftm_error(1,"input q_loc is INF")
-  if(gftm_isnan(q_prime))call gftm_error(1,"input q_prime_loc is NAN")
-  if(gftm_isinf(q_prime))call gftm_error(1,"input q_prime_loc is INF")
-  if(gftm_isnan(p_prime))call gftm_error(1,"input p_prime_loc is NAN")
-  if(gftm_isinf(p_prime))call gftm_error(1,"input p_prime_loc is INF")
-  if(gftm_isnan(kx0_m))call gftm_error(1,"input kx0_loc is NAN")
-  if(gftm_isinf(kx0_m))call gftm_error(1,"input kx0_loc is INF")
-
-  !
-  ! set geometry type flag for Miller
-  !
-  igeo = 1
-  !
-  ! set flow control switch
-  !
-  new_geometry = .TRUE.
-  !
-  ! transfer values
-  !
-  rmin_loc = rmin
-  rmaj_loc = rmaj
-  zmaj_loc = zmaj
-  q_loc = ABS(q)
-  q_in = q_loc   ! needed for kygrid_model_in = 3
-  p_prime_loc = p_prime
-  q_prime_loc = q_prime
-  drmindx_loc = drmindx
-  drmajdx_loc = drmajdx
-  dzmajdx_loc = dzmajdx
-  kappa_loc = kappa
-  s_kappa_loc = s_kappa
-  delta_loc = delta
-  s_delta_loc = s_delta
-  zeta_loc = zeta
-  s_zeta_loc = s_zeta
-  kx0_loc = kx0_m
-  !
-  ! validatiy checks
-  !
-  if(rmin_loc.ge.rmaj_loc)rmin_loc = 0.999*rmaj_loc
-  if(drmajdx_loc.le.-1.0)drmajdx_loc=-0.999
-  !
-END SUBROUTINE put_Miller_geometry
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_Fourier_geometry(q,q_prime,p_prime,nf,f)
-  !
-  ! This routine transfers the inputs for the fourier_geo model 
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: nf
-  REAL,INTENT(IN) :: q,q_prime,p_prime
-  REAL,INTENT(IN) :: f(8,0:max_fourier)
-  INTEGER :: i,j
-  !
-  ! validatiy checks
-  !
-  if(nf.gt.max_fourier)call gftm_error(1,"input nfourier_in exceeds maximum")
-  if(gftm_isnan(q))call gftm_error(1,"input q_fourier_in is NAN")
-  if(gftm_isinf(q))call gftm_error(1,"input q_fourier_in is INF")
-  if(gftm_isnan(q_prime))call gftm_error(1,"input q_prime_fourier_in is NAN")
-  if(gftm_isinf(q_prime))call gftm_error(1,"input q_prime_fourier_in is INF")
-  if(gftm_isnan(p_prime))call gftm_error(1,"input p_prime_fourier_in is NAN")
-  if(gftm_isinf(p_prime))call gftm_error(1,"input p_prime_fourier_in is INF")
-  do i=1,nf
-    do j=1,8
-      if(gftm_isnan(f(j,i)))call gftm_error(1,"input fourrier_in is NAN")
-      if(gftm_isinf(f(j,i)))call gftm_error(1,"input fourrier_in is INF")
-    enddo
-  enddo
-  !
-  ! set geometry type flag for Fourier
-  !
-  igeo = 2
-  !
-  ! set flow control switch
-  !
-  new_geometry = .TRUE.
-  !
-  ! transfer values
-  !
-  q_fourier_in = ABS(q)
-  q_in = q_loc   ! needed for kygrid_model_in = 3
-  p_prime_fourier_in = p_prime
-  q_prime_fourier_in = q_prime
-  nfourier_in = nf
-  fourier_in(:,:)=f(:,:)
-END SUBROUTINE put_Fourier_geometry
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE put_ELITE_geometry(nc,q,q_prime,p_prime,r_c,z_c,bp_c)
-  !
-  ! This routine requires having read the data from an ELITE geometry file
-  ! giving R,Z,Bp on a flux surface contour with nc points.
-  !
-  USE gftm_global
-  USE gftm_sgrid
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: nc
-  REAL,INTENT(IN) :: q,q_prime,p_prime
-  REAL,INTENT(IN) :: r_c(0:max_ELITE),z_c(0:max_ELITE),bp_c(0:max_ELITE)
-  !
-  INTEGER i
-  !
-  ! set geometry type flag for ELITE
-  !
-  igeo = 2
-  !
-  ! set flow control switch
-  !
-  new_geometry = .TRUE.
-  !
-  ! validatiy checks
-  !
-  if(nc.gt.max_ELITE)call gftm_error(1,"input n_ELITE exceeds limit")
-  if(nc.lt.ms)call gftm_error(1,"input n_ELITE is too small")
-  if(gftm_isnan(q_prime))call gftm_error(1,"input q_ELITE is NAN")
-  if(gftm_isinf(q_prime))call gftm_error(1,"input q_ELITE is INF")
-  do i=0,nc
-    if(gftm_isnan(r_c(i)))call gftm_error(1,"input R_ELITE is NAN")
-    if(gftm_isinf(r_c(i)))call gftm_error(1,"input R_ELITE is INF")
-    if(gftm_isnan(z_c(i)))call gftm_error(1,"input Z_ELITE is NAN")
-    if(gftm_isinf(z_c(i)))call gftm_error(1,"input Z_ELITE is INF")
-    if(gftm_isnan(bp_c(i)))call gftm_error(1,"input Bp_ELITE is NAN")
-    if(gftm_isinf(bp_c(i)))call gftm_error(1,"input Bp_ELITE is INF")
-  enddo
-  !
-  ! transfer values
-  !
-  n_ELITE = nc
-  q_ELITE = q
-  q_in = q   ! needed for kygrid=3
-  q_prime_ELITE = q_prime
-  p_prime_ELITE = p_prime
-  ! note direction change for contour angle
-  do i=0,n_ELITE
-     R_ELITE(n_ELITE-i) = r_c(i)
-     Z_ELITE(n_ELITE-i) = z_c(i)
-     Bp_ELITE(n_ELITE-i) = bp_c(i)
-  enddo
-  !
-END SUBROUTINE put_ELITE_geometry
-!
-!-----------------------------------------------------------------
-!  output routines
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_growthrate(index1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: index1
-  INTEGER :: i3
-  !
-  i3 = SIZE(gamma_out)
-  if(index1.gt.i3)then
-     write(*,*)"requested growthrate index out of bounds",i3
-     get_growthrate = 0.0
-  else
-     get_growthrate = gamma_out(index1)
-  endif
-  !
-END FUNCTION get_growthrate
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_frequency(index1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: index1
-  INTEGER :: i3
-  !
-  i3 = SIZE(freq_out)
-  if(index1.gt.i3)then
-     write(*,*)"requested frequency index is of bounds",i3
-     get_frequency = 0.0
-  else
-     get_frequency = freq_out(index1)
-  endif
-  !
-END FUNCTION get_frequency
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_particle_flux(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i4
-  !
-  i4=SIZE(particle_QL_out)
-  if(i1*i2.gt.i4)then
-     write(*,*)"requested QL particle flux index is of bounds",i4
-     get_QL_particle_flux = 0.0
-  else
-     get_QL_particle_flux = particle_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_particle_flux
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_energy_flux(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i4
-  !
-  i4=SIZE(energy_QL_out)
-  if(i1*i2.gt.i4)then
-     write(*,*)"requested QL energy flux index is of bounds",i4
-     get_QL_energy_flux = 0.0
-  else
-     get_QL_energy_flux = energy_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_energy_flux
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_stress_par(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i4
-  !
-  i4=SIZE(stress_par_QL_out)
-  if(i1*i2.gt.i4)then
-     write(*,*)"requested QL stress_par index is of bounds",i4
-     get_QL_stress_par = 0.0
-  else
-     get_QL_stress_par = stress_par_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_stress_par
-!
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_stress_tor(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i4
-  !
-  i4=SIZE(stress_tor_QL_out)
-  if(i1*i2.gt.i4)then
-     write(*,*)"requested QL stress_tor index is of bounds",i4
-     get_QL_stress_tor = 0.0
-  else
-     get_QL_stress_tor = stress_tor_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_stress_tor
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_exchange(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i4
-  !
-  i4=SIZE(exchange_QL_out)
-  if(i1*i2.gt.i4)then
-     write(*,*)"requested QL exchange index is of bounds",i4
-     get_QL_exchange = 0.0
-  else
-     get_QL_exchange = exchange_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_exchange
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_density(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i3
-  !
-  i3=SIZE(N_QL_out)
-  if(i1*i2.gt.i3)then
-     write(*,*)"requested QL_density index is of bounds",i3
-     get_QL_density = 0.0
-  else
-     get_QL_density = N_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_density
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_QL_temperature(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i3
-  !
-  i3=SIZE(T_QL_out)
-  if(i1*i2.gt.i3)then
-     write(*,*)"requested QL_temperature index is of bounds",i3
-     get_QL_temperature = 0.0
-  else
-     get_QL_temperature = T_QL_out(i1,i2)
-  endif
-  !
-END FUNCTION get_QL_temperature
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_ne_te_phase(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(ne_te_phase_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested ne_te_phase index is of bounds",i3
-     get_ne_te_phase = 0.0
-  else
-     get_ne_te_phase = ne_te_phase_out(i1)
-  endif
-  !
-END FUNCTION get_ne_te_phase
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_phi_bar(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(phi_bar_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested phi_bar index is of bounds",i3
-     get_phi_bar = 0.0
-  else
-     get_phi_bar = phi_bar_out(i1)
-  endif
-  !
-END FUNCTION get_phi_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_kpar_bar(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(kpar_bar_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested kpar_bar index is of bounds",i3
-     get_kpar_bar = 0.0
-  else
-     get_kpar_bar = kpar_bar_out(i1)
-  endif
-  !
-END FUNCTION get_kpar_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_v_bar(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(v_bar_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested v_bar index is of bounds",i3
-     get_v_bar = 0.0
-  else
-     get_v_bar = v_bar_out(i1)
-  endif
-  !
-END FUNCTION get_v_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_n_bar(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i3
-  !
-  i3=SIZE(n_bar_out)
-  if(i1*i2.gt.i3)then
-     write(*,*)"requested n_bar index is of bounds",i3
-     get_n_bar = 0.0
-  else
-     get_n_bar = n_bar_out(i1,i2)
-  endif
-  !
-END FUNCTION get_n_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_t_bar(i1,i2)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1,i2
-  INTEGER :: i3
-  !
-  i3=SIZE(t_bar_out)
-  if(i1*i2.gt.i3)then
-     write(*,*)"requested t_bar index is of bounds",i3
-     get_t_bar = 0.0
-  else
-     get_t_bar = t_bar_out(i1,i2)
-  endif
-  !
-END FUNCTION get_t_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_gaussian_width()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_gaussian_width = width_in
-  !
-END FUNCTION get_gaussian_width
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_R_unit()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_R_unit = R_unit
-  !
-END FUNCTION get_R_unit
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_ft()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_ft = ft
-  !
-END FUNCTION get_ft
-!-----------------------------------------------------------------
-REAL FUNCTION get_B_unit()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_B_unit = B_unit
-  !
-END FUNCTION get_B_unit
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_q_unit()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_q_unit = q_unit
-  !
-END FUNCTION get_q_unit
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_B2_ave()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_B2_ave = B2_ave_out
-  !
-END FUNCTION get_B2_ave
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_R2_ave()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_R2_ave = R2_ave_out
-  !
-END FUNCTION get_R2_ave
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_B_ave()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_B_ave = B_ave_out
-  !
-END FUNCTION get_B_ave
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_Bt_ave()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_Bt_ave = Bt_ave_out
-  !
-END FUNCTION get_Bt_ave
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_Bp0()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_Bp0 = Bp0_out
-  !
-END FUNCTION get_Bp0
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_RBt_ave()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_RBt_ave = RBt_ave_out
-  !
-END FUNCTION get_RBt_ave
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_b0_bar(n1)
-  !
-  USE gftm_global
-  USE gftm_coeff
-  !
-  IMPLICIT NONE
-  ! 
-  INTEGER,INTENT(IN):: n1
-  !
-  get_b0_bar = b0_bar_out(n1)
-  !
-END FUNCTION get_b0_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_wd_bar(n1)
-  !
-  USE gftm_global
-  USE gftm_coeff
-  !
-  IMPLICIT NONE
-  ! 
-  INTEGER,INTENT(IN):: n1
-  !
-  get_wd_bar = wd_bar_out(n1)
-  !
-END FUNCTION get_wd_bar
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_particle_flux(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(particle_flux_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested particle flux index is of bounds",i3
-     get_particle_flux = 0.0
-  else
-     get_particle_flux = particle_flux_out(i1)
-  endif
-  !
-END FUNCTION get_particle_flux
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_energy_flux(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(energy_flux_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested energy flux index is of bounds",i3
-     get_energy_flux = 0.0
-  else
-     get_energy_flux = energy_flux_out(i1)
-  endif
-  !
-END FUNCTION get_energy_flux
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_stress_par(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(stress_par_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested stress_par index is of bounds",i3
-     get_stress_par = 0.0
-  else
-     get_stress_par = stress_par_out(i1)
-  endif
-  !
-END FUNCTION get_stress_par
-!!-----------------------------------------------------------------
-!
-REAL FUNCTION get_stress_tor(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(stress_tor_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested stress_tor index is of bounds",i3
-     get_stress_tor = 0.0
-  else
-     get_stress_tor = stress_tor_out(i1)
-  endif
-  !
-END FUNCTION get_stress_tor
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_exchange(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(exchange_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested exchange index is of bounds",i3
-     get_exchange = 0.0
-  else
-     get_exchange = exchange_out(i1)
-  endif
-  !
-END FUNCTION get_exchange
-!
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_n_bar_sum(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(n_bar_sum_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested n_bar_sum index is of bounds",i3
-     get_n_bar_sum = 0.0
-  else
-     get_n_bar_sum = n_bar_sum_out(i1)
-  endif
-  !
-END FUNCTION get_n_bar_sum
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_q_low(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(q_low_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested energy flux index is of bounds",i3
-     get_q_low = 0.0
-  else
-     get_q_low = q_low_out(i1)
-  endif
-  !
-END FUNCTION get_q_low
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_t_bar_sum(i1)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(IN) :: i1
-  INTEGER :: i3
-  !
-  i3=SIZE(t_bar_sum_out)
-  if(i1.gt.i3)then
-     write(*,*)"requested t_bar_sum index is of bounds",i3
-     get_t_bar_sum = 0.0
-  else
-     get_t_bar_sum = t_bar_sum_out(i1)
-  endif
-  !
-END FUNCTION get_t_bar_sum
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_phi_bar_sum()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_phi_bar_sum = phi_bar_sum_out
-  !
-END FUNCTION get_phi_bar_sum
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_v_bar_sum()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_v_bar_sum = v_bar_sum_out
-  !
-END FUNCTION get_v_bar_sum
-!-----------------------------------------------------------------
-!
-INTEGER FUNCTION get_nky_out()
-  !
-  USE gftm_global
-  USE gftm_kyspectrum
-  !
-  IMPLICIT NONE
-  !
-  get_nky_out = nky
-  !
-END FUNCTION get_nky_out
-!----------------------------------------------------------------
-!
-REAL FUNCTION get_flux_spectrum_out(itype,ispec,iky,imode)
-  !
-  USE gftm_global
-  !   
-  IMPLICIT NONE
-  !
-  INTEGER,INTENT(IN) :: itype,ispec,iky,imode
-  INTEGER :: error
-  !
-  error=0
-  get_flux_spectrum_out = 0.0
-  if(itype.lt.1.or.itype.gt.5)then
-     write(*,*)"itype out of bounds",1,5
-     error=1
-  elseif(ispec.lt.1.or.ispec.gt.nsm)then
-     write(*,*)"ispec out of bounds",1,nsm
-     error=1
-  elseif(iky.lt.1.or.iky.gt.nkym)then
-     write(*,*)"iky out of bounds",1,nkym
-     error=1
-  elseif(imode.lt.1.or.imode.gt.maxmodes)then
-     write(*,*)"imode out of bounds",1,maxmodes
-     error=1
-  endif
-  !
-  if(error.eq.0)then
-     get_flux_spectrum_out=flux_spectrum_out(itype,ispec,iky,imode)
-  endif
-  !
-END FUNCTION get_flux_spectrum_out
-!----------------------------------------------------------------
-!
-REAL FUNCTION get_eigenvalue_spectrum_out(itype,iky,imode)
-  !
-  USE gftm_global
-  !   
-  IMPLICIT NONE
-  !
-  INTEGER,INTENT(IN) :: itype,iky,imode
-  INTEGER :: error
-  !
-  error=0
-  get_eigenvalue_spectrum_out = 0.0
-  if(itype.lt.1.or.itype.gt.2)then
-     write(*,*)"ntype out of bounds",1,2
-     error=1
-  elseif(iky.lt.1.or.iky.gt.nkym)then
-     write(*,*)"iky out of bounds",1,nkym
-     error=1
-  elseif(imode.lt.1.or.imode.gt.maxmodes)then
-     write(*,*)"imode out of bounds",1,maxmodes
-     error=1
-  endif
-  !
-  if(error.eq.0)then
-     get_eigenvalue_spectrum_out=eigenvalue_spectrum_out(itype,iky,imode)
-  endif
-  !
-END FUNCTION get_eigenvalue_spectrum_out
-!----------------------------------------------------------------
-!
-REAL FUNCTION get_intensity_spectrum_out(itype,ispec,iky,imode)
-  !
-  USE gftm_global
-  !   
-  IMPLICIT NONE
-  !
-  INTEGER,INTENT(IN) :: itype,ispec,iky,imode
-  INTEGER :: error
-  !
-  error=0
-  get_intensity_spectrum_out = 0.0
-  if(itype.lt.1.or.itype.gt.4)then
-     write(*,*)"ntype out of bounds",1,4
-     error=1
-  elseif(ispec.lt.1.or.ispec.gt.nsm)then
-     write(*,*)"ispec out of bounds",1,nsm
-     error=1        
-  elseif(iky.lt.1.or.iky.gt.nkym)then
-     write(*,*)"iky out of bounds",1,nkym
-     error=1
-  elseif(imode.lt.1.or.imode.gt.maxmodes)then
-     write(*,*)"imode out of bounds",1,maxmodes
-     error=1
-  endif
-  !
-  if(error.eq.0)then
-     get_intensity_spectrum_out=intensity_spectrum_out(itype,ispec,iky,imode)
-  endif
-  !
-END FUNCTION get_intensity_spectrum_out
-!----------------------------------------------------------------
-!
-REAL FUNCTION get_field_spectrum_out(itype,iky,imode)
-  !
-  USE gftm_global
-  !   
-  IMPLICIT NONE
-  !
-  INTEGER,INTENT(IN) :: itype,iky,imode
-  INTEGER :: error
-  !
-  error = 0
-  get_field_spectrum_out = 0.0
-  if(itype.lt.1.or.itype.gt.4)then
-     write(*,*)"itype out of bounds",1,2
-     error=1
-  elseif(iky.lt.1.or.iky.gt.nkym)then
-     write(*,*)"nky out of bounds",1,nkym
-     error=1
-  elseif(imode.lt.1.or.imode.gt.maxmodes)then
-     write(*,*)"imode out of bounds",1,maxmodes
-     error=1
-  endif
-  !
-  if(error.eq.0)then
-     get_field_spectrum_out=field_spectrum_out(itype,iky,imode)
-  endif
-  !
-END FUNCTION get_field_spectrum_out
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_ky_spectrum_out(iky)
-  !
-  USE gftm_global
-  USE gftm_kyspectrum
-  !
-  IMPLICIT NONE
-  !
-  INTEGER,INTENT(IN) :: iky
-  !
-  if(iky.lt.1.or.iky.gt.nkym)then
-     write(*,*)"iky out of bounds",1,nkym
-     get_ky_spectrum_out = 0.0
-  else
-     get_ky_spectrum_out = ky_spectrum(iky)
-  endif
-  !
-END FUNCTION get_ky_spectrum_out
-!-----------------------------------------------------------------
-!
-
-REAL FUNCTION get_DM()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_DM = DM_out
-  !
-END FUNCTION get_DM
-!-----------------------------------------------------------------
-!
-REAL FUNCTION get_DR()
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  get_DR = DR_out
-  !
-END FUNCTION get_DR
-!-----------------------------------------------------------------
-!
-SUBROUTINE get_DEP_parameters(r_dep,rmaj_dep,q_dep,taui_dep,rlni_dep,rlti_dep,ni_dep)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  !
-  REAL,INTENT(OUT) :: r_dep,rmaj_dep,q_dep,taui_dep,rlni_dep,rlti_dep,ni_dep
-  !
-  ! warning this routine assumes that the call put_species set the main ion species to be index 2
-  !
-  taui_dep = taus_in(2)
-  rlni_dep = rlns_in(2)
-  rlti_dep = rlts_in(2)
-  ni_dep = as_in(2)
-  ! note that rmin_input,Rmaj_input,q_input are set the different geometry routines 
-  r_dep = rmin_input
-  rmaj_dep = Rmaj_input
-  q_dep = q_in
-  !
-END SUBROUTINE get_DEP_parameters
-!-----------------------------------------------------------------
-!
-SUBROUTINE get_wavefunction_out(nmodes,nfields,nplot,angle,wavefunction)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-  INTEGER,INTENT(OUT) :: nmodes,nfields,nplot
-  REAL,INTENT(OUT) :: angle(max_plot)
-  COMPLEX,INTENT(OUT) :: wavefunction(maxmodes,3,max_plot)
-  !
-  if(new_start)then
-     write(*,*)"error: gftm must be called before get_wavefunction_out"
-  else
-     call get_wavefunction
-     nmodes = nmodes_out
-     nfields = nfields_out
-     nplot = max_plot
-     angle(:) = plot_angle_out(:)
-     wavefunction(:,:,:) = plot_field_out(:,:,:)
-  endif
-  !
-END SUBROUTINE get_wavefunction_out
-!-----------------------------------------------------------------
-
-
-
-SUBROUTINE get_error_status(message,status)
-!-------------------------------------------------------------------
-! Determine internal gftm error status and return string and integer
-!
-! gftm success:
-!  status=0
-!  message='null'
-!
-! gftm failure
-!  status=1
-!  message=<error description>
-!
-! gftm warning
-!  status=2
-!  message=<warning description>
-!-------------------------------------------------------------------
-
-  use gftm_global
-
-  implicit none
-
-  character (len=*), intent(inout) :: message
-  integer, intent(inout) :: status
-
-  message = trim(error_msg)
-
-  if (message == 'null') then
-     status = 0
-  else
-     status = 1
-  endif
-
-END SUBROUTINE get_error_status
-!
-!-----------------------------------------------------------------
-!
-SUBROUTINE write_wavefunction_out(datafile)
-  !
-  USE gftm_global
-  !
-  IMPLICIT NONE
-
-  character (len=*), intent(in) :: datafile
-
-  INTEGER :: i,n,k,noff
-  REAL :: wave(maxmodes*6)
-  CHARACTER(len=81) :: header
-  CHARACTER(len=11) :: theta="    theta  "
-  CHARACTER(len=22) :: phi="  RE(phi)    IM(phi)  "
-  CHARACTER(len=24) :: Bper="  RE(Bper)    IM(Bper)  "
-  CHARACTER(len=24) :: Bpar="  RE(Bpar)    IM(Bpar)  "
-  !
-  if(new_start)then
-     write(*,*)"error: gftm must be called before write_wavefunction_out"
-  else
-     call get_wavefunction
-     !
-     open(unit=33,file=datafile,status='replace')
-     header = theta//phi
-     if(use_bper_in)header = theta//phi//Bper
-     if(use_bpar_in)header = theta//phi//Bpar
-     if(use_bper_in.and.use_bpar_in)header = theta//phi//Bper//Bpar
-     !
-     write(33,*)nmodes_out,nfields_out,max_plot
-     write(33,*)header
-     do i = 1,max_plot
-        do n=1,nmodes_out
-           noff=2*nfields_out*(n-1)
-           wave(noff+1) = REAL(plot_field_out(n,1,i))
-           wave(noff+2) = AIMAG(plot_field_out(n,1,i))
-           if(use_bper_in)then
-              wave(noff+3) = REAL(plot_field_out(n,2,i))
-              wave(noff+4) = AIMAG(plot_field_out(n,2,i))
-           endif
-           if(use_bpar_in)then
-              wave(noff+5) = REAL(plot_field_out(n,3,i))
-              wave(noff+6) = AIMAG(plot_field_out(n,3,i))
-           endif
-        enddo
-        write(33,*)plot_angle_out(i),(wave(k),k=1,nmodes_out*nfields_out*2)
-     enddo
-     close(33)
-  endif
-  !
-END SUBROUTINE write_wavefunction_out
-!-----------------------------------------------------------------
-!
-SUBROUTINE write_gftm_sum_flux_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(26) :: fluxfile="out.gftm.sum_flux_spectrum"
-  INTEGER :: i,j,is,imax,jmax
-  REAL :: dky
-  REAL :: dky0,dky1,ky0,ky1
-  REAL :: pflux0(nsm),eflux0(nsm)
-  REAL :: stress_par0(nsm),stress_tor0(nsm)
-  REAL :: exch0(nsm)
-  REAL :: pflux1(nsm),eflux1(nsm)
-  REAL :: stress_par1(nsm),stress_tor1(nsm)
-  REAL :: exch1(nsm)
-  REAL :: pflux_out,eflux_out,mflux_tor_out,mflux_par_out,exch_out
-
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_flux_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-  !
-  !
-  ! initialize fluxes
-  !
-!  write(*,*)"ns0,ns,nky,nmodes",ns0,ns,nky,nmodes_in
-!
-  do is=ns0,ns
-    pflux0(is) = 0.0
-    eflux0(is) = 0.0
-    stress_par0(is) = 0.0
-    stress_tor0(is) = 0.0
-    exch0(is) = 0.0
-  enddo
-  ! loop over species
-  do is=ns0,ns
-    write(33,*)"species = ",is
-    write(33,*)" particle flux,energy flux,toroidal stress,parallel stress,exchange"
-        !
-        ! loop over ky spectrum
-        !
-        iflux_in=.TRUE. 
-        dky0=0.0
-        ky0=0.0 
-        do i=1,nky
-           ky_in = ky_spectrum(i)
-           dky = dky_spectrum(i)
-           ky1=ky_in
-           if(i.eq.1)then
-              dky1=ky1
-           elseif(kygrid_model_in.ne.0)then
-              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(taus_in(1)*mass_in(2))
-!           dky1 = dky1*SQRT(taus_in(1)*mass_in(2))
-           !
-           ! compute the fluxes in the same way as gftm_TM.f90
-           !
-           pflux1(is) = 0.0
-           eflux1(is) = 0.0
-           stress_tor1(is) = 0.0
-           stress_par1(is) = 0.0
-           exch1(is) = 0.0
-           do imax = 1,nmodes_in
-              pflux1(is) = pflux1(is) + flux_spectrum_out(1,is,i,imax)
-              eflux1(is) = eflux1(is) + flux_spectrum_out(2,is,i,imax)
-              stress_tor1(is) = stress_tor1(is) + &
-                   flux_spectrum_out(3,is,i,imax)
-              stress_par1(is) = stress_par1(is) + &
-                   flux_spectrum_out(4,is,i,imax)
-              exch1(is) = exch1(is) + flux_spectrum_out(5,is,i,imax)
-           enddo !imax
-           pflux_out = dky0*pflux0(is) + dky1*pflux1(is)
-           eflux_out = dky0*eflux0(is) + dky1*eflux1(is)
-           mflux_tor_out = dky0*stress_tor0(is) + dky1*stress_tor1(is)
-           mflux_par_out = dky0*stress_par0(is) + dky1*stress_par1(is)
-           exch_out = dky0*exch0(is) + dky1*exch1(is)
-           write(33,*)pflux_out,eflux_out,mflux_tor_out,mflux_par_out,exch_out
-           pflux0(is) = pflux1(is)
-           eflux0(is) = eflux1(is)
-           stress_par0(is) = stress_par1(is)
-           stress_tor0(is) = stress_tor1(is)
-           exch0(is) = exch1(is)
-           ky0 = ky1
-    enddo  ! i
-  enddo  ! is 
-  !
-  CLOSE(33)
-  !
-END SUBROUTINE write_gftm_sum_flux_spectrum
-!-----------------------------------------------------------------
-
-SUBROUTINE write_gftm_density_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(25) :: fluxfile="out.gftm.density_spectrum"
-  INTEGER :: i,is,n
-  REAL :: density(nsm)
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_density_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"gyro-bohm normalized density fluctuation amplitude spectra"
-  write(33,*)"(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,*)(density(is),is=1,ns)
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_density_spectrum
-!-----------------------------------------------------------------
-
-SUBROUTINE write_gftm_temperature_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(29) :: fluxfile="out.gftm.temperature_spectrum"
-  INTEGER :: i,is,n
-  REAL :: temp(nsm)
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_temperature_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"gyro-bohm normalized temperature fluctuation amplitude spectra"
-  write(33,*)"(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,*)(temp(is),is=1,ns)
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_temperature_spectrum
-!-----------------------------------------------------------------
-
-SUBROUTINE write_gftm_intensity_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(36) :: fluxfile="out.gftm.intensity_spectrum"
-  INTEGER :: i,is,n
-  REAL :: den,tem, u_par, q_tot
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_intensity_spectrum_per_mode"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"gyro-bohm normalized fluctuation intensity 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
-      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,tem,u_par,q_tot
-      enddo
-    enddo
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_intensity_spectrum
-
-!-----------------------------------------------------------------
-
-SUBROUTINE write_gftm_field_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(36) :: fluxfile="out.gftm.field_spectrum"
-  INTEGER :: i,n
-  REAL :: v,phi,a_par,b_par
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_field_spectrum_per_mode"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_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,*)"vector,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
-      v = field_spectrum_out(1,i,n)
-      phi = field_spectrum_out(2,i,n)
-      a_par = field_spectrum_out(3,i,n)
-      b_par = field_spectrum_out(4,i,n)
-      write(33,*)v,phi,a_par,b_par
-    enddo
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_field_spectrum
-!-----------------------------------------------------------------
-
-SUBROUTINE write_gftm_eigenvalue_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(28) :: fluxfile="out.gftm.eigenvalue_spectrum"
-  INTEGER :: i,n
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_eigenvalue_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"gyro-bohm normalized eigenvalue spectra"
-  write(33,*)"(gamma(n),freq(n),n=1,nmodes_in)"
-  do i=1,nky
-    write(33,*)(eigenvalue_spectrum_out(1,i,n), &
-              eigenvalue_spectrum_out(2,i,n),n=1,nmodes_in)
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_eigenvalue_spectrum
-!-----------------------------------------------------------------
-
-SUBROUTINE write_gftm_nete_crossphase_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !   
-  IMPLICIT NONE
-  CHARACTER(33) :: fluxfile="out.gftm.nete_crossphase_spectrum"
-  INTEGER :: i,n
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_nete_crossphase_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"electron density-temperature cross phase spectra per mode"
-  write(33,*)"(ne_te_phase,n=1,nmodes_in)"
-  do i=1,nky
-    write(33,*)(ne_te_phase_spectrum_out(i,n),n=1,nmodes_in)
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_nete_crossphase_spectrum
-!-----------------------------------------------------------------
-!
-SUBROUTINE write_gftm_nsts_crossphase_spectrum
-  !
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-  !
-  IMPLICIT NONE
-  CHARACTER(33) :: fluxfile="out.gftm.nsts_crossphase_spectrum"
-  INTEGER :: is,i,n
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_nsts_crossphase_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"density-temperature cross phase spectra per mode for ",ns_in," species"
-   do is=1,ns_in
-    write(33,*)"species index = ",is
-    write(33,*)"(nsts_phase_spectrum_out,n=1,nmodes_in)"
-    do i=1,nky
-      write(33,*)(nsts_phase_spectrum_out(is,i,n),n=1,nmodes_in)
-    enddo
-  enddo
-!
-  CLOSE(33)
-!
-END SUBROUTINE write_gftm_nsts_crossphase_spectrum
-!-----------------------------------------------------------------
-!
- SUBROUTINE write_gftm_QL_flux_spectrum
-!
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-! 
-  IMPLICIT NONE
-  CHARACTER(33) :: fluxfile="out.gftm.QL_flux_spectrum"
-  INTEGER :: i,j,k,is,m
-  REAL,PARAMETER :: small=1.0E-10
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_QL_weight_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=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,*)"QL_flux_spectrum_out(type,nspecies,field,ky,mode)"
-  write(33,*)"index limits: type,ns,field,nky,nmodes"
-  write(33,*)5,ns,nky,nmodes_in
-  do is=ns0,ns
-    write(33,*)"species = ",is
-    do m=1,nmodes_in
-        write(33,*)"mode = ",m
-        do i=1,nky
-          write(33,*)(QL_flux_spectrum_out(k,is,i,m),k=1,5)
-        enddo  ! i
-    enddo ! m
- enddo  ! is
-
-  CLOSE(33)
-!
- END SUBROUTINE write_gftm_QL_flux_spectrum
-!-----------------------------------------------------------------
-!
- SUBROUTINE write_gftm_ky_spectrum
-!
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-!
-  IMPLICIT NONE
-  CHARACTER(20) :: fluxfile="out.gftm.ky_spectrum"
-  INTEGER :: i
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_spectral_shift"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"index limits: nky"
-  write(33,*)nky
-!
-  do i=1,nky
-    write(33,*)ky_spectrum(i)
-  enddo
-  CLOSE(33)
-!
- END SUBROUTINE write_gftm_ky_spectrum
-!-----------------------------------------------------------------
-!
- SUBROUTINE write_gftm_spectral_shift_spectrum
-!
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-!
-  IMPLICIT NONE
-  CHARACTER(33) :: fluxfile="out.gftm.spectral_shift_spectrum"
-  INTEGER :: i
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_spectral_shift"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"kx spectral shift model is used when ALPHA_QUENCH=0 and ALPHA_E=1.0"
-  write(33,*)"note: the model for the spectral shift (kx_e) = <phi|kx/ky|phi>/<phi|phi>"
-  write(33,*)"depends on which staturation model is being used: SAT_RULE and UNITS settings"
-  write(33,*)"index limits: nky"
-  write(33,*)nky
-!
-  do i=1,nky
-    write(33,*)spectral_shift_out(i)
-  enddo
-  CLOSE(33)
-!
- END SUBROUTINE write_gftm_spectral_shift_spectrum
-!
-!______________________________________________________________
-!
-SUBROUTINE write_gftm_ave_p0_spectrum
-!
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-!
-  IMPLICIT NONE
-  CHARACTER(33) :: fluxfile="out.gftm.ave_p0_spectrum"
-  INTEGER :: i
-!
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_ave_p0_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-!
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"ave_p0 is used for normalization of SAT0"
-  write(33,*)"index limits: nky"
-  write(33,*)nky
-!
-  do i=1,nky
-    write(33,*)ave_p0_spectrum_out(i)
-  enddo
-  CLOSE(33)
-!
- END SUBROUTINE write_gftm_ave_p0_spectrum
-!
-!______________________________________________________________
-!
- SUBROUTINE write_gftm_width_spectrum
-!
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-!
-  IMPLICIT NONE
-  CHARACTER(33) :: fluxfile="out.gftm.width_spectrum"
-  INTEGER :: i
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_width_spectrum"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"width of the Gaussian envelope for the Hermite basis functions"
-  write(33,*)"index limits: nky"
-  write(33,*)nky
-!
-  do i=1,nky
-    write(33,*)width_out(i)
-  enddo
-  CLOSE(33)
-!
- END SUBROUTINE write_gftm_width_spectrum
-!-----------------------------------------------------------------
-!
- SUBROUTINE write_gftm_scalar_saturation_parameters
-!
-  USE gftm_dimensions
-  USE gftm_global
-  USE gftm_species
-  USE gftm_kyspectrum
-!
-  IMPLICIT NONE
-  CHARACTER(37) :: fluxfile="out.gftm.scalar_saturation_parameters"
-  !
-  if(new_start)then
-     write(*,*)"error: gftm_TM must be called before write_gftm_saturation_parameters"
-     write(*,*)"       NN doesn't compute spectra -> if needed set gftm_nn_max_error_in=-1"
-  endif
-  !
-  OPEN(unit=33,file=fluxfile,status='replace')
-!
-  write(33,*)"!This file has all of the scalar staturation parameters used for different SAT_RULE options"
-  write(33,*)"SAT_RULE = ", sat_rule_in
-  write(33,*)"UNITS = ", units_in
-  write(33,*)"XNU_MODEL = ",xnu_model_in
-  write(33,*)"!   SAT0 model "
-  write(33,*)"ETG_FACTOR = ",etg_factor_in
-  write(33,*)"B_unit = ",B_unit
-  write(33,*)"R_unit = ",R_unit
-  write(33,*)"q_unit = ",q_unit
-  write(33,*)"!   SAT1 & SAT2 models "
-  write(33,*)"ALPHA_ZF = ",alpha_zf_in
-  write(33,*)"SAT_geo0_out = ",SAT_geo0_out
-  write(33,*)"SAT_geo1_out = ",SAT_geo1_out
-  write(33,*)"SAT_geo2_out = ",SAT_geo2_out
-  write(33,*)"Bt0_out = ",Bt0_out
-  write(33,*)"B_geo0_out = ",B_geo0_out
-  write(33,*)"grad_r0_out = ",grad_r0_out
-  write(33,*)"rho_ion = ",rho_ion
-  write(33,*)"rho_e = ",rho_e
-  write(33,*)"kymax_out = ",kymax_out
-  write(33,*)"vzf_out = ",vzf_out
-!
-  CLOSE(33)
-!
- END SUBROUTINE write_gftm_scalar_saturation_parameters
-
-
-
-
diff --git a/gftm/src/gftm_interface.f90 b/gftm/src/gftm_interface.f90
deleted file mode 100644
index 80cbd39e5..000000000
--- a/gftm/src/gftm_interface.f90
+++ /dev/null
@@ -1,567 +0,0 @@
-!-------------------------------------------------------------------------
-! gftm_interface.f90
-!
-! PURPOSE:
-!  Provides interface description for gftm.
-!
-! CALLING SEQUENCE:
-!  call gftm_init(...)
-!  set gftm_*_in variables
-!  call gftm_run(...)
-!  get gftm_*_out variables
-!
-! NOTES:
-!  gftm_path:        working directory
-!  gftm_dump_flag:   TRUE = call dump routines, FALSE = do NOT call dump routines
-!  gftm_dump_suffix: appended to name of dump file
-!
-!  gftm_dump_local and gftm_dump_global are called by gftm_run
-!
-! NAMING CONVENTION:
-!  Interface parameter names are formed from gftm variable names by
-!  prepending 'gftm_' and appending '_in'
-!
-! INITIALIZATION:
-!  We initialize input arrays/vectors to zero unlike original gftm module
-!
-!-------------------------------------------------------------------------
-
-module gftm_interface
-
-  use gftm_max_dimensions
-
-  !  NOTE: gftm_max_dimensions defines
-  !   nsm=6
-  !   maxmodes=4
-
-  implicit none
-
-  ! CONTROL PARAMETERS
-  character (len=256)  :: gftm_path_in       = ''
-  character (len=20)   :: file_dump_local = 'out.gftm.localdump'
-  logical              :: gftm_dump_flag_in  = .false.
-  logical              :: gftm_quiet_flag_in = .true.
-  integer              :: gftm_test_flag_in  = 0
-
-! units switch
-  character (len=8) :: gftm_units_in = 'GYRO'
-
-! INPUT PARAMETERS
-  logical :: gftm_use_transport_model_in = .true.
-  integer :: gftm_geometry_flag_in = 1
-  integer :: gftm_write_wavefunction_flag_in=0
-
-  ! Data passed to: put_signs
-  real    :: gftm_sign_bt_in        = 1.0
-  real    :: gftm_sign_it_in        = 1.0
-
-  ! Data passed to: put_rare_switches
-  real    :: gftm_theta_trapped_in  = 0.7
-  real    :: gftm_wdia_trapped_in   = 0.0
-  real    :: gftm_park_in           = 1.0
-  real    :: gftm_ghat_in           = 1.0
-  real    :: gftm_gchat_in          = 1.0
-  real    :: gftm_wd_zero_in        = 0.1
-  real    :: gftm_linsker_factor_in = 0.0
-  real    :: gftm_gradb_factor_in   = 0.0
-  real    :: gftm_filter_in         = 2.0
-  real    :: gftm_damp_psi_in       = 0.0
-  real    :: gftm_damp_sig_in       = 0.0
-
-  ! Data passed to: put_switches
-  logical :: gftm_iflux_in          = .true.
-  logical :: gftm_use_bper_in       = .false.
-  logical :: gftm_use_bpar_in       = .false.
-  logical :: gftm_use_mhd_rule_in   = .true.
-  logical :: gftm_use_bisection_in  = .true.
-  logical :: gftm_use_inboard_detrapped_in = .false.
-  logical :: gftm_use_ave_ion_grid_in = .false.
-  integer :: gftm_ibranch_in        = -1
-  integer :: gftm_nmodes_in         = 2
-  integer :: gftm_nbasis_max_in     = 4
-  integer :: gftm_nbasis_min_in     = 2
-  integer :: gftm_nxgrid_in         = 16
-  integer :: gftm_nky_in            = 12
-
-  ! Data passed to: put_model_parameters
-  logical :: gftm_adiabatic_elec_in = .false.
-  real    :: gftm_alpha_mach_in     = 0.0
-  real    :: gftm_alpha_e_in        = 1.0
-  real    :: gftm_alpha_p_in        = 1.0
-  real    :: gftm_alpha_quench_in   = 0.0
-  real    :: gftm_alpha_zf_in       = 1.0
-  real    :: gftm_xnu_factor_in     = 1.0
-  real    :: gftm_debye_factor_in   = 1.0
-  real    :: gftm_etg_factor_in     = 1.25
-  real    :: gftm_rlnp_cutoff_in     = 18.0
-  integer :: gftm_sat_rule_in       = 0
-  integer :: gftm_kygrid_model_in   = 1
-  integer :: gftm_xnu_model_in      = 2
-  integer :: gftm_vpar_model_in     = 0
-  integer :: gftm_vpar_shear_model_in = 1
-
-  ! Data passed to: put_species
-  integer :: gftm_ns_in             = 2
-  real    :: gftm_mass_in(nsm)      = 0.0
-  real    :: gftm_zs_in(nsm)        = 0.0
-
-  ! Data passed to: put_kys
-  real    :: gftm_ky_in             = 0.3
-
-  ! Data passed to: put_gaussian_width
-  real    :: gftm_width_in          = 1.65
-  real    :: gftm_width_min_in      = 0.3
-  integer :: gftm_nwidth_in         = 21
-  logical :: gftm_find_width_in     = .true.
-
-  ! Data passed to: put_gradients
-  real    :: gftm_rlns_in(nsm)      = 0.0
-  real    :: gftm_rlts_in(nsm)      = 0.0
-  real    :: gftm_vpar_shear_in(nsm)= 0.0
-  real    :: gftm_vexb_shear_in     = 0.0
-
-  ! Data passed to: put_profile_shear
-  real    :: gftm_vns_shear_in(nsm) = 0.0
-  real    :: gftm_vts_shear_in(nsm) = 0.0
-
-  ! Data passed to: put_averages
-  real    :: gftm_taus_in(nsm)    = 0.0
-  real    :: gftm_as_in(nsm)      = 0.0
-  real    :: gftm_vpar_in(nsm)    = 0.0
-  real    :: gftm_vexb_in         = 0.0
-  real    :: gftm_betae_in        = 0.0
-  real    :: gftm_xnue_in         = 0.0
-  real    :: gftm_zeff_in         = 1.0
-  real    :: gftm_debye_in        = 0.0
-
-  ! Data passed to: put_eikonal
-  logical :: gftm_new_eikonal_in    = .true.
-
-  ! Data passed to: put_s_alpha_geometry
-  real    :: gftm_rmin_sa_in        = 0.5
-  real    :: gftm_rmaj_sa_in        = 3.0
-  real    :: gftm_q_sa_in           = 2.0
-  real    :: gftm_shat_sa_in        = 1.0
-  real    :: gftm_alpha_sa_in       = 0.0
-  real    :: gftm_xwell_sa_in       = 0.0
-  real    :: gftm_theta0_sa_in      = 0.0
-  integer :: gftm_b_model_sa_in     = 1
-  integer :: gftm_ft_model_sa_in    = 1
-
-  ! Data passed to: put_Miller_geometry
-  real    :: gftm_rmin_loc_in       = 0.5
-  real    :: gftm_rmaj_loc_in       = 3.0
-  real    :: gftm_zmaj_loc_in       = 0.0
-  real    :: gftm_drmindx_loc_in    = 1.0
-  real    :: gftm_drmajdx_loc_in    = 0.0
-  real    :: gftm_dzmajdx_loc_in    = 0.0
-  real    :: gftm_kappa_loc_in      = 1.0
-  real    :: gftm_s_kappa_loc_in    = 0.0
-  real    :: gftm_delta_loc_in      = 0.0
-  real    :: gftm_s_delta_loc_in    = 0.0
-  real    :: gftm_zeta_loc_in       = 0.0
-  real    :: gftm_s_zeta_loc_in     = 0.0
-  real    :: gftm_q_loc_in          = 2.0
-  real    :: gftm_q_prime_loc_in    = 16.0
-  real    :: gftm_p_prime_loc_in    = 0.0
-  real    :: gftm_kx0_loc_in        = 0.0
-
-  ! Data passed to Fourier_geometry
-  integer :: gftm_nfourier_in        = 16
-  real :: gftm_q_fourier_in          = 2.0
-  real :: gftm_q_prime_fourier_in    = 16.0
-  real :: gftm_p_prime_fourier_in    = 0.0
-  real :: gftm_fourier_in(8,0:max_fourier)=0.0
-
-  ! Data passed to: put_ELITE_geometry
-  integer  :: gftm_n_elite_in   = 700
-  real     :: gftm_q_elite_in   = 2.0
-  real     :: gftm_q_prime_elite_in = 16.0
-  real     :: gftm_R_elite_in(max_ELITE)
-  real     :: gftm_Z_elite_in(max_ELITE)
-  real     :: gftm_Bp_elite_in(max_ELITE)
-  
-  ! TRANSPORT OUTPUT PARAMETERS
-  real :: gftm_elec_pflux_out = 0.0
-  real :: gftm_elec_eflux_out = 0.0
-  real :: gftm_elec_eflux_low_out = 0.0
-  real :: gftm_elec_mflux_out = 0.0
-  real :: gftm_elec_expwd_out = 0.0
-
-  real, dimension(nsm-1) :: gftm_ion_pflux_out = 0.0
-  real, dimension(nsm-1) :: gftm_ion_eflux_out = 0.0
-  real, dimension(nsm-1) :: gftm_ion_eflux_low_out = 0.0
-  real, dimension(nsm-1) :: gftm_ion_mflux_out = 0.0
-  real, dimension(nsm-1) :: gftm_ion_expwd_out = 0.0
-
-  real, dimension(nsm-1, 3) :: gftm_particle_flux_out = 0.0
-  real, dimension(nsm-1, 3) :: gftm_energy_flux_out = 0.0
-  real, dimension(nsm-1, 3) :: gftm_stress_tor_out = 0.0
-  real, dimension(nsm-1, 3) :: gftm_stress_par_out = 0.0
-  real, dimension(nsm-1, 3) :: gftm_exchange_out = 0.0
-  
-  ! LINEAR OUTPUT PARAMETERS
-  complex :: gftm_eigenvalue_out(maxmodes)
-
-  ! GYRO gftm input
-  real, allocatable, dimension(:, :, :) :: gftm_eigenvalue_spectrum_out
-  real, allocatable, dimension(:) :: gftm_ky_spectrum_out, gftm_dky_spectrum_out
-
-  real, allocatable, dimension(:, :, :) :: gftm_field_spectrum_out
-  real, allocatable, dimension(:, :, :, :, :) :: gftm_flux_spectrum_out
-  
-  
-  
-  ! DIAGNOSTIC OUTPUT PARAMETERS
-  real :: interchange_DR = 0.0
-  real :: interchange_DM = 0.0
-
-  ! ERROR OUTPUT
-  character (len=80) :: gftm_error_message='null'
-  integer :: gftm_error_status=0
-  
-  ! Set threshold for gftm-NN execution versus full gftm calculation
-  real    :: gftm_nn_max_error_in = 0.0
-
- ! CHECK <<<---------------------------------------------<<<
- !write(*,*) 'gftm_interface --> gftm_nn_max_error_in: ', gftm_nn_max_error_in
-
- 
-  
-contains
-
-  ! Dump LOCAL INTERFACE variables
-  subroutine gftm_dump_local()
-
-    implicit none
-
-    integer :: ierr, i
-
-    open(unit=1,file=trim(gftm_path_in)//trim(file_dump_local),&
-         status='replace',iostat=ierr)
-
-    if (gftm_geometry_flag_in == 2 ) then
-       write(1,*) 'DUMP NOT SUPPORTED FOR FOURIER GEOMETRY'
-       close(1)
-       return
-    endif
-
-    write(1,*) '# input.gftm generated by gftm_dump_local()'
-    write(1,*) '#'
-    write(1,*) '# See https://fusion.gat.com/theory/gftminput'
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Control parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,50) 'UNITS', gftm_units_in
-    write(1,20) 'NS',gftm_ns_in
-    write(1,10) 'USE_TRANSPORT_MODEL',gftm_use_transport_model_in
-    write(1,20) 'GEOMETRY_FLAG',gftm_geometry_flag_in
-    write(1,10) 'USE_BPER',gftm_use_bper_in
-    write(1,10) 'USE_BPAR',gftm_use_bpar_in
-    write(1,10) 'USE_MHD_RULE',gftm_use_mhd_rule_in
-    write(1,10) 'USE_BISECTION',gftm_use_bisection_in
-    write(1,10) 'USE_INBOARD_DETRAPPED',gftm_use_inboard_detrapped_in
-    write(1,10) 'USE_AVE_ION_GRID',gftm_use_ave_ion_grid_in
-    write(1,20) 'SAT_RULE',gftm_sat_rule_in
-    write(1,20) 'KYGRID_MODEL',gftm_kygrid_model_in
-    write(1,20) 'XNU_MODEL',gftm_xnu_model_in
-    write(1,20) 'VPAR_MODEL',gftm_vpar_model_in
-    write(1,20) 'VPAR_SHEAR_MODEL',gftm_vpar_shear_model_in
-    write(1,30) 'SIGN_BT',gftm_sign_bt_in
-    write(1,30) 'SIGN_IT',gftm_sign_it_in
-    write(1,30) 'KY',gftm_ky_in
-    write(1,10) 'NEW_EIKONAL',gftm_new_eikonal_in
-    write(1,30) 'VEXB',gftm_vexb_in
-    write(1,30) 'VEXB_SHEAR',gftm_vexb_shear_in
-    write(1,30) 'BETAE',gftm_betae_in
-    write(1,30) 'XNUE',gftm_xnue_in
-    write(1,30) 'ZEFF',gftm_zeff_in
-    write(1,30) 'DEBYE',gftm_debye_in
-    write(1,10) 'IFLUX',gftm_iflux_in
-    write(1,20) 'IBRANCH',gftm_ibranch_in
-    write(1,20) 'NMODES',gftm_nmodes_in
-    write(1,20) 'NBASIS_MAX',gftm_nbasis_max_in
-    write(1,20) 'NBASIS_MIN',gftm_nbasis_min_in
-    write(1,20) 'NXGRID',gftm_nxgrid_in
-    write(1,20) 'NKY',gftm_nky_in
-    write(1,10) 'ADIABATIC_ELEC',gftm_adiabatic_elec_in
-    write(1,30) 'ALPHA_MACH',gftm_alpha_mach_in
-    write(1,30) 'ALPHA_E',gftm_alpha_e_in
-    write(1,30) 'ALPHA_P',gftm_alpha_p_in
-    write(1,30) 'ALPHA_QUENCH',gftm_alpha_quench_in
-    write(1,30) 'ALPHA_ZF',gftm_alpha_zf_in
-    write(1,30) 'XNU_FACTOR',gftm_xnu_factor_in
-    write(1,30) 'DEBYE_FACTOR',gftm_debye_factor_in
-    write(1,30) 'ETG_FACTOR',gftm_etg_factor_in
-    write(1,30) 'RLNP_CUTOFF',gftm_rlnp_cutoff_in
-    write(1,20) 'WRITE_WAVEFUNCTION_FLAG',gftm_write_wavefunction_flag_in
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Species vectors:'
-    write(1,*) '#---------------------------------------------------'
-    do i = 1,gftm_ns_in
-        write(1,40) 'ZS_',i,gftm_zs_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'MASS_',i,gftm_mass_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'RLNS_',i,gftm_rlns_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'RLTS_',i,gftm_rlts_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'TAUS_',i,gftm_taus_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'AS_',i,gftm_as_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'VPAR_',i,gftm_vpar_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'VPAR_SHEAR_',i,gftm_vpar_shear_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'VNS_SHEAR_',i,gftm_vns_shear_in(i)
-    enddo
-    do i = 1,gftm_ns_in
-        write(1,40) 'VTS_SHEAR_',i,gftm_vts_shear_in(i)
-    enddo
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Gaussian width parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'WIDTH',gftm_width_in
-    write(1,30) 'WIDTH_MIN',gftm_width_min_in
-    write(1,10) 'FIND_WIDTH',gftm_find_width_in
-    write(1,20) 'NWIDTH',gftm_nwidth_in
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Miller geometry parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'RMIN_LOC',gftm_rmin_loc_in
-    write(1,30) 'RMAJ_LOC',gftm_rmaj_loc_in
-    write(1,30) 'ZMAJ_LOC',gftm_zmaj_loc_in
-    write(1,30) 'DRMINDX_LOC',gftm_drmindx_loc_in
-    write(1,30) 'DRMAJDX_LOC',gftm_drmajdx_loc_in
-    write(1,30) 'DZMAJDX_LOC',gftm_dzmajdx_loc_in
-    write(1,30) 'Q_LOC',gftm_q_loc_in
-    write(1,30) 'KAPPA_LOC',gftm_kappa_loc_in
-    write(1,30) 'S_KAPPA_LOC',gftm_s_kappa_loc_in
-    write(1,30) 'DELTA_LOC',gftm_delta_loc_in
-    write(1,30) 'S_DELTA_LOC',gftm_s_delta_loc_in
-    write(1,30) 'ZETA_LOC',gftm_zeta_loc_in
-    write(1,30) 'S_ZETA_LOC',gftm_s_zeta_loc_in
-    write(1,30) 'P_PRIME_LOC',gftm_p_prime_loc_in
-    write(1,30) 'Q_PRIME_LOC',gftm_q_prime_loc_in
-    write(1,30) 'KX0_LOC',gftm_kx0_loc_in
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# s-alpha geometry parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'RMIN_SA',gftm_rmin_sa_in
-    write(1,30) 'RMAJ_SA',gftm_rmaj_sa_in
-    write(1,30) 'Q_SA',gftm_q_sa_in
-    write(1,30) 'SHAT_SA',gftm_shat_sa_in
-    write(1,30) 'ALPHA_SA',gftm_alpha_sa_in
-    write(1,30) 'XWELL_SA',gftm_xwell_sa_in
-    write(1,30) 'THETA0_SA',gftm_theta0_sa_in
-    write(1,20) 'B_MODEL_SA',gftm_b_model_sa_in
-    write(1,20) 'FT_MODEL_SA',gftm_ft_model_sa_in
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Expert parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'DAMP_PSI',gftm_damp_psi_in
-    write(1,30) 'DAMP_SIG',gftm_damp_sig_in
-    write(1,30) 'PARK',gftm_park_in
-    write(1,30) 'GHAT',gftm_ghat_in
-    write(1,30) 'GCHAT',gftm_gchat_in
-    write(1,30) 'WD_ZERO',gftm_wd_zero_in
-    write(1,30) 'LINSKER_FACTOR',gftm_linsker_factor_in
-    write(1,30) 'GRADB_FACTOR',gftm_gradB_factor_in
-    write(1,30) 'FILTER',gftm_filter_in
-    write(1,30) 'THETA_TRAPPED',gftm_theta_trapped_in
-    write(1,30) 'NN_MAX_ERROR', gftm_nn_max_error_in
-
-    close(1)
-
-10  format(t2,a,'=',l1)
-20  format(t2,a,'=',i3)
-30  format(t2,a,'=',1pe12.5)
-40  format(t2,a,i1,'=',1pe12.5)
-50  format(t2,a,'=',a8)
-
-  end subroutine gftm_dump_local
-
-  ! Dump GLOBAL MODULE variables
-  subroutine gftm_dump_global()
-
-    use gftm_global
-
-    implicit none
-
-    integer :: ierr, i
-
-    open(unit=1,file=trim(gftm_path_in)//'out.gftm.globaldump',&
-         status='replace',iostat=ierr)
-    if (gftm_geometry_flag_in == 2 ) then
-       write(1,*) 'DUMP NOT SUPPORTED FOR FOURIER GEOMETRY'
-       close(1)
-       return
-    endif
-
-    write(1,*) '# input.gftm generated by gftm_dump_global()'
-    write(1,*) '#'
-    write(1,*) '# See https://fusion.gat.com/theory/gftminput'
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Control parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,50) 'UNITS',gftm_units_in
-    write(1,20) 'NS',ns_in
-    write(1,10) 'USE_TRANSPORT_MODEL',.TRUE.
-    write(1,20) 'GEOMETRY_FLAG',igeo
-    write(1,10) 'USE_BPER',use_bper_in
-    write(1,10) 'USE_BPAR',use_bpar_in
-    write(1,10) 'USE_MHD_RULE',use_mhd_rule_in
-    write(1,10) 'USE_BISECTION',use_bisection_in
-    write(1,10) 'USE_INBOARD_DETRAPPED',use_inboard_detrapped_in
-    write(1,10) 'USE_AVE_ION_GRID',use_ave_ion_grid_in
-    write(1,20) 'SAT_RULE',sat_rule_in
-    write(1,20) 'KYGRID_MODEL',kygrid_model_in
-    write(1,20) 'XNU_MODEL',xnu_model_in
-    write(1,20) 'VPAR_MODEL',vpar_model_in
-    write(1,20) 'VPAR_SHEAR_MODEL',vpar_shear_model_in 
-    write(1,30) 'SIGN_BT',sign_bt_in
-    write(1,30) 'SIGN_IT',sign_it_in
-    write(1,30) 'KY',ky_in
-    write(1,10) 'NEW_EIKONAL',new_eikonal_in
-    write(1,30) 'VEXB',vexb_in
-    write(1,30) 'VEXB_SHEAR',vexb_shear_in
-    write(1,30) 'BETAE',betae_in
-    write(1,30) 'XNUE',xnue_in
-    write(1,30) 'ZEFF',zeff_in
-    write(1,30) 'DEBYE',debye_in
-    write(1,10) 'IFLUX',iflux_in
-    write(1,20) 'IBRANCH',ibranch_in
-    write(1,20) 'NMODES',nmodes_in
-    write(1,20) 'NBASIS_MAX',nbasis_max_in
-    write(1,20) 'NBASIS_MIN',nbasis_min_in
-    write(1,20) 'NXGRID',nxgrid_in
-    write(1,20) 'NKY',nky_in
-    write(1,10) 'ADIABATIC_ELEC',adiabatic_elec_in
-    write(1,30) 'ALPHA_MACH',alpha_mach_in
-    write(1,30) 'ALPHA_E',alpha_e_in
-    write(1,30) 'ALPHA_P',alpha_p_in
-    write(1,30) 'ALPHA_QUENCH',alpha_quench_in
-    write(1,30) 'ALPHA_ZF',alpha_zf_in
-    write(1,30) 'XNU_FACTOR',xnu_factor_in
-    write(1,30) 'DEBYE_FACTOR',debye_factor_in
-    write(1,30) 'ETG_FACTOR',etg_factor_in
-    write(1,30) 'RLNP_CUTOFF',rlnp_cutoff_in
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Species vectors:'
-    write(1,*) '#---------------------------------------------------'
-    do i = 1,ns_in
-        write(1,40) 'ZS_',i,zs_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'MASS_',i,mass_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'RLNS_',i,rlns_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'RLTS_',i,rlts_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'TAUS_',i,taus_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'AS_',i,as_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'VPAR_',i,vpar_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'VPAR_SHEAR_',i,vpar_shear_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'VNS_SHEAR_',i,vns_shear_in(i)
-    enddo
-    do i = 1,ns_in
-        write(1,40) 'VTS_SHEAR_',i,vts_shear_in(i)
-    enddo
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Gaussian width parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'WIDTH',width_in
-    write(1,30) 'WIDTH_MIN',width_min_in
-    write(1,10) 'FIND_WIDTH',find_width_in
-    write(1,20) 'NWIDTH',nwidth_in
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Miller geometry parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'RMIN_LOC',rmin_loc
-    write(1,30) 'RMAJ_LOC',rmaj_loc
-    write(1,30) 'ZMAJ_LOC',zmaj_loc
-    write(1,30) 'DRMINDX_LOC',drmindx_loc
-    write(1,30) 'DRMAJDX_LOC',drmajdx_loc
-    write(1,30) 'DZMAJDX_LOC',dzmajdx_loc
-    write(1,30) 'Q_LOC',q_loc
-    write(1,30) 'KAPPA_LOC',kappa_loc
-    write(1,30) 'S_KAPPA_LOC',s_kappa_loc
-    write(1,30) 'DELTA_LOC',delta_loc
-    write(1,30) 'S_DELTA_LOC',s_delta_loc
-    write(1,30) 'ZETA_LOC',zeta_loc
-    write(1,30) 'S_ZETA_LOC',s_zeta_loc
-    write(1,30) 'P_PRIME_LOC',p_prime_loc
-    write(1,30) 'Q_PRIME_LOC',q_prime_loc
-    write(1,30) 'KX0_LOC',kx0_loc
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# s-alpha geometry parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'RMIN_SA',rmin_sa
-    write(1,30) 'RMAJ_SA',rmaj_sa
-    write(1,30) 'Q_SA',q_sa
-    write(1,30) 'SHAT_SA',shat_sa
-    write(1,30) 'ALPHA_SA',alpha_sa
-    write(1,30) 'XWELL_SA',xwell_sa
-    write(1,30) 'THETA0_SA',theta0_sa
-    write(1,20) 'B_MODEL_SA',b_model_sa
-    write(1,20) 'FT_MODEL_SA',ft_model_sa
-    write(1,*) ' '
-    write(1,*) '#---------------------------------------------------'
-    write(1,*) '# Expert parameters:'
-    write(1,*) '#---------------------------------------------------'
-    write(1,30) 'DAMP_PSI',damp_psi_in
-    write(1,30) 'DAMP_SIG',damp_sig_in
-    write(1,30) 'PARK',park_in
-    write(1,30) 'GHAT',ghat_in
-    write(1,30) 'GCHAT',gchat_in
-    write(1,30) 'WD_ZERO',wd_zero_in
-    write(1,30) 'LINSKER_FACTOR',linsker_factor_in
-    write(1,30) 'GRADB_FACTOR',gradB_factor_in
-    write(1,30) 'FILTER',filter_in
-    write(1,30) 'THETA_TRAPPED',theta_trapped_in
-    write(1,30) 'NN_MAX_ERROR', nn_max_error_in
-
-    close(1)
-
-10  format(t2,a,'=',l1)
-20  format(t2,a,'=',i3)
-30  format(t2,a,'=',1pe12.5)
-40  format(t2,a,i1,'=',1pe12.5)
-50  format(t2,a,'=',a8)
-
-  end subroutine gftm_dump_global
-
-end module gftm_interface
diff --git a/gftm/src/gftm_isinf.f90 b/gftm/src/gftm_isinf.f90
deleted file mode 100644
index d1728d067..000000000
--- a/gftm/src/gftm_isinf.f90
+++ /dev/null
@@ -1,15 +0,0 @@
-
-  logical function gftm_isinf(x)
-  ! 
-  ! test real variables for NAN 
-  !
-  implicit none
-  real, intent(in) :: x
-
-  gftm_isinf = .false.
-
-  if (ABS(x) > HUGE(x)) gftm_isinf = .true.
-
-  end function gftm_isinf
-   
-      
diff --git a/gftm/src/gftm_isnan.cray.f90 b/gftm/src/gftm_isnan.cray.f90
deleted file mode 100644
index 88c08db14..000000000
--- a/gftm/src/gftm_isnan.cray.f90
+++ /dev/null
@@ -1,12 +0,0 @@
-  logical function gftm_isnan(x)
-  ! 
-  ! test real variables for NAN 
-  !
-  implicit none
-  real, intent(in) :: x
-
-  gftm_isnan = ISNAN(x)
-
-  end function gftm_isnan
-   
-      
diff --git a/gftm/src/gftm_isnan.f90 b/gftm/src/gftm_isnan.f90
deleted file mode 100644
index a38fa0e7d..000000000
--- a/gftm/src/gftm_isnan.f90
+++ /dev/null
@@ -1,15 +0,0 @@
-  logical function gftm_isnan(x)
-  ! 
-  ! test function for platforms where isnan is not intrinsic.
-  ! This numerical test may not work depending on the compiler
-  !
-  implicit none
-  real, intent(in) :: x
-
-  gftm_isnan = .false.
-
-  if (x/=x) gftm_isnan = .true.
-
-  end function gftm_isnan
-   
-      
diff --git a/gftm/src/gftm_isnan.ieee.f90 b/gftm/src/gftm_isnan.ieee.f90
deleted file mode 100644
index 6ee8be085..000000000
--- a/gftm/src/gftm_isnan.ieee.f90
+++ /dev/null
@@ -1,13 +0,0 @@
-  logical function gftm_isnan(x)
-  ! 
-  ! test real variables for NAN 
-  !
-  use ieee_arithmetic, only : ieee_is_nan
-  implicit none
-  real, intent(in) :: x
-
-  gftm_isnan = IEEE_IS_NAN(x)
-
-  end function gftm_isnan
-   
-      
diff --git a/gftm/src/gftm_kygrid.f90 b/gftm/src/gftm_kygrid.f90
deleted file mode 100644
index ca8f10995..000000000
--- a/gftm/src/gftm_kygrid.f90
+++ /dev/null
@@ -1,227 +0,0 @@
-!-------------------------------------------------------------------------------
-!
-      SUBROUTINE get_ky_spectrum
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_kyspectrum
-      IMPLICIT NONE
-!
-      integer :: nk_zones,nky0,nky1,nky2 
-      INTEGER :: spectrum_type=0
-      INTEGER :: i
-      INTEGER :: ntest
-      REAL :: ky_min=0.05
-      REAL :: ky_max=0.7
-      REAL :: ky0,ky1,lnky,dky0
-      REAL :: ky_cut
-      REAL :: ky_factor
-
-!
-!  spectrum_type = 0 for linear GYRO spectrum
-!  spectrum_type = 1 for APS07 spectrum
-!  spectrum_type = 2 for IAEA08 spectrum
-!  spectrum_type = 3 for spectrum with ky_min = ky_cut
-!
-      new_kyspectrum=.FALSE.
-!
-!
-      spectrum_type = kygrid_model_in
-!
-      nk_zones=3
-!
-      nky = nky_in
-!
-      if(units_in.eq.'GYRO')then
-        ky_factor = 1.0
-      else
-        ky_factor = grad_r0_out
-      endif
-      ky0 = ky_min
-      ky1 = ky_max
-      if(nk_zones.ge.2)ky1 = ky_max/SQRT(mass(1))
-!
-      if(spectrum_type.eq.0)then
-!        dky0 = (ky_max-ky_min)/REAL(nky-1)
-        ky1=ky_in
-        dky0=ky1/REAL(nky)
-!        write(*,*)" ky_in = ", ky_in
-        do i=1,nky
-!          ky_spectrum(i) = ky0 + REAL(i-1)*dky0
-          ky_spectrum(i) = REAL(i)*dky0
-          dky_spectrum(i) = dky0
-        enddo
-!        if(use_highk)then
-!          ky0=1.0
-!          dky0 = (ky1-ky0)/REAL(nky-1)
-!          do i=1,nky
-!            ky_spectrum(nky+i) = ky0 + REAL(i-1)*dky0
-!            dky_spectrum(nky+i) = dky0
-!          enddo
-!          nky=2*nky
-!        endif
-      endif
-      if(spectrum_type.eq.1)then   ! APS07 spectrum
-        nky=9
-!        ky_max = 0.9*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))  !k_theta*rho_ion = 0.9
-        ky_max = 0.9*ky_factor/rho_ion  !k_theta*rho_ion = 0.9
-        dky0 = ky_max/REAL(nky)
-        do i=1,nky
-          ky_spectrum(i) = REAL(i)*dky0
-          dky_spectrum(i) = dky0
-        enddo
-        ky0 = ky_max+dky0
-!        ky1 = 0.4*ky_factor*ABS(zs(1))/SQRT(taus(1)*mass(1))  !k_theta*rho_e = 0.4
-        ky1 = 0.4*ky_factor/rho_e  !k_theta*rho_e = 0.4
-        dky0 = LOG(ky1/ky0)/REAL(nky_in-1)
-        lnky = LOG(ky0)
-        if(nky_in.gt.0)then
-          do i=nky+1,nky+nky_in     
-            ky_spectrum(i) = EXP(lnky)
-            dky_spectrum(i) = ky_spectrum(i)*dky0
-            lnky = lnky + dky0
-          enddo
-        endif
-        nky = nky + nky_in
-      endif
-      if(spectrum_type.eq.2)then  ! IAEA08 spectrum
-        nky1=8
-!        dky0=0.05*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))
-        dky0=0.05*ky_factor/rho_ion
-        do i=1,nky1
-          ky_spectrum(i) = REAL(i)*dky0
-          dky_spectrum(i) = dky0
-        enddo
-!        dky0 = ky_max/REAL(nky)
-!        dky0=0.2/SQRT(taus(2)*mass(2))
-        dky0=0.2/rho_ion
-        ky0 = ky_spectrum(nky1)
-        nky2=7
-        nky = nky1+nky2
-        do i=nky1+1,nky
-          ky_spectrum(i) = ky0 + REAL(i-nky1)*dky0
-          dky_spectrum(i) = dky0
-        enddo
-!        ky_max = 0.9*ABS(zs(2))/SQRT(taus(2)*mass(2))  !k_theta*rho_ion = 0.9
-!        ky0 = ky_max+dky0
-        ky0 = ky_spectrum(nky) + dky0
-!        ky1 = 0.4*ky_factor*ABS(zs(1))/SQRT(taus(1)*mass(1))  !k_theta*rho_e = 0.4
-        ky1 = 0.4*ky_factor/rho_e    !k_theta*rho_e = 0.4
-        dky0 = LOG(ky1/ky0)/REAL(nky_in-1)
-        lnky = LOG(ky0)
-        if(nky_in.gt.0)then
-          do i=nky+1,nky+nky_in     
-            ky_spectrum(i) = EXP(lnky)
-            dky_spectrum(i) = ky_spectrum(i)*dky0
-            lnky = lnky + dky0
-          enddo
-          nky = nky + nky_in
-        endif
-      endif
-      if(spectrum_type.eq.3)then   ! ky_min=ky_in spectrum similar to APS07
-!      the value of ky_in must be set externally e.g. ky_in = rhos*q/r
-!        ky_max = 6.0*ky_min  ! n=6
-!        nky0=6
-!        ky_max = 1.0*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))  !k_theta*rho_ion = 1.0
-        ky_max = 1.0*ky_factor/rho_ion  !k_theta*rho_ion = 1.0
-        nky0 = INT(ky_max/ky_in)-1
-        ky_min = ky_in
-        dky0 = ky_min
-        ky_spectrum(1) = ky_min
-        dky_spectrum(1) = ky_min
-        do i=2,nky0
-          ky_spectrum(i) = ky_spectrum(i-1) + dky0
-          dky_spectrum(i) = dky0
-        enddo
-        if(ky_spectrum(nky0).lt.ky_max)then
-          nky1 = 1
-          ky_min = ky_spectrum(nky0)
-          dky0 = (ky_max-ky_min)/REAL(nky1)
-          do i=1,nky1
-            ky_spectrum(nky0+i) = ky_spectrum(nky0+i-1) + dky0
-            dky_spectrum(nky0+i) = dky0
-          enddo 
-        else
-          nky1=0
-          ky_max = ky_spectrum(nky0)
-        endif       
-        ky0 = ky_max
-!        ky1 = 0.4*ky_factor*ABS(zs(1))/SQRT(taus(1)*mass(1))  !k_theta*rho_e = 0.4
-        ky1 = 0.4*ky_factor/rho_e !k_theta*rho_e = 0.4        dky0 = LOG(ky1/ky0)/REAL(nky_in)
-        lnky = LOG(ky0+dky0)
-        do i=1,nky_in     
-          ky_spectrum(nky0+nky1+i) = EXP(lnky)
-          dky_spectrum(nky0+nky1+i) = ky_spectrum(nky0+nky1+i)*dky0
-          lnky = lnky + dky0
-        enddo
-        nky = nky0 + nky1 + nky_in
-      endif
-      if(spectrum_type.eq.4)then   ! APS07 spectrum with ky_min=0.05
-        nky=12
-!        ky_min = 0.05*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))
-        ky_min = 0.05*ky_factor/rho_ion
-        ky_spectrum(1) = ky_min
-        dky_spectrum(1) = ky_min
-        ky_spectrum(2) = 2.0*ky_min
-        dky_spectrum(2) = ky_min
-        ky_spectrum(3) = 3.0*ky_min
-        dky_spectrum(3) = ky_min
-        ky_spectrum(4) = 4.0*ky_min
-        dky_spectrum(4) = ky_min
-        ky_spectrum(5) = 5.0*ky_min
-        dky_spectrum(5) = ky_min        
-        ky_min = ky_spectrum(5)
-!        ky_max = 1.0*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))
-        ky_max = 1.0*ky_factor/rho_ion
-!        dky0 = 0.1*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))
-        dky0 = 0.1*ky_factor/rho_ion
-        do i=6,nky
-          ky_spectrum(i) = ky_min + REAL(i-4)*dky0
-          dky_spectrum(i) = dky0
-        enddo
-!        ky0 = 1.0*ky_factor*ABS(zs(2))/SQRT(taus(2)*mass(2))
-!        ky1 = 0.4*ky_factor*ABS(zs(1))/SQRT(taus(1)*mass(1))  !k_theta*rho_e = 0.4
-        ky0 = 1.0*ky_factor/rho_ion
-        ky1 = 0.4*ky_factor/rho_e  !k_theta*rho_e = 0.4
-        dky0 = LOG(ky1/ky0)/REAL(nky_in-1)
-        lnky = LOG(ky0)
-        if(nky_in.gt.0)then
-          dky_spectrum(nky)=ky0-ky_spectrum(nky)
-          do i=nky+1,nky+nky_in     
-            ky_spectrum(i) = EXP(lnky)
-            dky_spectrum(i) = ky_spectrum(i)*dky0
-            lnky = lnky + dky0
-          enddo
-        endif
-        nky = nky + nky_in
-      endif
-!
-      if(spectrum_type.eq.5)then
-        nky=nky_in
-        ky1=ky_in
-        dky0=ky1/REAL(nky)
-        ntest=INT(0.5/dky0)+1
-        nky=11 + nky_in - ntest
-        do i=1,10
-          ky_spectrum(i) = REAL(i)*0.05
-          dky_spectrum(i) = 0.05
-        enddo
-        ky_spectrum(11) = REAL(ntest)*dky0
-        dky_spectrum(i) = ky_spectrum(11)-0.5
-        do i=12,nky
-          ky_spectrum(i) = ky_spectrum(i-1) + dky0
-          dky_spectrum(i) = dky0
-        enddo
-      endif
-
-
-! debug
-!      write(*,*)"ky_min=",ky_min,"ky_max=",ky_max
-!      write(*,*)"nky = ",nky,"ky0 = ",ky0," ky1 = ",ky1
-!      do i=1,nky
-!      write(*,*)i,"ky=",ky_spectrum(i),"dky=",dky_spectrum(i)
-!      enddo
-!
-      END SUBROUTINE get_ky_spectrum
-
diff --git a/gftm/src/gftm_matrix.f90 b/gftm/src/gftm_matrix.f90
deleted file mode 100644
index 1fe389c09..000000000
--- a/gftm/src/gftm_matrix.f90
+++ /dev/null
@@ -1,786 +0,0 @@
-!         
-      SUBROUTINE get_matrix
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_coeff
-!
-      IMPLICIT NONE
-      INTEGER :: i,j,k 
-!
-      new_matrix=.FALSE.
-!      write(*,*)"get_matrix"
-!
-      call get_gyro_average_xgrid
-!
-      call get_gyro_average_matrix
-!
-      call ave_theta
-!
-!      write(*,*)"ave_bp(1,1)=",ave_bp(1,1)
-      call ave_inv0(ave_p0,ave_p0inv)
-      call ave_inv0(ave_b0,ave_b0inv)
-!          write(*,*)"ave_b0inv(i,j)=",ave_b0inv(1,1)
-! debug
-!      do i=1,nbasis
-!      do j=1,nbasis
-!        p0 = 0.0
-!        do k=1,nbasis
-!          p0 = p0 + ave_b0(i,k)*ave_b0inv(k,j)
-!        enddo
-!        write(*,*)"check b0/b0",i,j,p0
-!      enddo
-!      enddo
-! debug
-!
-!
-      END SUBROUTINE get_matrix
-!
-      SUBROUTINE get_gyro_average_matrix
-!***************************************************************
-!
-!   compute the average h-bessel functions
-!
-!***************************************************************
-      USE gftm_dimensions
-      USE gftm_hermite
-      USE gftm_xgrid
-      USE gftm_coeff
-      USE gftm_gyro_average
-!
-      IMPLICIT NONE
-      INTEGER :: is,ie,ix,ib,jb
-
-
-      REAL :: ww, zero_cut
-!
-      zero_cut = 1.E-12
-!
-      do is = ns0,ns
-      do ie = 1,ne
-      do ib=1,nbasis
-      do jb=ib,nbasis
-        mat_pe1j0s(is,ie,ib,jb) = 0.0
-        mat_pe2j0s(is,ie,ib,jb) = 0.0
-        mat_pe1j1s(is,ie,ib,jb) = 0.0
-        mat_pe2j1s(is,ie,ib,jb) = 0.0
-!
-        do ix=1,nx
-         ww = wx(ix)*h(ib,ix)*h(jb,ix)
-!        write(*,*)i,j,k,ww,wx(k),h(i,k),h(j,k)
-         mat_pe1j0s(is,ie,ib,jb) = mat_pe1j0s(is,ie,ib,jb) + ww*pe1j0sx(is,ie,ix)
-         mat_pe2j0s(is,ie,ib,jb) = mat_pe2j0s(is,ie,ib,jb) + ww*pe2j0sx(is,ie,ix)
-         mat_pe1j1s(is,ie,ib,jb) = mat_pe1j1s(is,ie,ib,jb) + ww*pe1j1sx(is,ie,ix)/SQRT(b2x(ix))
-         mat_pe2j1s(is,ie,ib,jb) = mat_pe2j1s(is,ie,ib,jb) + ww*pe2j1sx(is,ie,ix)/SQRT(b2x(ix))
-        enddo
-! symmetrize
-         mat_pe1j0s(is,ie,jb,ib) = mat_pe1j0s(is,ie,ib,jb)
-         mat_pe2j0s(is,ie,jb,ib) = mat_pe2j0s(is,ie,ib,jb)
-         mat_pe1j1s(is,ie,jb,ib) = mat_pe1j1s(is,ie,ib,jb)
-         mat_pe2j1s(is,ie,jb,ib) = mat_pe2j1s(is,ie,ib,jb)
-      enddo
-      enddo
-      enddo
-      enddo
-!
-      END SUBROUTINE get_gyro_average_matrix
-!
-      SUBROUTINE ave_theta
-!***********************************************************
-!  compute  k-independent hermite basis averages
-!***********************************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_hermite
-      USE gftm_xgrid
-      USE gftm_coeff
-      USE gftm_sgrid
-!
-      IMPLICIT NONE
-      INTEGER :: i,j,k,is
-      REAL :: ww
-      REAL :: zero_cut
-      REAL :: debye
-      INTEGER :: lwork,info
-      REAL :: w(nbasis)
-      REAL :: rwork(3*nbasis-2)
-      COMPLEX :: work(34*nbasis)
-      COMPLEX :: a(nbasis,nbasis),b(nbasis,nbasis)
-
-!
-      zero_cut = 1.E-12
-
-! fill the Poisson equation phi multiplier px0 x-grid array
-! note that pol is set in get_species
-!
-      do i=1,nx
-        debye = debye_factor_in*b0x(i)*(ky*debye_s)**2  ! (k_per*debye length unit)^2
-        p0x(i) = debye + pol
-      enddo
-!debug
-!      write(*,*)"check p0",nx
-!      do i=1,nx
-!        write(*,*)i,b0x(i)
-!      enddo
-!      write(*,*)"debye_s = ",debye_s
-!      write(*,*)"pol = ",pol
-!      write(*,*)"ky = ", ky
-!      write(*,*)"width_in =",width_in
-!debug
-!
-!  compute the guass-hermite intregrals
-!
-       do i=1,nbasis
-       do j=1,nbasis
-         ave_kpar(i,j) = 0.0
-       enddo
-       enddo
-       do i=1,nbasis        
-        if(i.lt.nbasis)then
-         ave_kpar(i,i+1)=SQRT(REAL(i)/2.0)
-! ave_kpar is an odd function
-          ave_kpar(i+1,i)=-ave_kpar(i,i+1)
-        endif
-       enddo
-!
-       do i=1,nbasis
-       do j=i,nbasis
-!   initialize the averages
-        ave_wdpar(i,j) = 0.0
-        ave_wdper(i,j)= 0.0
-        ave_wb(i,j) = 0.0
-        ave_b0(i,j) = 0.0
-        ave_Binv(i,j) = 0.0
-        ave_p0inv(i,j) = 0.0
-        ave_p0(i,j) = 0.0
-        ave_kx(i,j) = 0.0
-        ave_c_tor_par(i,j) = 0.0
-        ave_c_tor_per(i,j) = 0.0
-        ave_c_par_par(i,j) = 0.0
-!
-        do k=1,nx
-         ww=wx(k)*h(i,k)*h(j,k)
-!           ave_kpar(i,j) = ave_kpar(i,j) + 0.5*wx(k)*   &
-!           (h(i+1,k)*SQRT(2.0*REAL(i))*h(j,k)           &
-!           -h(i,k)*SQRT(2.0*REAL(j))*h(j+1,k))/Bx(k)
-         ave_wdpar(i,j)    = ave_wdpar(i,j)  + ww*wdx(k)
-         ave_wdper(i,j)   = ave_wdper(i,j) + ww*(wdx(k)+wdpx(k))
-         ave_wb(i,j)   = ave_wb(i,j) + ww*wbx(k)
-         ave_b0(i,j)    = ave_b0(i,j)  + ww*b0x(k)*ky*ky
-         ave_Binv(i,j)   = ave_Binv(i,j) + ww*Log(SQRT(b2x(k)))
-         ave_p0inv(i,j) = ave_p0inv(i,j) + ww/p0x(k)
-         ave_p0(i,j) = ave_p0(i,j) + ww*p0x(k)
-         ave_kx(i,j) = ave_kx(i,j) + ww*kxx(k)
-         ave_c_tor_par(i,j) = ave_c_tor_par(i,j) + ww*cx_tor_par(k)
-         ave_c_tor_per(i,j) = ave_c_tor_per(i,j) + ww*cx_tor_per(k)
-         ave_c_par_par(i,j) = ave_c_par_par(i,j) + ww*cx_par_par(k)
-        enddo
-!        if(ABS(ave_kpar(i,j)).lt.zero_cut)ave_kpar(i,j) = 0.0
-        if(ABS(ave_wdpar(i,j)).lt.zero_cut)ave_wdpar(i,j) = 0.0
-        if(ABS(ave_wdper(i,j)).lt.zero_cut)ave_wdper(i,j) = 0.0
-        if(ABS(ave_wb(i,j)).lt.zero_cut)ave_wb(i,j) = 0.0
-        if(ABS(ave_b0(i,j)).lt.zero_cut)ave_b0(i,j) = 0.0
-        if(ABS(ave_Binv(i,j)).lt.zero_cut)ave_Binv(i,j) = 0.0
-        if(ABS(ave_p0inv(i,j)).lt.zero_cut)ave_p0inv(i,j) = 0.0
-        if(ABS(ave_p0(i,j)).lt.zero_cut)ave_p0(i,j) = 0.0
-        if(ABS(ave_kx(i,j)).lt.zero_cut)ave_kx(i,j) = 0.0
-        if(ABS(ave_c_tor_par(i,j)).lt.zero_cut)ave_c_tor_par(i,j) = 0.0
-        if(ABS(ave_c_tor_per(i,j)).lt.zero_cut)ave_c_tor_per(i,j) = 0.0
-        if(ABS(ave_c_par_par(i,j)).lt.zero_cut)ave_c_par_par(i,j) = 0.0
-! symmetrize
-        ave_wdpar(j,i)    = ave_wdpar(i,j)
-        ave_wdper(j,i)    = ave_wdper(i,j)
-        ave_wb(j,i)    = ave_wb(i,j)
-        ave_b0(j,i)    = ave_b0(i,j)
-        ave_Binv(j,i)   = ave_Binv(i,j)
-        ave_p0inv(j,i) = ave_p0inv(i,j)
-        ave_p0(j,i) = ave_p0(i,j)
-        ave_kx(j,i) = ave_kx(i,j)
-        ave_c_tor_par(j,i) = ave_c_tor_par(i,j)
-        ave_c_tor_per(j,i) = ave_c_tor_per(i,j)
-        ave_c_par_par(j,i) = ave_c_par_par(i,j)
-        enddo
-       enddo
-       ave_p0_out = ave_p0(1,1)
-!       write(*,*)"ave_wdpar(1,1)=",ave_wdpar(1,1)
-!       write(*,*)"ave_wdper(1,1)=",ave_wdper(1,1)
-!       write(*,*)"ave_wb(1,1)=",ave_wb(1,1)
-!       write(*,*)"ave_p0inv(1,1) = ",ave_p0inv(1,1)
-!       write(*,*)"ave_p0(1,1) = ",ave_p0(1,1)
-!       write(*,*)"ave_b0(1,1) = ",ave_b0(1,1)
-!       write(*,*)"ave_kx(1,1) = ",ave_kx(1,1)
-!       write(*,*)"ave_tor_par(1,1) = ",ave_c_tor_par(1,1)
-!       write(*,*)"ave_tor_per(1,1) = ",ave_c_tor_per(1,1)
-!       write(*,*)"ave_par_par(1,1) = ",ave_c_par_par(1,1)
-!
-       do i=1,nbasis
-       do j=1,nbasis
-         gradB = 0.0
-         do k=1,nbasis
-           gradB = gradB + ave_kpar(i,k)*ave_Binv(k,j)         &
-           - ave_Binv(i,k)*ave_kpar(k,j)
-         enddo
-         ave_gradB(i,j) = gradB
-!         write(*,*)i,j,"gradB = ",gradB,"  wb = ",ave_wb(i,j)
-       enddo
-       enddo
-!
-        do i=1,nbasis
-        do j=i,nbasis
-          a(i,j) = xi*ave_kpar(i,j)
-        enddo
-        enddo
-        lwork=34*nbasis
-        call ZHEEV('V','U',nbasis,a,nbasis,w,work,lwork,rwork,info)
-        if(info.ne.0)CALL gftm_error(1,"ZHEEV failed in modkpar")
-!       write(*,*)"kpar eigenvalues"
-!       do i=1,nbasis
-!       write(*,*)i,w(i)
-!       enddo
-!       write(*,*)"kpar eigenvectors"
-!       do i=1,nbasis
-!       write(*,*)"******",i
-!       do j=1,nbasis
-!       write(*,*)j,a(i,j)
-!       enddo
-!       enddo
-! construct mod_kpar
-! note modkpar is a real symmetric matrix
-!       write(*,*)"modkpar"
-         do i=1,nbasis
-         do j=1,nbasis
-           b(i,j) = 0.0
-           do k=1,nbasis
-             b(i,j) = b(i,j)+ ABS(w(k))*a(i,k)*CONJG(a(j,k))
-           enddo
-!         write(*,*)i,j,b(i,j)
-           ave_modkpar(i,j)=REAL(b(i,j))
-         enddo
-         enddo
-!
-!
-!
-!  debug
-!       write(*,*)"check ave_p0inv"
-!       do i=1,nbasis
-!         write(*,*)"ave_p0inv(i,j) = ",(ave_p0inv(i,j),j=1,nbasis)
-!       enddo
-!       write(*,*)"check ave_kpar "
-!       do i=1,nbasis
-!       do j=1,nbasis
-!        write(*,*)i,j,ave_kpar(i,j)
-!       enddo
-!       enddo
-!
-!       write(*,*)"check ave_wdpar "
-!       do i=1,nbasis
-!       do j=1,nbasis
-!        write(*,*)i,j,ave_wdpar(i,j)
-!       enddo
-!       enddo
-!       write(*,*)"check ave_wdper "
-!       do i=1,nbasis
-!       do j=1,nbasis
-!        write(*,*)i,j,ave_wdper(i,j)
-!       enddo
-!       enddo
-!       write(*,*)"check ave_gradB "
-!       do i=1,nbasis
-!       do j=1,nbasis
-!        write(*,*)i,j,ave_gradB(i,j)
-!       enddo
-!       enddo
-!
-      END SUBROUTINE ave_theta
-!
-!
-      SUBROUTINE ave_inv(ave_m,ave_minv)
-!***************************************************************
-!
-!   compute the inverse matrix ave_minv
-!   of the symmetric real matrix ave_m
-!
-!***************************************************************
-!
-      USE gftm_dimensions
-! 
-      IMPLICIT NONE
-      INTEGER :: nm,is,i,j,k
-      INTEGER :: lwork,info
-      REAL,INTENT(IN),DIMENSION(ns,nbasis_max,nbasis_max) :: ave_m
-      REAL,INTENT(OUT),DIMENSION(ns,nbasis_max,nbasis_max) :: ave_minv
-      REAL :: detm,zero
-!      REAL :: check
-      REAL :: a(nbasis,nbasis)
-      REAL :: w(nbasis)
-      REAL,ALLOCATABLE,DIMENSION(:) :: work
-!
-      nm = nbasis
-!
-      if(nm.eq.1)then
-        do is=ns0,ns
-          ave_minv(is,1,1) = 1.0/ave_m(is,1,1)
-        enddo
-        go to 100
-      endif
-!
-      if(nm.eq.2)then
-        do is=ns0,ns
-         detm = ave_m(is,1,1)*ave_m(is,2,2)-ave_m(is,1,2)*ave_m(is,2,1)
-         if(detm.eq.0.0)detm = 1.E-12
-         ave_minv(is,1,1) = ave_m(is,2,2)/detm
-         ave_minv(is,2,2) = ave_m(is,1,1)/detm
-         ave_minv(is,1,2) = -ave_m(is,1,2)/detm
-         ave_minv(is,2,1) = -ave_m(is,2,1)/detm
-        enddo
-        go to 100
-      endif
-!
-!  for nm > 2 need to use eigensytem solver
-!
-!  find the eigenvalues of ave_m
-!
-      zero = 1.0E-10
-      do is = ns0,ns
-       do i=1,nm
-       do j=i,nm
-         a(i,j) = ave_m(is,i,j)
-       enddo
-       enddo
-       lwork=34*nm
-       ALLOCATE(work(lwork))
-! call LAPACK routine for symmetric real eigenvalue problem DSYEV
-       call DSYEV('V','U',nm,a,nm,w,work,lwork,info)
-       if(info.ne.0)CALL gftm_error(1,"DSYEV failed in ave_inv")
-       DEALLOCATE(work)
-
-!
-! debug
-!       write(*,*)"ave_m eigenvalues"
-!       do i=1,nm
-!       write(*,*)i,rr(i),ri(i)
-!       enddo
-!       write(*,*)"ave_m eigenvectors"
-!       do i=1,nm
-!       write(*,*)"******",i
-!       do j=1,nm
-!       write(*,*)j,vr(j,i),vi(j,i)
-!       enddo
-!       enddo
-!
-! regularize the eigenvalues
-       do k=1,nm
-           if(ABS(w(k)).lt.zero)then
-             if(w(k).ge.0.0)then
-               w(k)=zero
-             else
-               w(k)=-zero
-             endif
-           endif
-       enddo
-! compute ave_inv
-       do i=1,nm
-       do j=1,nm
-         ave_minv(is,i,j) = 0.0
-         do k=1,nm
-           ave_minv(is,i,j) = ave_minv(is,i,j) + a(i,k)*a(j,k)/w(k)
-         enddo
-       enddo
-       enddo
-      enddo ! is loop
- 100  continue
-! debug check minv
-!      do is=ns0,ns
-!       write(*,*)"check minv",is
-!        do i=1,nm
-!        do j=1,nm
-!         check = 0.0
-!         do k=1,nm
-!           check = check + ave_m(is,i,k)*ave_minv(is,k,j)
-!         enddo
-!         write(*,*)i,j,check
-!        enddo
-!        enddo
-!      enddo
-!
-!
-      END SUBROUTINE ave_inv
-!
-      SUBROUTINE ave_inv0(ave_m,ave_minv)
-!***************************************************************
-!
-!   compute the inverse matrix ave_minv
-!   of the symmetric real matrix ave_m
-!
-!***************************************************************
-      USE gftm_dimensions
-!
-      IMPLICIT NONE
-      INTEGER :: nm,i,j,k
-      INTEGER :: lwork,info
-      REAL :: detm,zero
-!      REAL :: check
-      REAL :: a(nbasis,nbasis)
-      REAL :: w(nbasis)
-      REAL :: work(34*nbasis)
-      REAL,INTENT(IN),DIMENSION(nbasis_max,nbasis_max) :: ave_m
-      REAL,INTENT(OUT),DIMENSION(nbasis_max,nbasis_max) :: ave_minv
-!
-      nm = nbasis
-      zero = 1.0E-12
-!
-      if(nm.eq.1)then
-        ave_minv(1,1) = 1.0/ave_m(1,1)
-        go to 100
-      endif
-!
-      if(nm.eq.2)then
-        detm = ave_m(1,1)*ave_m(2,2)-ave_m(1,2)*ave_m(2,1)
-        if(detm.eq.0.0)detm = zero
-        ave_minv(1,1) = ave_m(2,2)/detm
-        ave_minv(2,2) = ave_m(1,1)/detm
-        ave_minv(1,2) = -ave_m(1,2)/detm
-        ave_minv(2,1) = -ave_m(2,1)/detm
-        go to 100
-      endif
-!
-!  for nm > 2 need to use eigensytem solver
-!
-!
-!  find the eigenvalues of ave_m
-!
-       do i=1,nm
-       do j=i,nm
-         a(i,j) = ave_m(i,j)
-       enddo
-       enddo
-       lwork=34*nm
-! call LAPACK routine for symmetric real eigenvalue problem DSYEV
-       call DSYEV('V','U',nm,a,nm,w,work,lwork,info)
-       if(info.ne.0)CALL gftm_error(1,"DSYEV failed in ave_inv0")
-!
-! debug
-!       write(*,*)"ave_m eigenvalues"
-!       do i=1,nm
-!       write(*,*)i,rr(i),ri(i)
-!       enddo
-!       write(*,*)"ave_m eigenvectors"
-!       do i=1,nm
-!       write(*,*)"******",i
-!       do j=1,nm
-!       write(*,*)j,vr(j,i),vi(j,i)
-!       enddo
-!       enddo
-!
-! regularize the eigenvalues
-       do k=1,nm
-           if(ABS(w(k)).lt.zero)then
-             if(w(k).ge.0.0)then
-               w(k)=zero
-             else
-               w(k)=-zero
-             endif
-           endif
-       enddo
-! compute ave_inv
-       do i=1,nm
-       do j=1,nm
-         ave_minv(i,j) = 0.0
-         do k=1,nm
-           ave_minv(i,j) = ave_minv(i,j) + a(i,k)*a(j,k)/w(k)
-         enddo
-       enddo
-       enddo
- 100   continue
-! debug check minv
-!       write(*,*)"check minv"
-!        do i=1,nm
-!        do j=1,nm
-!         check = 0.0
-!         do k=1,nm
-!           check = check + ave_m(i,k)*ave_minv(k,j)
-!         enddo
-!         write(*,*)i,j,check
-!        enddo
-!        enddo
-!
-      END SUBROUTINE ave_inv0
-! **************** begin gftm-2.0 velocity space matricies
-!
-      SUBROUTINE get_velocity_matrix
-!
-!  This subroutine initializes the parallel velocity and perpendicular energy
-!  matricies and the corresponding derivative matricies needed for the
-!  mirror force operator
-!  G. M. Staebler Jan 6, 2022
-!
-      USE gftm_velocity_matrix
-      IMPLICIT NONE
-      INTEGER :: i
-!
-!  upar matrix
-      mat_upar(:,:) = 0.0
-      mat_upar(1,2) = SQRT(0.5)
-      mat_upar(2,1) = SQRT(0.5)
-      mat_upar(2,3) = 1.0
-      mat_upar(3,2) = 1.0
-      mat_upar(3,4) = SQRT(1.5)
-      mat_upar(4,3) = SQRT(1.5)
-      mat_upar(4,5) = SQRT(2.0)
-      mat_upar(5,4) = SQRT(2.0)
-      mat_upar(5,6) = SQRT(2.5)
-      mat_upar(6,5) = SQRT(2.5)
-      mat_upar(6,7) = SQRT(3.0)
-      mat_upar(7,6) = SQRT(3.0)
-      mat_upar(7,8) = SQRT(3.5)
-      mat_upar(8,7) = SQRT(3.5)
-      mat_upar(8,9) = 2.0
-      mat_upar(9,8) = 2.0
-      mat_upar(9,10) = SQRT(4.5)
-      mat_upar(10,9) = SQRT(4.5)
-      mat_upar(10,11) = SQRT(5.0)
-      mat_upar(11,10) = SQRT(5.0)
-      mat_upar(11,12) = SQRT(5.5)
-      mat_upar(12,11) = SQRT(5.5)
-      mat_upar(12,13) = SQRT(6.0)
-      mat_upar(13,11) = SQRT(6.0)
-! upar derivative matrix  d/dupar
-      mat_dupar(:,:) = 0.0
-      mat_dupar(1,2) = SQRT(0.5)
-      mat_dupar(2,1) = -SQRT(0.5)
-      mat_dupar(2,3) = 1.0
-      mat_dupar(3,2) = -1.0
-      mat_dupar(3,4) = SQRT(1.5)
-      mat_dupar(4,3) = -SQRT(1.5)
-      mat_dupar(4,5) = SQRT(2.0)
-      mat_dupar(5,4) = -SQRT(2.0)
-      mat_dupar(5,6) = SQRT(2.5)
-      mat_dupar(6,5) = -SQRT(2.5)
-      mat_dupar(6,7) = SQRT(3.0)
-      mat_dupar(7,6) = -SQRT(3.0)
-      mat_dupar(7,8) = SQRT(3.5)
-      mat_dupar(8,7) = -SQRT(3.5)
-      mat_dupar(8,9) = 2.0
-      mat_dupar(9,8) = -2.0
-      mat_dupar(9,10) = SQRT(4.5)
-      mat_dupar(10,9) = -SQRT(4.5)
-      mat_dupar(10,11) = SQRT(5.0)
-      mat_dupar(11,10) = -SQRT(5.0)
-      mat_dupar(11,12) = SQRT(5.5)
-      mat_dupar(12,11) = -SQRT(5.5)
-      mat_dupar(12,13) = SQRT(6.0)
-      mat_dupar(13,12) = -SQRT(6.0)
-!  eper matrix
-      mat_eper(:,:) = 0.0
-      mat_eper(1,1) = 1.0
-      mat_eper(1,2) = 1.0
-      mat_eper(2,1) = 1.0
-      mat_eper(2,2) = 3.0
-      mat_eper(2,3) = 2.0
-      mat_eper(3,2) = 2.0
-      mat_eper(3,3) = 5.0
-      mat_eper(3,4) = 3.0
-      mat_eper(4,3) = 3.0
-      mat_eper(4,4) = 7.0
-      mat_eper(4,5) = 4.0
-      mat_eper(5,4) = 4.0
-      mat_eper(5,5) = 9.0
-      mat_eper(5,6) = 5.0
-      mat_eper(6,5) = 5.0
-      mat_eper(6,6) = 11.0
-      mat_eper(6,7) = 6.0
-      mat_eper(7,6) = 6.0
-      mat_eper(7,7) = 13.0
-!  eper derivative matrix  eper*d/deper
-      mat_deper(:,:) = 0.0
-      mat_deper(1,2) = 0.5
-      mat_deper(2,1) = -0.5
-      mat_deper(2,3) = 1.0
-      mat_deper(3,2) = -1.0
-      mat_deper(3,4) = 1.5
-      mat_deper(4,3) = -1.5
-      mat_deper(4,5) = 2.0
-      mat_deper(5,4) = -2.0
-      mat_deper(5,6) = 2.5
-      mat_deper(6,5) = -2.5
-      mat_deper(6,7) = 3.0
-      mat_deper(7,6) = -3.0
-!
-      END SUBROUTINE get_velocity_matrix
-!
-!     gyro_average integrals
-!
-      SUBROUTINE get_gyro_average(b,n)
-!
-! Soubroutine to evaluate the perpendicular energy moments of the
-! Bessel functions J0, J1. 
-! Note: This routine is called many times to compute the polidal angle matricies
-! so it needs to be reduce the output to just the n specified moments
-!
-      USE gftm_gyro_average
-      IMPLICIT NONE
-!
-      INTEGER,INTENT(IN) :: n
-      REAL,INTENT(IN)  :: b
-      REAL :: w, b2, b4, b6, b8, b10, b12
-!
-      b2=b*b
-      b4 = b2*b2
-      b6 = b4*b2
-      b8 = b6*b2
-      b10 = b8*b2
-      b12 = b10*b2
-      w = EXP(- 0.25*b2)
-      if(n.ge.1)then
-        pe1j0(1)= w
-        pe2j0(1) = -b2*w/4.0
-        pe1j1(1) = w/2.0
-        pe2j1(1) = -(b2 - 4.0)*w/8.0
-      endif
-      if(n.ge.2)then
-        pe1j0(2) = -b2*w/4.0
-        pe2j0(2) = ((b2 -4.0)**2)*w/16.0
-        pe1j1(2) = -(b2 -4.0)*w/8.0
-        pe2j1(2) = (b4 -16.0*b2 +48.0)*w/32.0
-      endif
-      if(n.ge.3)then
-        pe1j0(3) = b4*w/32.0
-        pe2j0(3) = -((b2 -8.0)**2)*b2*w/128.0
-        pe1j1(3) = (b2 -8.0)*b2*w/64.0
-        pe2j1(3) = -(b2 -8.0)*(b4 -20.0*b2 +32.0)*w/256.0
-      endif
-      if(n.ge.4)then
-        pe1j0(4) = -b6*w/384.0
-        pe2j0(4) = ((b2 -12.0)**2)*b4*w/1536.0
-        pe1j1(4) = -(b2 -12.0)*b4*w/768.0
-        pe2j1(4) = (b2 -4.0)*(b2 -12.0)*(b2 -24.0)*b2*w/3072.0
-      endif
-      if(n.ge.5)then
-        pe1j0(5) = b8*w/6144.0
-        pe2j0(5) = -((b2 -16.0)**2)*b6*w/24576.0
-        pe1j1(5) = (b2 -16.0)*b6*w/12288.0
-        pe2j1(5) = -(b2 -16.0)*(b4 -36.0*b2 +192.0)*b4*w/49152.0
-      endif
-      if(n.ge.6)then
-        pe1j0(6) = -b10*w/122880.0
-        pe2j0(6) = ((b2 -20.0)**2)*b8*w/491520.0
-        pe1j1(6) = -(b2 -20.0)*b8*w/245760.0
-        pe2j1(6) = (b2 - 20.0)*(b4 -44.0*b2 +320.0)*b6*w/983040.0
-      endif
-      if(n.ge.7)then
-        pe1j0(7) = b12*w/2949120.0
-        pe2j0(7) = -((b2 -24.0)**2)*b10*w/11796480.0
-        pe1j1(7) = (b2 -24.0)*b10*w/5898240.0
-        pe2j1(7) = -(b2 -40.0)*(b2 -24.0)*(b2 -12.0)*b8*w/23592960.0
-      endif
-!
-      END SUBROUTINE get_gyro_average
-!
-      SUBROUTINE get_gyro_average_xgrid
-!
-!*************************************************************
-!  Compute the gyro-average integrals at the hermite quadrature nodes
-!*************************************************************
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_xgrid
-      USE gftm_gyro_average
-!
-      IMPLICIT NONE
-!
-      REAL :: b
-      INTEGER :: ix, is, ie
-!
-      do ix=1,nx
-      do is=ns0,ns
-        b= ky*sqrt_two*vs(is)*mass(is)*SQRT(b0x(ix)/b2x(ix))/ABS(zs(is))
-        CALL get_gyro_average(b,ne)
-        do ie=1,ne
-          pe1j0sx(is,ie,ix) = pe1j0(ie)
-          pe2j0sx(is,ie,ix) = pe2j0(ie)
-          pe1j1sx(is,ie,ix) = pe1j1(ie)
-          pe2j1sx(is,ie,ix) = pe2j1(ie)
-        enddo
-      enddo
-      enddo
-!
-      END SUBROUTINE get_gyro_average_xgrid
-!
-! **************** end
-!
-      SUBROUTINE get_mat_uparc
-!***************************************************************
-!
-!   compute the regularized mat_upar matrix
-!
-!***************************************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_velocity_matrix
-!
-      IMPLICIT NONE
-      INTEGER :: i,j,k
-      INTEGER :: lwork,info
-      REAL :: a(nu,nu)
-      REAL :: w(nu)
-      REAL :: work(34*nu)
-!
-!  find the eigenvalues of matu
-!
-       do i=1,nu
-       do j=i,nu
-         a(i,j) = mat_upar(i,j)
-       enddo
-       enddo
-       lwork=34*nu
-! call LAPACK routine for symmetric real eigenvalue problem DSYEV
-       call DSYEV('V','U',nu,a,nu,w,work,lwork,info)
-       if(info.ne.0)CALL gftm_error(1,"DSYEV failed in mat_uparc")
-! debug
-!       write(*,*)"mat_upar eigenvalues"
-!       do i=1,nu
-!       write(*,*)i,w(i)
-!       enddo
-!       write(*,*)"mat_upar eigenvectors"
-!       do i=1,nu
-!       write(*,*)"******",i
-!       do j=1,nu
-!       write(*,*)j,a(j,i)
-!       enddo
-!       enddo
-!
-! regularize the eigenvalues
-!
-       do k=1,nu
-         if(ABS(w(k)).lt.0.01)then
-          write(*,*)"w = ",w(k),"  etg_factor_in = ",etg_factor_in
-          w(k) = etg_factor_in
-         endif
-       enddo
-! compute mat_uparc with regularized eigenvalues
-! note that the DSYEV normalized eigenvectors are now in a(i,j)
-       do i=1,nu
-       do j=1,nu
-         mat_uparc(i,j) = 0.0
-         do k=1,nu
-           mat_uparc(i,j) = mat_uparc(i,j) + w(k)*a(i,k)*a(j,k)
-         enddo
-       enddo
-       enddo
-!
-! debug check mat_uparc eigenvalues
-!       do i=1,nu
-!       do j=i,nu
-!         a(i,j) = mat_uparc(i,j)
-!       enddo
-!       enddo
-!       call DSYEV('V','U',nu,a,nu,w,work,lwork,info)
-!       write(*,*)"mat_uparc eigenvalues"
-!       do i=1,nu
-!       write(*,*)i,w(i)
-!       enddo
-!
-      END SUBROUTINE get_mat_uparc
diff --git a/gftm/src/gftm_max.f90 b/gftm/src/gftm_max.f90
deleted file mode 100644
index c5fbdc900..000000000
--- a/gftm/src/gftm_max.f90
+++ /dev/null
@@ -1,335 +0,0 @@
-!
-      SUBROUTINE gftm_max
-!
-      USE gftm_global
-      USE gftm_dimensions
-      USE gftm_species
-      USE gftm_pkg
-!
-      IMPLICIT NONE
-      LOGICAL :: save_iflux
-      LOGICAL :: save_bper
-      LOGICAL :: save_bpar
-      INTEGER :: nt,i,is,imax
-      INTEGER :: save_nbasis
-      INTEGER :: save_ibranch
-      INTEGER :: save_nu, save_ne
-      REAL :: width_max=1.65
-      REAL :: width_min=0.15
-      REAL :: tp,dt
-      REAL :: t1,t2,tm,g1,g2,gm
-      REAL :: tmax,tmin,gamma_max,gmax
-      REAL :: save_width,dtmin
-      REAL :: gamma_n(nt0),freq_n(nt0),width_n(nt0)
-!      REAL :: save_vexb_shear
-      REAL :: wgp_max,width_p_max
-      REAL :: kyi,ft2
-!
-      CALL gftm_setup_geometry
-!
-!      do i=1,nmodes_in
-!        gamma_reference_kx0(i)=0.0
-!        freq_reference_kx0(i)=0.0
-!      enddo
-!      save_iflux = iflux_in
-      save_ibranch = ibranch_in
-      save_nbasis = nbasis_max_in
-      save_width = width_in
-      save_bper = use_bper_in
-      save_bpar = use_bpar_in
-!      save_nu = nu
-!      save_ne = ne
-!      nu = 5
-!      ne = 3
-!      save_vexb_shear = vexb_shear_s
-!      if(alpha_quench_in.eq.0.0)vexb_shear_s = 0.0
-      ibranch_in = -1
-      width_min = width_min_in
-      width_max = ABS(width_in)
-!      write(*,*)"width_min = ",width_min,"  width_max = ", width_max
-!
-!      write(*,*)"R_unit=",R_unit,"q_unit=",q_unit
-!      write(*,*)ns0,ns,ky_s
-!    if(alpha_p_in.gt.0.0)then
-!      do is=ns0,ns
-!        kyi = ky_s*SQRT(taus(is)*mass(is))/ABS(zs(is))
-!        wgp_max = ABS((taus(is)/zs(is))*vpar_shear_s(is)/vs(is))*ky_s/(1+kyi**2)
-!        width_p_max = 3.6*vs(is)/(sqrt_two*R_unit*q_unit*MAX(wgp_max,0.001))
-!        width_p_max=MAX(width_p_max,0.1)
-!         if(width_p_max.lt.width_min_in)then
-!          width_min = width_p_max
-!        endif
-!      enddo
- !   endif
-!        kyi = ky_s*SQRT(taus(2)*mass(2))/ABS(zs(2))
-!        wgp_max = ABS(vpar_shear_in(2)/vs(2))*kyi/(1+kyi**2)
-!        width_p_max = 3.6/(sqrt_two*R_unit*q_unit*MAX(wgp_max,0.001))
-!        width_p_max=MAX(width_p_max,0.01)
-!         if(width_p_max.lt.width_min_in)then
-!          width_min = width_p_max
-!        endif
-!      write(*,*)ky," width_p_max = ", width_p_max,width_min
-!
-! for ibranch_in > 0 the most unstable positive frequency mode is stored 
-! in gamma_out(1) and the most unstable negative frequency mode 
-! (ion diamagnetic drift direction) is stored in gamma_out(2)
-! for ibranch_in = -1 the unstable modes in rank order are stored in
-! gamma_out(i) i=1,nmodes_in
-!
-!      iflux_in=.FALSE.
-      if(nbasis_min_in.ne.0)then
-        nbasis = nbasis_min_in
-      endif
-!      if(sat_rule_in.eq.2)then
-!        use_bper_in = .false.
-!        use_bpar_in = .false.
-!      endif
-!       write(*,*)"nbasis = ",nbasis
-      tmin=LOG10(width_min)
-      tmax=LOG10(width_max)
-      nt=nwidth_in
-      dtmin=(tmax-tmin)/REAL(nt-1)
-      if(use_bisection_in)nt=5
-!
-!      open(2,file = 'width.dat',status='unknown')
-      dt = (tmax-tmin)/REAL(nt-1)
-      tp = tmin
-      do i=1,nt
-       gamma_n(i)=0.0
-       freq_n(i)=0.0
-       width_n(i)=0.0
-       tp = tmin + REAL(i-1)*dt
-       width_in = 10.0**tp
-!       write(*,*)"width_in = ",width_in
-       new_width = .TRUE.
-       call gftm_LS
-       write(*,*)i,width_in,nbasis,gamma_out(1),freq_out(1)
-       width_n(i)=width_in
-       gamma_n(i) = gamma_out(1)
-       freq_n(i) = freq_out(1)
-      enddo
-!      close(2)
-! find the global maximum
-      gamma_max=gamma_n(nt)
-      imax=nt
-      do i=nt-1,1,-1
-        if(gamma_n(i).gt.gamma_max)then
-          gamma_max=gamma_n(i)
-          imax=i
-        endif
-!        write(*,*)"debug",i,imax,gamma_max,gamma_n(i)
-      enddo
-      width_in = width_n(imax)
-!
-      if(use_bisection_in.and.gamma_max.gt.0.0)then
-!
-! use bounded bisection search to refine width
-!
-         if(imax.eq.1)then
-! maximum is against bottom width
-           g1 = gamma_n(1)
-           t1 = tmin
-           g2 = gamma_n(2)
-           t2 = LOG10(width_n(2))
-           tp = (t2+t1)/2.0    
-           width_in = 10.0**tp
-           new_width = .TRUE.
-           call gftm_LS
-           gm = gamma_out(1)
-           tm = tp
-         elseif(imax.eq.nt)then
-! maximum is against top width
-           g1 = gamma_n(nt-1)
-           t1 = LOG10(width_n(nt-1))
-           g2 = gamma_n(nt)
-           t2 = tmax           
-           tp = (t2+t1)/2.0    
-           width_in = 10.0**tp
-           new_width = .TRUE.
-           call gftm_LS
-           gm = gamma_out(1)
-           tm = tp
-         else
-! maximum is away from boundaries
-           g1 = gamma_n(imax-1)
-           t1 = LOG10(width_n(imax-1))
-           g2 = gamma_n(imax+1)
-           t2 = LOG10(width_n(imax+1))
-           gm = gamma_n(imax)
-           tm = LOG10(width_n(imax))
-         endif
-! start bisection search
-         dt=(t2-t1)/2.0
-!         write(*,*)"dtmin=",dtmin,"tmin=",tmin,"tmax=",tmax
-         do while(dt.gt.dtmin)
-           dt=dt/2.0
-           gmax = MAX(gm,MAX(g1,g2))
-!           write(*,*)"dt=",dt,gmax
-!           write(*,*)g1,gm,g2
-!           write(*,*)t1,tm,t2
-!
-           if(g1.eq.gmax)then  
-             if(t1.gt.tmin)then
-! shift past t1 and compute new g1,t1 
-               tp = t1-dt
-               width_in = 10.0**tp
-               new_width = .TRUE.
-               call gftm_LS
-               tm = t1
-               gm = g1
-               g1 = gamma_out(1)
-               t1 = tp
-! compute new g2,t2
-               tp = tm+dt
-               width_in = 10.0**tp
-               new_width = .TRUE.
-               call gftm_LS
-               g2 = gamma_out(1)
-               t2 = tp
-             else   ! t1 at tmin
-! shrink towards t1
-               tp = t1 + dt
-               width_in = 10.0**tp
-               new_width = .TRUE.
-               call gftm_LS
-               g2 = gm
-               t2 = tm
-               gm = gamma_out(1)
-               tm = tp               
-             endif
-           elseif(g2.eq.gmax)then
-             if(t2.lt.tmax)then
-! shift past t2 and compute new g2,t2
-               tp = t2 + dt
-               width_in = 10.0**tp
-               new_width = .TRUE.
-               call gftm_LS
-               gm = g2
-               tm = t2
-               g2 = gamma_out(1)
-               t2 = tp
-! compute new g1,t1
-               tp = tm - dt
-               width_in = 10.0**tp
-               new_width = .TRUE.
-               call gftm_LS
-               g1 = gamma_out(1)
-               t1 = tp
-             else  ! t2 at tmax 
-! shrink towards t2
-               tp = t2 - dt
-               width_in = 10.0**tp
-               new_width = .TRUE.
-               call gftm_LS
-               g1 = gm
-               t1 = tm
-               gm = gamma_out(1)
-               tm = tp               
-             endif
-           else  ! gm.eq.gmax
-! compute new g1,t1 and g2,t2 closer to gm,tm
-             tp = tm - dt
-             width_in = 10.0**tp
-             new_width = .TRUE.
-             call gftm_LS
-             g1 = gamma_out(1)
-             t1 = tp
-!
-             tp = tm + dt
-             width_in = 10.0**tp
-             new_width = .TRUE.
-             call gftm_LS
-             g2 = gamma_out(1)
-             t2 = tp
-           endif           
-         enddo  ! end of bisection search main loop
-! find final maximum
-         gmax=gm
-         tp=tm
-         if(g1.gt.gmax)then
-          gmax=g1
-          tp=t1
-         endif
-         if(g2.gt.gmax)then
-          gmax=g2
-          tp=t2
-         endif
-         gamma_max = gmax
-         width_in = 10.0**tp        
-      endif ! done with bisection search
-!      write(*,*)"gamma_max=",gamma_max,"width_in=",width_in
-       gamma_nb_min_out = gamma_max
-!  reset ibranch_in
-       ibranch_in = save_ibranch
-!
-       if(gamma_max.ne.0.0)then
-! refine eigenvalue with more basis functions
-         nbasis = save_nbasis
-!         nu = save_nu
-!         ne = save_ne
-         if(sat_rule_in.eq.2)then
-          use_bper_in = save_bper
-          use_bpar_in = save_bpar
-         endif
-         write(*,*)"nbasis=",nbasis, "width_in = ",width_in
-         iflux_in=save_iflux
-         new_width=.TRUE.
-         call gftm_LS
-!         if(ibranch_in.eq.-1)then
-! check for inward ballooning modes
-!         write(*,*) ky_s,use_inboard_detrapped_in
-!         write(*,*)"modB_test = ",modB_test
-!         write(*,*)"ft_test = ",ft_test
-!           if(use_inboard_detrapped_in.and.ft_test.gt.modB_test)then
-!             fts(:) =  ft_min
-!           write(*,*)"changed ft",ft
-!             new_geometry = .FALSE.
-!             new_width = .FALSE.
-!             new_matrix = .TRUE.
-!             call gftm_LS
-!           endif
-!           if(alpha_quench_in.eq.0.0)then
-!             if(save_vexb_shear.ne.0.0.or.wgp_max.ne.0.0)then
-!               do i=1,nmodes_out
-!                 gamma_reference_kx0(i) = gamma_out(i)
-!                 freq_reference_kx0(i) = freq_out(i)
-!               enddo
-!               vexb_shear_s = save_vexb_shear
-!               iflux_in=save_iflux
-!               new_width=.TRUE.
-!               call gftm_LS
-!             endif
-!           endif
-!         endif  ! ibranch_in == -1
-         gamma_max = MAX(gamma_out(1),gamma_out(2))  ! works for both ibranch_in cases
-!
-!        write(*,*)"width_p_max = ", width_p_max,width_in,gamma_max
-!        write(*,*)ky,width_in,gamma_out(1),freq_out(1)
-!        write(*,*)" maximum gamma for nbasis = ",nbasis_max_in
-!        write(*,*)"gamma_out(1) = ",gamma_out(1)
-!        write(*,*)"freq_out(1) = ",freq_out(1)
-!        write(*,*)"gamma_out(2) = ",gamma_out(2)
-!        write(*,*)"freq_out(2) = ",freq_out(2)
-!        gamma_n(igamma)=gamma_out(branch)
-!        freq_n(igamma) = freq_out(branch)
-       endif
-!
-       if(gamma_max.eq.0.0)then
-         width_in=save_width
-         if(sat_rule_in.eq.2)then
-          use_bper_in = save_bper
-          use_bpar_in = save_bpar
-         endif
-         do i=1,nmodes_in
-          gamma_out(i)=0.0
-          freq_out(i)=0.0
- !         gamma_reference_kx0(i)=0.0
- !         freq_reference_kx0(i)=0.0
-         enddo
-       endif
-!
-       nbasis=save_nbasis
-!       iflux_in=save_iflux
-!       vexb_shear_s = save_vexb_shear
-!
-      END SUBROUTINE gftm_max   
diff --git a/gftm/src/gftm_modules.f90 b/gftm/src/gftm_modules.f90
deleted file mode 100644
index 8a97ee266..000000000
--- a/gftm/src/gftm_modules.f90
+++ /dev/null
@@ -1,538 +0,0 @@
-      MODULE gftm_max_dimensions
-!
-! global dimensions for shared arrays
-!
-      IMPLICIT NONE
-      SAVE
-!
-      INTEGER, PARAMETER :: nb=32
-      INTEGER, PARAMETER :: nxm=2*(nb+1)-1
-      INTEGER, PARAMETER :: nsm=12, nt0=40
-      INTEGER, PARAMETER :: nkym=512
-      INTEGER, PARAMETER :: maxmodes=16
-      INTEGER, PARAMETER :: max_ELITE=700
-      INTEGER, PARAMETER :: max_fourier = 24
-      INTEGER, PARAMETER :: ms = 128  ! ms needs to be divisible by 8
-      INTEGER, PARAMETER :: max_plot =18*ms/8+1
-      INTEGER, PARAMETER :: num = 13
-      INTEGER, PARAMETER :: nem = 7
-!
-      END MODULE gftm_max_dimensions
-!
-      MODULE gftm_dimensions
-      USE gftm_max_dimensions
-!
-! dimensions determined by inputs
-! 
-      IMPLICIT NONE
-      SAVE
-!
-! global dimensions
-!
-      INTEGER nx,nbasis,nbasis_max,ns0,ns,nky
-      INTEGER :: nu=3, ne=2, nz, nune, nphase, ntot
-!
-      END MODULE gftm_dimensions
-!
-      MODULE gftm_global
-      USE gftm_max_dimensions
-!
-!  global controls for the gftm driver routine
-!
-      IMPLICIT NONE
-      SAVE
-! global constants
-      REAL :: pi
-      REAL :: pi_2
-      REAL :: sqrt_pi
-      REAL :: sqrt_two
-      COMPLEX :: xi=(0.0,1.0)
-! internal flow control switches
-      LOGICAL :: new_eikonal_in=.TRUE.
-      LOGICAL :: new_start=.TRUE.
-      LOGICAL :: new_matrix=.TRUE.
-      LOGICAL :: new_geometry=.TRUE.
-      LOGICAL :: new_width=.TRUE.
-      LOGICAL :: new_kyspectrum=.TRUE.
-      LOGICAL :: gauher_uncalled=.TRUE.
-      LOGICAL :: gauss_hermite_uncalled=.TRUE.
-      LOGICAL :: eikonal_unsaved=.TRUE.
-      INTEGER :: igeo=1
-      LOGICAL :: use_default_species=.TRUE.
-      INTEGER,DIMENSION(8) :: trace_path=0
-      LOGICAL,EXTERNAL :: gftm_isnan
-      LOGICAL,EXTERNAL :: gftm_isinf
-! input units switch
-      CHARACTER (len=8) :: units_in = 'GYRO'
-! Input Gaussian width
-      REAL :: width_in=1.65
-      REAL :: width_min_in=0.3
-      INTEGER :: nwidth_in=21
-      LOGICAL :: find_width_in=.TRUE.
-! Input kys
-      REAL :: ky_in=0.3
-! Input species 
-      INTEGER :: ns_in=2, nstotal_in = 2
-      REAL,DIMENSION(nsm) :: mass_in
-      REAL,DIMENSION(nsm) :: zs_in
-! input switches
-      LOGICAL :: iflux_in=.TRUE.
-      LOGICAL :: use_bper_in=.FALSE.
-      LOGICAL :: use_bpar_in=.FALSE.
-      LOGICAL :: use_mhd_rule_in=.TRUE.
-      LOGICAL :: use_bisection_in=.TRUE.
-      LOGICAL :: use_inboard_detrapped_in=.FALSE.
-      LOGICAL :: use_ave_ion_grid_in=.FALSE.
-      INTEGER :: ibranch_in=-1
-      INTEGER :: nmodes_in=2
-      INTEGER :: nbasis_max_in=4
-      INTEGER :: nbasis_min_in=2
-      INTEGER :: nxgrid_in=16
-      INTEGER :: nky_in=12
-      INTEGER :: mainion=2
-! input rare switches
-      REAL :: theta_trapped_in=0.7
-      REAL :: wdia_trapped_in=0.0
-      REAL :: park_in=1.0
-      REAL :: ghat_in=1.0
-      REAL :: gchat_in=1.0
-      REAL :: wd_zero_in=0.1
-      REAL :: Linsker_factor_in=0.0
-      REAL :: gradB_factor_in=0.0
-      REAL :: filter_in=2.0
-      REAL :: damp_psi_in = 0.0
-      REAL :: damp_sig_in = 0.0
-! Input model paramaters
-      LOGICAL :: adiabatic_elec_in=.FALSE.
-      REAL :: alpha_e_in=1.0
-      REAL :: alpha_p_in=1.0
-      REAL :: alpha_mach_in=0.0
-      REAL :: alpha_quench_in=0.0
-      REAL :: alpha_zf_in = 1.0
-      REAL :: xnu_factor_in=1.0
-      REAL :: debye_factor_in=1.0
-      REAL :: etg_factor_in=1.25
-      REAL :: rlnp_cutoff_in = 18.0
-      INTEGER :: sat_rule_in=0
-      INTEGER :: kygrid_model_in=1
-      INTEGER :: xnu_model_in=2
-      INTEGER :: vpar_model_in=0
-      INTEGER :: vpar_shear_model_in=1    
-      REAL :: alpha_n_in =0.0  !not used
-      REAL :: alpha_t_in =0.0  !not used
-! Input signs
-      REAL :: sign_Bt_in = 1.0
-      REAL :: sign_It_in = 1.0
-! Input field gradients
-      REAL,DIMENSION(nsm) :: rlns_in=0.0
-      REAL,DIMENSION(nsm) :: rlts_in=0.0
-      REAL,DIMENSION(nsm) :: vpar_shear_in=0.0
-      REAL :: vexb_shear_in=0.0
-! Input profile shear
-      REAL,DIMENSION(nsm) :: vns_shear_in=0.0
-      REAL,DIMENSION(nsm) :: vts_shear_in=0.0
-! Input field averages
-      REAL,DIMENSION(nsm) :: as_in=0.0
-      REAL,DIMENSION(nsm) :: taus_in=0.0
-      REAL,DIMENSION(nsm) :: vpar_in=0.0
-      REAL :: vexb_in = 0.0
-      REAL :: betae_in=0.0
-      REAL :: xnue_in=0.0
-      REAL :: zeff_in=1.0
-      REAL :: debye_in=0.0
-! Shifted circle (s-alpha) inputs
-      REAL :: rmin_sa=0.5
-      REAL :: rmaj_sa=3.0
-      REAL :: q_sa=2.0
-      REAL :: shat_sa=1.0
-      REAL :: alpha_sa=0.0
-      REAL :: xwell_sa=0.0
-      REAL :: theta0_sa=0.0
-! Shifted circle flags
-      INTEGER :: b_model_sa=1
-      INTEGER :: ft_model_sa=1
-! Miller inputs
-      REAL :: rmin_loc=0.5
-      REAL :: rmaj_loc=3.0
-      REAL :: zmaj_loc=0.0
-      REAL :: q_loc=2.0
-!      REAL :: shat_loc=1.0
-      REAL :: dlnpdr_loc=0.0
-      REAL :: drmindx_loc=1.0
-      REAL :: drmajdx_loc=0.0
-      REAL :: dzmajdx_loc=0.0
-      REAL :: kappa_loc=1.0
-      REAL :: s_kappa_loc=0.0
-      REAL :: delta_loc=0.0
-      REAL :: s_delta_loc=0.0
-      REAL :: zeta_loc=0.0
-      REAL :: s_zeta_loc=0.0
-      REAL :: p_prime_loc=0.0 
-      REAL :: q_prime_loc=16.0
-      REAL :: kx0_loc = 0.0
-! Fourier geometry inputs
-      INTEGER :: nfourier_in        = 16
-      REAL :: q_fourier_in          = 2.0
-      REAL :: q_prime_fourier_in    = 16.0
-      REAL :: p_prime_fourier_in    = 0.0
-      REAL :: fourier_in(8,0:max_fourier) = 0.0
-! ELITE geometry inputs
-      INTEGER :: n_ELITE
-      REAL :: R_ELITE(0:max_ELITE)
-      REAL :: Z_ELITE(0:max_ELITE)
-      REAL :: Bp_ELITE(0:max_ELITE)
-      REAL :: q_ELITE
-      REAL :: q_prime_ELITE
-      REAL :: p_prime_ELITE
-! global variables
-      REAL :: ft=0.5
-      REAL :: ft_min=0.01
-      REAL :: ft_test
-      REAL :: modB_test
-      REAL :: modB_min
-      REAL :: ky=0.3
-      REAL :: R_unit=3.0
-      REAL :: q_unit=2.0
-      REAL :: B_unit=1.0
-      REAL :: Rmaj_input = 3.0
-      REAL :: q_in = 2.0
-      REAL :: rmin_input=0.5
-      REAL,DIMENSION(maxmodes) :: gamma_reference_kx0 =0.0
-      REAL,DIMENSION(maxmodes) :: freq_reference_kx0 =0.0
-      REAL,DIMENSION(2,nkym,maxmodes) :: eigenvalue_first_pass =0.0
-      REAL :: pol=1.0
-      REAL :: U0=0.0
-      REAL :: kx0=0.0
-      REAL :: kx0_e=0.0
-      REAL :: kx0_p = 0.0
-      REAL :: midplane_shear=1.0
-      REAL :: kx0_factor=1.0
-      REAL :: rho_ion=1.0
-      REAL :: rho_e=1.0
-! output
-      COMPLEX,DIMENSION(3,nb) :: field_weight_QL_out=0.0
-      COMPLEX,DIMENSION(maxmodes,3,nb) :: field_weight_out=0.0
-      COMPLEX,DIMENSION(maxmodes,3,max_plot) :: plot_field_out=0.0
-      REAL,DIMENSION(max_plot) :: plot_angle_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: particle_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: energy_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: stress_par_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: stress_tor_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: exchange_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: N_QL_out=0.0,T_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: U_QL_out=0.0,Q_QL_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: n_bar_out=0.0,t_bar_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: u_bar_out=0.0,q_bar_out=0.0
-      REAL,DIMENSION(maxmodes,nsm) :: Ns_Ts_phase_out=0.0
-      REAL,DIMENSION(nsm) :: particle_flux_out=0.0,energy_flux_out=0.0
-      REAL,DIMENSION(nsm) :: exchange_out=0.0
-      REAL,DIMENSION(nsm) :: stress_par_out=0.0,stress_tor_out=0.0
-      REAL,DIMENSION(maxmodes) :: gamma_out=0.0,freq_out=0.0
-      REAL,DIMENSION(maxmodes) :: v_QL_out=0.0,a_par_QL_out=0.0,b_par_QL_out=0.0
-      REAL,DIMENSION(maxmodes) :: phi_bar_out=0.0,v_bar_out=0.0
-      REAL,DIMENSION(maxmodes) :: a_par_bar_out=0.0,b_par_bar_out=0.0
-      REAL,DIMENSION(maxmodes) :: wd_bar_out=0.0,b0_bar_out=0.0
-      REAL,DIMENSION(maxmodes) :: ne_te_phase_out=0.0
-      REAL,DIMENSION(maxmodes) :: kx_bar_out=0.0,kpar_bar_out=0.0
-      REAL,DIMENSION(maxmodes) :: modB_bar_out=0.0
-      REAL,DIMENSION(nsm) :: n_bar_sum_out=0.0,t_bar_sum_out=0.0
-      REAL,DIMENSION(nsm) :: q_low_out=0.0
-      REAL,DIMENSION(4,nkym,maxmodes) :: field_spectrum_out=0.0
-      REAL,DIMENSION(4,nkym,maxmodes) :: QL_field_spectrum_out=0.0
-      REAL,DIMENSION(4,nsm,nkym,maxmodes) :: intensity_spectrum_out=0.0
-      REAL,DIMENSION(4,nsm,nkym,maxmodes) :: QL_intensity_spectrum_out=0.0
-      REAL,DIMENSION(5,nsm,nkym,maxmodes) :: flux_spectrum_out=0.0
-      REAL,DIMENSION(5,nsm,nkym,maxmodes) :: QL_flux_spectrum_out=0.0
-      REAL,DIMENSION(2,nkym,maxmodes) :: eigenvalue_spectrum_out=0.0
-      REAl,DIMENSION(nkym,maxmodes) :: ne_te_phase_spectrum_out=0.0
-      REAl,DIMENSION(nsm,nkym,maxmodes) :: nsts_phase_spectrum_out=0.0
-      REAL,DIMENSION(nkym) :: spectral_shift_out=0.0
-      REAL,DIMENSION(nkym) :: ave_p0_spectrum_out=0.0
-      REAL,DIMENSION(nkym) :: width_out=0.0
-      REAL,DIMENSION(nsm,5,5) :: diff_out=0.0
-      REAL,DIMENSION(nsm,5) :: conv_out=0.0
-      REAL,DIMENSION(nsm,5) :: flux_out=0.0
-      REAL,DIMENSION(nsm) :: delta_out
-      REAL :: Vzf_out = 0.0
-      REAL :: kymax_out = 0.0
-      REAL :: phi_bar_sum_out=0.0
-      REAL :: v_bar_sum_out=0.0
-      REAL :: gamma_nb_min_out=0.0
-      REAL :: B2_ave_out=1.0
-      REAL :: R2_ave_out=1.0
-      REAL :: B_ave_out=1.0
-      REAL :: Bt_ave_out=1.0
-      REAL :: Bp0_out = 1.0
-      REAL :: RBt_ave_out=1.0
-      REAL :: Grad_r_ave_out=1.0
-      REAL :: grad_r0_out=1.0
-      REAL :: B_geo0_out = 1.0
-      REAL :: Bt0_out = 1.0
-      REAL :: SAT_geo0_out=1.0
-      REAL :: SAT_geo1_out=1.0
-      REAL :: SAT_geo2_out=1.0
-      REAL :: kx_geo0_out=1.0
-      REAL :: DM_out = 0.25
-      REAL :: DR_out = 0.0
-      REAL :: Bref_out = 1.0
-      REAL :: ave_p0_out = 1.0
-      INTEGER :: nmodes_out = 2
-      INTEGER :: nfields_out = 1
-      INTEGER :: jmax_out = 0
-      character (len=80) :: error_msg='null' 
-! NN activation parameters (thresholds)  
-      REAL :: nn_max_error_in = -1.0
-      LOGICAL :: valid_nn = .FALSE.
-    
-     
-!
-      END MODULE gftm_global
-!-------------------------------------------------
-      MODULE gftm_hermite
-! hermite basis functions and x-grid
-      USE gftm_max_dimensions
-      IMPLICIT NONE
-      SAVE
-!
-      REAL :: x(nxm),wx(nxm),h(nxm,nxm)
-!
-      END MODULE gftm_hermite
-!
-      MODULE gftm_species
-! species parameters
-!      USE gftm_max_dimensions
-      IMPLICIT NONE
-!
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ei_exch, resist
-      REAL,ALLOCATABLE,DIMENSION(:) :: zs, mass, vs, fts
-      REAL,ALLOCATABLE,DIMENSION(:) :: rlts, rlns
-      REAL,ALLOCATABLE,DIMENSION(:) :: as, taus
-      REAL,ALLOCATABLE,DIMENSION(:) :: vpar_s, vpar_shear_s
-      REAL :: xnue_s, vexb_shear_s, ky_s
-!
-      END MODULE gftm_species
-!-------------------------------------------------
-      MODULE gftm_kyspectrum
-!
-! ky spectrum for computing total fluxes and intensities
-!
-      USE gftm_dimensions
-      IMPLICIT NONE
-      SAVE
-
-!
-      REAL,DIMENSION(nkym) :: ky_spectrum
-      REAL,DIMENSION(nkym) :: dky_spectrum
-!
-      END MODULE gftm_kyspectrum
-!
-!-------------------------------------------------
-      MODULE gftm_eigen
-!
-! eigenvalues, eigenvectors and fluxes
-!
-!      USE gftm_dimensions
-      IMPLICIT NONE
-!
-      INTEGER matz
-      INTEGER,ALLOCATABLE,DIMENSION(:) :: grow_index
-      REAL,ALLOCATABLE,DIMENSION(:) :: fv1, fv2, fv3
-      REAL,ALLOCATABLE,DIMENSION(:) :: rr, ri
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ar, ai
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: vr, vi
-      COMPLEX :: we
-      COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: amat, bmat
-      COMPLEX,ALLOCATABLE,DIMENSION(:) :: he, alpha, beta
-      COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: hetot
-!
-      END MODULE gftm_eigen
-!
-!-------------------------------------------------
-!
-      MODULE gftm_weight
-!  
-!  quasilinear weights and eigenfunction averages
-!
-      USE gftm_dimensions
-      IMPLICIT NONE
-!
-      REAL :: N_weight(nsm),T_weight(nsm)
-      REAl :: U_weight(nsm),Q_weight(nsm)
-      REAL :: phi_weight,a_par_weight,b_par_weight,v_weight
-      REAL :: Ne_Te_phase,Ne_Te_cos,Ne_Te_sin
-      REAL :: Ns_Ts_phase(nsm),Ns_Ts_cos,Ns_Ts_sin
-      REAL :: wd_bar,b0_bar,modB_bar,kx_bar,kpar_bar
-!      
-      END MODULE gftm_weight
-!
-!-------------------------------------------------
-!      
-     MODULE gftm_xgrid
-!
-! functions on the x-grid
-!
-      USE gftm_max_dimensions
-      IMPLICIT NONE
-      SAVE
-!
-      REAL,DIMENSION(nxm) :: wdx, wdpx, b0x, b2x, kxx, wbx
-      REAL,DIMENSION(nxm) :: cx_tor_par, cx_tor_per
-      REAL,DIMENSION(nxm) :: cx_par_par
-      REAL,DIMENSION(nxm) :: p0x, Bx
-      INTEGER,DIMENSION(nkym) :: mask_save
-      REAL,DIMENSION(nkym) :: gamma_nb_min_save
-      REAL,DIMENSION(nkym) :: width_save, ft_save
-      REAL,DIMENSION(nkym) :: R_unit_save, q_unit_save
-      REAL,DIMENSION(nkym,nxm) :: wdx_save, b0x_save
-      REAL,DIMENSION(nkym,nxm) :: cx_par_par_save
-      REAL,DIMENSION(nkym,nxm) :: cx_tor_par_save
-      REAL,DIMENSION(nkym,nxm) :: cx_tor_per_save
-      REAL,DIMENSION(nkym,nxm) :: b2x_save, kxx_save
-! gftm2 additions
-      REAL,DIMENSION(nsm,nem,nxm) :: pe1j0sx,pe2j0sx,pe1j1sx,pe2j1sx
-!
-      END MODULE gftm_xgrid
-!
-!-------------------------------------------------
-!
-      MODULE gftm_sgrid
-!
-! functions on the s-grid
-!
-      USE gftm_max_dimensions
-      IMPLICIT NONE
-      SAVE
-!
-!---------------------------------------------------------------
-! s_grid.m
-! 
-! PURPOSE:
-!  include file which contains the data for mercier_luc.f :
-! INPUT
-!  R, Z and Bp on the s-grid with ms equally space intervals of length ds
-!  as defined by the polidal co-ordinate in the mercier-luc system. 
-!  B_unit = B0 (r/rho) dr/drho where B0 = magnetic field on axis
-!  Rmaj_s = major radius at magnetic axis
-!  rmin_s = minor radius of flux surface 
-!  q_s = local flux surface safety factor 
-!  q_prime_s = dq/dpsi
-!  p_prime_s = dp/dpsi 
-!
-! OUTPUT
-!  costheta_geo, sintheta_geo, costheta_p_geo, pk_geo, epsl_geo, qrat_geo
-!  kyoky_geo, b_geo
-!
-! 24 June 05: gms
-!  this version for gftm separated miller and mercier-luc components
-!  in GKS and GYRO versions
-!---------------------------------------------------------------
-! INPUT
-      REAL,DIMENSION(0:ms) :: R, Z, Bp
-      REAL :: ds, Ls
-      REAL :: Rmaj_s, Zmaj_s,rmin_s, q_s
-      REAL :: p_prime_s, q_prime_s
-      REAL :: p_prime_zero_s
-      REAL :: betae_s, debye_s
-! OUTPUT
-      REAL,DIMENSION(0:ms) :: costheta_geo, sintheta_geo
-      REAL,DIMENSION(0:ms) :: costheta_p_geo, s_p
-      REAL,DIMENSION(0:ms) :: pk_geo, epsl_geo, qrat_geo
-      REAL,DIMENSION(0:ms) :: kxoky_geo, b_geo, t_s
-      REAL,DIMENSION(0:ms) :: S_prime, kx_factor, y
-      REAL :: f,ff_prime
-!
-      END MODULE gftm_sgrid
-!
-!-------------------------------------------------
-!
-      MODULE gftm_coeff
-
- !  ave_theta
-      REAL :: gradB
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_kx
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_c_tor_par, ave_c_tor_per
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_c_par_par
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_wdpar
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_wdper
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_wb
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_gradB, ave_Binv
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_b0, ave_b0inv
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_kpar, ave_modkpar
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_p0, ave_p0inv
-      REAL,ALLOCATABLE,DIMENSION(:,:) :: ave_bp, ave_bpinv
-!
-      END MODULE gftm_coeff
-!
-!-----------------------------------------------------
-!
-       MODULE gftm_GFS
-       REAL,ALLOCATABLE,DIMENSION(:,:) :: matmirror
-       REAL,ALLOCATABLE,DIMENSION(:,:) :: matu, matuc,matdu, matuu
-       REAL,ALLOCATABLE,DIMENSION(:,:) :: mate, matde
-       REAL,ALLOCATABLE,DIMENSION(:,:) :: phib, psib, sigb
-       REAL,ALLOCATABLE,DIMENSION(:,:,:,:) :: pe1j0phib, pe1j0psib, pe1j1sigb
-       REAL,ALLOCATABLE,DIMENSION(:,:,:,:) :: pe2j0phib, pe2j0psib, pe2j1sigb
-       REAL,ALLOCATABLE,DIMENSION(:,:) :: pu1pe1PSI, pu1pe2PSI
-       REAL,ALLOCATABLE,DIMENSION(:,:) :: pu3pe1PSI,pu2pe1PSI
-       REAL,ALLOCATABLE,DIMENSION(:,:,:,:) :: p0invpe1j0s, b0invpe1j0s
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: mateq, mats, matb
-       COMPLEX,ALLOCATABLE,DIMENSION(:) :: zomega
-!
-       INTEGER,ALLOCATABLE,DIMENSION(:) :: di,de
-       INTEGER,ALLOCATABLE,DIMENSION(:) :: ipiv,ipive
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: emat,zmat, gmat
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:,:) :: gmatinv
-!
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:,:) :: pe1j0phi, pe1j0psi, pe1j1sig
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:,:) :: pe2j0phi, pe2j0psi, pe2j1sig
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: pwns,pwps,pwtpars,pwtpers,pwes
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: hwns,hwps,hwtpars,hwtpers,hwes,hes
-       COMPLEX,ALLOCATABLE,DIMENSION(:) :: phi,psi,sig
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:)  :: PSIpu1pe1, PSIpu2pe1
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:)  :: PSIpu3pe1, PSIpu1pe2
-!
-       COMPLEX,ALLOCATABLE,DIMENSION(:,:) :: rwn,rwp,rwtpar,rwtper,rwe,fluxe
-!
-       END MODULE gftm_GFS
-!
-!-------------------------------------------------
-!
-
-!-----------------------------------------------------
-!
-      MODULE gftm_gyro_average
-!
-!     integrals of gyro average operators
-!
-      USE gftm_max_dimensions
-      IMPLICIT NONE
-!
-      REAL,DIMENSION(nem) :: pe1j0=0.0
-      REAL,DIMENSION(nem) :: pe2j0=0.0
-      REAL,DIMENSION(nem) :: pe1j1=0.0
-      REAL,DIMENSION(nem) :: pe2j1=0.0
-      REAL,DIMENSION(nsm,nem,nb,nb) :: mat_pe1j0s=0.0
-      REAL,DIMENSION(nsm,nem,nb,nb) :: mat_pe2j0s=0.0
-      REAL,DIMENSION(nsm,nem,nb,nb) :: mat_pe1j1s=0.0
-      REAL,DIMENSION(nsm,nem,nb,nb) :: mat_pe2j1s=0.0
- !
-      END MODULE gftm_gyro_average
-!-----------------------------------------------------
-!
-      MODULE gftm_velocity_matrix
-!
-!     integrals of gyro average operators
-!
-      USE gftm_max_dimensions
-      IMPLICIT NONE
-!
-      REAL,DIMENSION(num,num) :: mat_upar
-      REAL,DIMENSION(num,num) :: mat_uparc
-      REAL,DIMENSION(num,num) :: mat_dupar
-!
-      REAL,DIMENSION(nem,nem) :: mat_eper
-      REAL,DIMENSION(nem,nem) :: mat_deper
- !
-      END MODULE gftm_velocity_matrix
-!-----------------------------------------------------
-!
diff --git a/gftm/src/gftm_mpi.f90 b/gftm/src/gftm_mpi.f90
deleted file mode 100644
index bf7318274..000000000
--- a/gftm/src/gftm_mpi.f90
+++ /dev/null
@@ -1,164 +0,0 @@
-program gftm
-
-  use gftm_mpi
-  use gftm_pkg
-  use gftm_interface
-  use gftm_global
-
-  implicit none
-
-  integer :: i
-  integer :: n
-  character (len=4) :: tag(6)=(/'ion1','ion2','ion3','ion4','ion5','ion6'/)
-  real(8) :: prec
-  integer :: ierr
-
-  ! initialize MPI
-  call MPI_INIT(ierr)
-
-  iCommgftm = MPI_COMM_WORLD
-  call MPI_COMM_RANK(iCommgftm,iProcgftm,ierr)
-  call MPI_COMM_SIZE(iCommgftm,nProcgftm,ierr)
-
-  call gftm_read_input()
-  call gftm_run_mpi()
-
-  if (iProcgftm == iProc0gftm) then
-    if(units_in.eq.'GENE')then
-       print 30,'GENE reference units used'
-       print 30,'Conversion to gftm units:'
-       print 30,'Bunit/Bref = ',1.0/Bref_out
-       print 30,'Te/Tref = ',taus_in(1)
-       print 30,'mi/mref = ',mass_in(2)
-       print 30,'a/Lref = ',1.0
-       print 30,'cs/cref = ',SQRT(taus_in(1)/mass_in(2))
-       print 30,'rhos/rhoref = ',SQRT(mass_in(2)*taus_in(1))*Bref_out
-    endif
-    if(alpha_zf_in.lt.0.0)print 30,' kx_geo0_out = ',kx_geo0_out, &
-        ' SAT_geo0_out = ',SAT_geo0_out
-
-
-! write interchange stability criteria with ELITE conventions
-      print 30,'  D(R) = ',-interchange_DR,'  D(I) = ',0.25-interchange_DM
-!  write species info
-      print 40,'  kinetic species = ',ns_in,'  non-kinetic species = ',nstotal_in - ns_in
-
-     if (gftm_use_transport_model_in) then
-
-        print 20,'Gam/Gam_GB',' Q/Q_GB','Q_low/Q_GB',' Pi/Pi_GB', ' S/S_GB'
-        print 10,'elec',&
-             gftm_elec_pflux_out,&
-             gftm_elec_eflux_out,&
-             gftm_elec_eflux_low_out,&
-             gftm_elec_mflux_out,&
-             gftm_elec_expwd_out
-
-        prec = abs(gftm_elec_pflux_out)+&
-             abs(gftm_elec_eflux_out)+&
-             abs(gftm_elec_eflux_low_out)+&
-             abs(gftm_elec_mflux_out)
-
-        do i=1,gftm_ns_in-1
-           print 10,tag(i),&
-                gftm_ion_pflux_out(i),&
-                gftm_ion_eflux_out(i),&
-                gftm_ion_eflux_low_out(i),&
-                gftm_ion_mflux_out(i),&
-                gftm_ion_expwd_out(i)
-
-           prec = prec+&
-                abs(gftm_ion_pflux_out(i))+&
-                abs(gftm_ion_eflux_out(i))+&
-                abs(gftm_ion_eflux_low_out(i))+&
-                abs(gftm_ion_mflux_out(i))
-        enddo
-
-        ! Output to file
-
-        n = gftm_ns_in-1
-        open(unit=1,file='out.gftm.gbflux',status='replace')
-        write(1,'(32(1pe11.4,1x))') gftm_elec_pflux_out,gftm_ion_pflux_out(1:n),&
-             gftm_elec_eflux_out,gftm_ion_eflux_out(1:n),&
-             gftm_elec_mflux_out,gftm_ion_mflux_out(1:n),&
-             gftm_elec_expwd_out,gftm_ion_expwd_out(1:n)
-        close(1)
-
-        open(unit=1,file='out.gftm.grid',status='replace')
-        write(1,'(i2)') gftm_ns_in,gftm_nxgrid_in
-        close(1)
-
-      ! write ky spectrum to file out.gftm.ky_spectrum
-      CALL write_gftm_ky_spectrum
-
-     ! write flux spectrum summed over nmodes to file out.gftm.sum_flux_spectrum
-     ! this can be compared directly with the flux spectrum from CGYRO
-
-      CALL write_gftm_sum_flux_spectrum
-
-     ! write density fluctuation amplitude spectrum to file out.gftm.density_spectrum
-      CALL write_gftm_density_spectrum
-
-     ! write temperature fluctuation amplitude spectrum to file out.gftm.temperature_spectrum
-      CALL write_gftm_temperature_spectrum
-
-      ! write intensity fluctuation amplitude spectrum per mode to file out.gftm.intensity_spectrum
-      CALL write_gftm_intensity_spectrum
-
-      ! write field fluctuation amplitude per mode spectrum to file out.gftm.field_spectrum
-      CALL write_gftm_field_spectrum
-
-      ! write eigenvalue spectrum to file out.gftm.eigenvalue_spectrum
-      CALL write_gftm_eigenvalue_spectrum
-
-      ! write ne-te crossphase spectrum to file out.gftm.nete_crossphase_spectrum
-      CALL write_gftm_nete_crossphase_spectrum
-
-      ! write ns-ts crossphase spectrum to file out.gftm.nsts_crossphase_spectrum
-      CALL write_gftm_nsts_crossphase_spectrum
-
-      ! write QL flux (weight) spectrum per mode to file out.gftm.QL_weight_spectrum
-      CALL write_gftm_QL_flux_spectrum
-
-      ! write kx/ky-spectral shift spectrum to file out.gftm.spectral_shift
-      CALL write_gftm_spectral_shift_spectrum
-
-      ! write ave_p0 spectrum to file out.gftm.ave_p0_spectrum
-      CALL write_gftm_ave_p0_spectrum
-
-      ! write intensity fluctuation amplitude spectrum per mode to file out.gftm.scalar_saturation_parameters
-      CALL write_gftm_scalar_saturation_parameters
-
-      ! write Gaussian width spectrum to file out.gftm.width_spectrum
-      CALL write_gftm_width_spectrum
-
-     else
-
-        print 10,'     ky:',gftm_ky_in
-        print 10,'Guassian width = ',get_gaussian_width()
-        ! Collect linear eigenvalues
-        do i=1,gftm_nmodes_in
-           print 10,'(wr,wi):',gftm_eigenvalue_out(i)
-        enddo
-
-        prec = sum(abs(gftm_eigenvalue_out))
-
-        ! write single ky-eigenmode wavefunction to file
-        CALL write_wavefunction_out('out.gftm.wavefunction')
-
-     endif
-
-     open(unit=1,file=trim(gftm_path_in)//'out.gftm.prec')
-     write(1,*) prec
-     close(1)
-
-  endif
-
-10 format(a,10(1x,1pe11.4))
-20 format(t7,a,t19,a,t31,a,t43,a,t55,a)
-30 format(a,1pe11.4,a,1pe11.4)
-40 format(a,I10,a,I10)
-
-! finalize MPI
-call MPI_FINALIZE(ierr)
-
-end program gftm
diff --git a/gftm/src/gftm_multiscale_spectrum.f90 b/gftm/src/gftm_multiscale_spectrum.f90
deleted file mode 100644
index 1fc5483ac..000000000
--- a/gftm/src/gftm_multiscale_spectrum.f90
+++ /dev/null
@@ -1,454 +0,0 @@
-!
-!--------------------------------------------------------------
-!
-      SUBROUTINE get_multiscale_spectrum
-!
-!***********************************************************************
-!  questions  should be addressed to
-!  Gary Staebler 858-455-3466  or email: gary.staebler@gat.com
-!***********************************************************************
-!
-!  gftm 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
-!  gftm multiscale saturation rule: sat_rule_in = 2 option
-!  Aug. 6, 2020 based on papers submitted to PPCF & NF
-!
-!***********************************************************************
-!
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-      USE gftm_kyspectrum
-      USE gftm_xgrid
-      IMPLICIT NONE
-      !
-      LOGICAL :: USE_MIX=.TRUE.
-      LOGICAL :: first_pass = .TRUE.
-      LOGICAL :: USE_SUB1=.FALSE.
-      INTEGER :: i,is,k,j,j1,j2,jmax1,jmax2
-      
-      INTEGER :: expsub=2, exp_ax, jmax_mix
-      REAL :: test,testmax1,testmax2
-      REAL :: gammamax1,kymax1,gammamax2,kymax2,ky0,ky1,ky2
-!      REAL :: f0,f1,f2,a,b,c,x0,x02,dky,xmax
-      REAL :: gamma0,gamma1,gammaeff,dgamma
-      REAL :: cnorm, phinorm, czf, cz1, cz2, kyetg
-      REAL :: kycut
-      REAL :: cky,sqcky,delta,ax,ay,kx
-      REAL :: mix1,mix2,mixnorm,gamma_ave
-      REAL :: vzf,dvzf,vzf1,vzf2
-      REAL :: vzf_mix, kymax_mix
-      REAL :: etg_streamer
-      REAL :: kxzf, sat_geo_factor
-      REAL :: b0,b1,b2,b3
-      REAL :: d1,d2,Gq,kx_width,dlnpdr,ptot
-      REAL :: measure
-      REAL,DIMENSION(nkym) :: gamma_net=0.0
-      REAL,DIMENSION(nkym) :: gamma=0.0
-      REAL,DIMENSION(nkym) :: gamma_kymix=0.0
-      REAL,PARAMETER :: small=1.0E-10
-      !
-       
-      if(jmax_out.eq.0)then
-         first_pass = .TRUE.
-      else
-        first_pass = .FALSE.
-      endif
-      if(first_pass)then  ! first pass for spectral shift model or only pass for quench rule
-        gamma_net(:) = eigenvalue_spectrum_out(1,:,1)
-        CALL get_zonal_mixing(nky,ky_spectrum,gamma_net,vzf_mix,kymax_mix,jmax_mix)
-        vzf_out = vzf_mix
-        kymax_out = kymax_mix
-        jmax_out = jmax_mix
-        gamma_net(:) = eigenvalue_spectrum_out(1,:,1)
-!        write(*,*)"FIRST PASS: vzf_out = ",vzf_out,"  jmax_out = ",jmax_out
-!        write(*,*)"FIRST PASS: kymax_out = ",kymax_out,"  gammamax_out = ",kymax_out*vzf_out
-      endif
-      ! model fit parameters
-      ! need to set alpha_zf_in = 1.0
-      ! Miller geometry values igeo=1
-      if(rlnp_cutoff_in.gt.0.0)then
-         dlnpdr = 0.0
-         ptot = 0.0
- !        do is=1,nstotal_in   ! include all species even non-kinetic ones like fast ions
-         do is=1,ns
-           ptot = ptot + as(is)*taus(is)
-           dlnpdr = dlnpdr + as(is)*taus(is)*(rlns(is)+rlts(is))
-         enddo
-         dlnpdr = rmaj_input*dlnpdr/MAX(ptot,0.01)
-         if(dlnpdr .ge. rlnp_cutoff_in)dlnpdr = rlnp_cutoff_in
-         if(dlnpdr .lt. 4.0)dlnpdr = 4.0
-      else
-         dlnpdr = 12.0
-      endif
-!         write(*,*)"dlnpdr = ",dlnpdr
-!
-      czf = ABS(alpha_zf_in)
-!
-! coefficients for SAT_RULE = 1
-      if(sat_rule_in.eq.1) then
-         kyetg=1.28
-         cnorm=14.21
-        if(USE_SUB1)then
-          cnorm=12.12
-          expsub=1
-        endif
-        cz1=0.48*czf
-        cz2=1.0*czf
-        cnorm = 14.29
-        measure = SQRT(taus(1)*mass(2))
-!
-!        if(USE_X3)then
-!         cnorm = 12.94  ! note this is normed to GASTD CGYRO units
-!         cz1 = 0.0
-!         cz2=1.4*czf
-!         etg_streamer = 1.0
-!         kyetg=etg_streamer*ABS(zs(2))/SQRT(taus(2)*mass(2))  ! fixed to ion gyroradius
-!         cky=3.0
-!         sqcky=SQRT(cky)
-!        endif
-        if(USE_MIX)then
-!original        kyetg=1.9*ABS(zs(2))/SQRT(taus(2)*mass(2))  ! fixed to ion gyroradius
-          cky=3.0
-          sqcky=SQRT(cky)
-          if(USE_SUB1)cnorm=12.12
-          cz1=0.48*czf
-!original         cz2=0.92*czf
-! retuned June 22,2017
-          cz2 = 1.0*czf
-          etg_streamer=1.05
-          if(alpha_quench_in .ne. 0.0)etg_streamer=2.1
-!          kyetg=etg_streamer*ABS(zs(2))/SQRT(taus(2)*mass(2))  ! fixed to ion gyroradius
-          kyetg=etg_streamer/rho_ion  ! fixed to ion gyroradius
-        endif
-        if(igeo.eq.0)then ! s-alpha
-           cnorm=14.63
-           cz1=0.90*czf
-           cz2=1.0*czf
-        endif
-     endif
-! coefficents for SAT_RULE = 2
-     if(sat_rule_in.eq.2)then
-       ! SAT2 fit for CGYRO linear modes NF 2021 paper
-!        b0 = 0.72
-        b0 = 0.76
-        b1 = 1.22
-!        b2 = 24.52  ! note this is b2**2 in PPCF paper 2020
-!        b2 = 11.21
-!        b2 = 8.44
-!        b2 = 2.13
-        b2 = 3.74
-        if(nmodes_in.gt.1)b2 = 3.55
-!        b3 = 0.88
-!        b3 = 2.4
-        b3 = 1.0
-!        d1 = 0.5475*((Bt0_out/B_geo0_out)**4)/grad_r0_out**2
-        d1 = (Bt0_out/B_geo0_out)**4    ! PPCF paper 2020
-        d1 = d1/grad_r0_out
-        Gq = B_geo0_out/grad_r0_out
-        d2 = b3/Gq**2
-        cnorm = b2*(12.0/dlnpdr)
-        kyetg = 1000.0   ! does not impact SAT2
-        cky=3.0
-        sqcky=SQRT(cky)
-        kycut = b0*kymax_out
-        cz1=0.0
-        cz2 = 1.05*czf
-        measure = 1.0/kymax_out     ! changed from alpha_i on Aug 8, 2021
-      endif
-!      write(*,*)"Bt0 = ",Bt0_out," B0 = ",B_geo0_out," gradr0 = ",grad_r0_out
-!      write(*,*)"G1 = ",sat_geo1_out,"  G2 = ",sat_geo2_out,"  sat_geo0 = ",sat_geo0_out
-!      write(*,*)"d1 = ",d1,"  d2 = ",d2
-! coefficients for spectral shift model for ExB shear
-      ax=0.0
-      ay=0.0
-      exp_ax = 1
-      if(alpha_quench_in.eq.0.0)then
-      !spectral shift model parameters
-        ax = 1.15
-        ay = 0.56
-        exp_ax = 4
-       if(sat_rule_in.eq.2)then
-         ax = 1.21
-         ay = 1.0
-         exp_ax = 2
-       endif
-      endif
-!    write(*,*)" ax= ",ax," ay= ",ay," kycut = ",kycut
-!  apply the spectral shift temporal suppression factor
-!
-     if(first_pass .eqv. .FALSE.)then  ! second pass for spectral shift model
-        do i=1,nky
-          kx = spectral_shift_out(i)
-          if(sat_rule_in.eq.2)then
-            ky0=ky_spectrum(i)
-            if(ky0.lt.kycut)then
-              kx_width = kycut/grad_r0_out
-            else
-              kx_width = kycut/grad_r0_out + b1*(ky0 - kycut)*Gq
-            endif
-            kx = kx*ky0/kx_width
-          endif
-          gamma_net(i) = eigenvalue_spectrum_out(1,i,1)/(1.0 + ABS(ax*kx)**exp_ax)
-!         write(*,*)ky0,kx,(ax*kx)**4
-!          write(*,*)i,"gamma_net = ",gamma_net(i)
-        enddo
-!     write(*,*)"gammamax_out = ",vzf_out*kymax_out, gamma_net(jmax_out),"  vexb_shear = ",vexb_shear_s!!
-! find the maximum of gamma_net/ky
-        if(sat_rule_in.eq.1)then
-          CALL get_zonal_mixing(nky,ky_spectrum,gamma_net,vzf_mix,kymax_mix,jmax_mix)
-          vzf_out = vzf_mix
-          kymax_out = kymax_mix
-          jmax_out = jmax_mix
-        else
-          vzf_out = vzf_out*gamma_net(jmax_out)/MAX(eigenvalue_spectrum_out(1,jmax_out,1),small)
-        endif
-!        write(*,*)"2nd PASS: vzf_out = ",vzf_out,"  jmax_out = ",jmax_out
-!        write(*,*)"2nd PASS: kymax_out = ",kymax_out,"  gammamax_out = ",kymax_out*vzf_out
-!        write(*,*)"2nd PASS: gamma_net(jmax) = ",gamma_net(jmax_out)
-      endif   ! second pass complete
-
-
-! compute multi-scale phi-intensity spectrum field_spectrum(2,,) = phi_bar_out
-      ! note that the field_spectrum(1,,) = v_bar_out = 1.0 for sat_rule_in = 1
-      gammamax1= vzf_out*kymax_out
-      kymax1 = kymax_out
-      jmax1 = jmax_out
-      vzf1 = vzf_out
-!      vzf2 = gammamax2/kymax2
-!      dvzf = MAX(vzf2-vzf1,0.0)
-!      dgamma= dvzf*kymax1
-!      gamma1=gammamax1
-!      write(*,*)"dvzf = ",dvzf," vzf1 = ",vzf1," vzf2 = ",vzf2
-!      write(*,*)"gammamax1 = ",gammamax1
-!      write(*,*)"kymax1 = ",kymax1,"  kycut = ",kycut
-      do j=1,nky
-! include zonal flow effects on growthrate model
-!          gamma=0.0
-          gamma0 = gamma_net(j)
-          ky0=ky_spectrum(j)
-          if(sat_rule_in.eq.1)then
-            if(ky0.lt.kymax1)then
-              gamma(j) = MAX(gamma0  - cz1*(kymax1 - ky0)*vzf1,0.0)
-            else
-              gamma(j) = cz2*gammamax1  +  Max(gamma0 - cz2*vzf1*ky0,0.0)          
-            endif
-          elseif(sat_rule_in.eq.2)then
-! note that the gamma mixing is for gamma_model not G*gamma_model
-            if(ky0.lt.kymax1)then
-              gamma(j) = gamma0
-            else
-              gamma(j) = gammamax1 +Max(gamma0 - cz2*vzf1*ky0,0.0)
-            endif
-          endif
-          gamma_kymix(j) = gamma(j)     ! used if USE_MIX=F 
-      enddo
-    if(USE_MIX)then
-      !mix over ky > kymax with integration weight = sqcky*ky0**2/(ky0**2 + cky*(ky-ky0)**2)
-      do j=jmax1+2,nky
-        gamma_ave = 0.0
-        ky0 = ky_spectrum(j)
-        mixnorm = ky0*(ATAN(sqcky*(ky_spectrum(nky)/ky0-1.0))-  &
-                  ATAN(sqcky*(ky_spectrum(jmax1+1)/ky0-1.0)))
-        do i=jmax1+1,nky-1
-          ky1 = ky_spectrum(i)
-          ky2 = ky_spectrum(i+1)
-          mix1 = ky0*(ATAN(sqcky*(ky2/ky0-1.0))- ATAN(sqcky*(ky1/ky0-1.0)))
-          delta = (gamma(i+1)-gamma(i))/(ky2-ky1)
-          mix2 = ky0*mix1 + (ky0*ky0/(2.0*sqcky))*(LOG(cky*(ky2-ky0)**2+ky0**2)- &
-                 LOG(cky*(ky1-ky0)**2+ky0**2))
-          gamma_ave = gamma_ave + (gamma(i)-ky1*delta)*mix1 + delta*mix2
-        enddo  
-        gamma_kymix(j) = gamma_ave/mixnorm
-!        write(*,*)j,ky0,gamma(j),gamma_kymix(j)
-      enddo  
-    endif      
-! intensity model
-       do j=1,nky
-        gamma0 = eigenvalue_spectrum_out(1,j,1)
-        ky0 = ky_spectrum(j)
-        kx = spectral_shift_out(j)
-        if(sat_rule_in.eq.1)then
-          sat_geo_factor = SAT_geo0_out
-          kx_width = ky0
-        endif
-        if(sat_rule_in.eq.2)then
-          if(ky0.lt. kycut)then
-            kx_width = kycut/grad_r0_out
-            sat_geo_factor = SAT_geo0_out*d1*SAT_geo1_out
-           else
-             kx_width = kycut/grad_r0_out + b1*(ky0 - kycut)*Gq
-             sat_geo_factor = SAT_geo0_out*(d1*SAT_geo1_out*kycut +  &
-                              (ky0 - kycut)*d2*SAT_geo2_out)/ky0
-           endif
-           kx = kx*ky0/kx_width
-    !       write(*,*)"sat2 ",B_geo0_out,grad_r0_out,SAT_geo1_out,SAT_geo2_out,sat_geo_factor
-        endif
-        do i=1,nmodes_in
-          gammaeff = 0.0
-          if(gamma0.gt.small)gammaeff = &
-               gamma_kymix(j)*(eigenvalue_spectrum_out(1,j,i)/gamma0)**expsub
-          if(ky0.gt.kyetg)gammaeff = gammaeff*SQRT(ky0/kyetg)
-          field_spectrum_out(2,j,i) = measure*cnorm*((gammaeff/(kx_width*ky0))/(1.0+ay*kx**2))**2
-          if(units_in.ne.'GYRO')field_spectrum_out(2,j,i) = sat_geo_factor*field_spectrum_out(2,j,i)
-        enddo
-     enddo
-     ! recompute the intensity and flux spectra
-      do j=1,nky
-         do i=1,nmodes_in
-            phinorm=field_spectrum_out(2,j,i) 
-            field_spectrum_out(1,j,i) = phinorm
-            field_spectrum_out(3,j,i) = QL_field_spectrum_out(3,j,i)*phinorm
-            field_spectrum_out(4,j,i) = QL_field_spectrum_out(4,j,i)*phinorm
-            do is=1,ns
-               intensity_spectrum_out(1,is,j,i) = QL_intensity_spectrum_out(1,is,j,i)*phinorm
-               intensity_spectrum_out(2,is,j,i) = QL_intensity_spectrum_out(2,is,j,i)*phinorm
-               intensity_spectrum_out(3,is,j,i) = QL_intensity_spectrum_out(3,is,j,i)*phinorm
-               intensity_spectrum_out(4,is,j,i) = QL_intensity_spectrum_out(4,is,j,i)*phinorm
-               flux_spectrum_out(1,is,j,i) = QL_flux_spectrum_out(1,is,j,i)*phinorm
-               flux_spectrum_out(2,is,j,i) = QL_flux_spectrum_out(2,is,j,i)*phinorm
-               flux_spectrum_out(3,is,j,i) = QL_flux_spectrum_out(3,is,j,i)*phinorm
-               flux_spectrum_out(4,is,j,i) = QL_flux_spectrum_out(4,is,j,i)*phinorm
-               flux_spectrum_out(5,is,j,i) = QL_flux_spectrum_out(5,is,j,i)*phinorm
-           enddo
-        enddo
-      enddo    
-
-      END SUBROUTINE get_multiscale_spectrum
-!
-!-------------------------------------------------------------------------------
-!
-
- SUBROUTINE get_zonal_mixing(nmix,ky_mix,gamma_mix,vzf_mix,kymax_mix,jmax_mix)
-!
-!  finds the maximum of gamma/ky spectrum vzf_out and kymax_out
-!
-    USE gftm_dimensions
-    USE gftm_global
-    USE gftm_species
-    IMPLICIT NONE
-    LOGICAL :: use_kymin = .false.
-    INTEGER :: nmix,i,k,j,j1,j2,jmax1,jmin
-    REAL :: test,testmax,peakmax
-    REAL :: kx, kyhigh, kycut, kymin
-    REAL :: gammamax1,kymax1,testmax1,ky0,ky1,ky2
-    REAL :: f0,f1,f2,a,b,c,x1,deltaky,xmax,xmin
-    REAL :: vzf1, vzf2
-    REAL :: kymax_mix, vzf_mix
-    INTEGER :: jmax_mix, down
-    REAL, DIMENSION(nkym) :: gamma_mix, ky_mix
-!  initialize output of subroutine
-    vzf_mix = 0.0
-    kymax_mix = 0.0
-    jmax_mix = 1
-    xmin = 0.0
-    if(alpha_zf_in.lt.0.0)use_kymin = .true. 
-!
-! find the local maximum of gamma_mix/ky_mix with the largest gamma_mix/ky_mix^2
-!
-      gammamax1= gamma_mix(1)
-      kymax1 = ky_mix(1)
-      testmax = 0.0
-      peakmax=0.0
-      jmax_mix=1
-      kycut=0.8/rho_ion
-      kymin = 0.0
-      jmin = 0
-      if(use_kymin)kymin = 0.173*sqrt(2.0)/rho_ion
-      if(sat_rule_in.eq.2)then
-        kycut = grad_r0_out*kycut
-        kymin = grad_r0_out*kymin
-      endif
-!      write(*,*)" kycut = ",kycut," kymin = ",kymin
-      ! find the low and high ky peaks of gamma/ky
-      do j=1,nky-1
-       if(ky_mix(j).lt.kymin)jmin = j
-       if((ky_mix(j+1).ge.kymin).and.(ky_mix(j).le.kycut))then
-         j1=j
-         kymax1 = ky_mix(j)
-         testmax1 = gamma_mix(j)/kymax1
-!         write(*,*)"j=",j,"ky = ",ky0," gamma_net = ",gamma_net(j)
-         if(testmax1.gt.testmax)then
-           testmax = testmax1
-           jmax_mix = j
-          endif
-         endif
-      enddo
-      if(testmax.eq.0.0)jmax_mix=j1
-! no unstable modes in range set kymax index to end of range
-! this is cut of at j1 since a maximum may not exist in the low-k range
-      kymax1 = ky_mix(jmax_mix)
-      gammamax1 = gamma_mix(jmax_mix)
-      if(kymax1.lt.kymin)then
-          kymax1 = kymin
-!interpolate to find a more accurate low-k maximum gamma/ky
-         gammamax1 = gamma_mix(1)   &
-          +(gamma_mix(2)-gamma_mix(1))*(kymin-ky_mix(1))/(ky_mix(2)-ky_mix(1))
-      endif
-!        write(*,*)" jmax_mix = ",jmax_mix,"  gammamax1 = ",gammamax1," kymax1 = ",kymax1
-      if(jmax_mix .gt. 1 .and. jmax_mix .lt. j1)then
- !        write(*,*)"refining low-k maximum"
-! determine kymax1 and gammamax1 bounded by the tree points f0,f1,f2
-! use a quadratic fit: f = a + b x + c x^2  to f = gamma/ky centered at jmax1
-         jmax1 = jmax_mix
-         f0 =  gamma_mix(jmax1-1)/ky_mix(jmax1-1)
-         f1 =  gamma_mix(jmax1)/ky_mix(jmax1)
-         f2 =  gamma_mix(jmax1+1)/ky_mix(jmax1+1)
-         deltaky = ky_mix(jmax1+1)-ky_mix(jmax1-1)
-         x1 = (ky_mix(jmax1)-ky_mix(jmax1-1))/deltaky
-         a = f0
-         b = (f1 - f0*(1-x1*x1)-f2*x1*x1)/(x1-x1*x1)
-         c = f2 - f0 - b
-!         write(*,*)"f0 = ",f0,"  f1 = ",f1,"  f2 = ",f2,"  x1 = ",x1
-         if(f0 .ge.f1)then
-! if f0>f1 then f1 is not a local maximum
-             kymax1 = ky_mix(jmax1-1)
-             gammamax1 = f0*kymax1
-             if(kymax1.lt.kymin)then
-!interpolate to find the value of gammamax1 at kymin
-               kymax1 = kymin
-               xmin = (kymin - ky_mix(jmax1-1))/deltaky
-               gammamax1 = (a + b*xmin + c*xmin*xmin)*kymin
-             endif
-        endif
-        if(f0.lt.f1  )then
-!        if f0<f1 then f1>f2 due to the maximum search
-! use the quadratic fit to refine the local maximum:
-             xmax = -b/(2.0*c)
-             xmin = 0.0
-             if(ky_mix(jmax1-1).lt.kymin)then
-               xmin = (kymin - ky_mix(jmax1-1))/deltaky
-             endif
-             if(xmax .ge. 1.0)then
-! if xmax >= 1  use f2 as the maximum
-               kymax1 = ky_mix(jmax1+1)
-               gammamax1 = f2*kymax1
-             elseif(xmax.le.xmin)then
-               if(xmin .gt. 0.0)then
-                 kymax1 = kymin
-! use the quadratic fit to determine gammamax1 at kymin
-                 gammamax1 = (a + b*xmin + c*xmin*xmin)*kymin
-               elseif(xmax .le. 0.0)then
-! if xmax<=0 use f0 as the maximum
-                 kymax1 = ky_mix(jmax1-1)
-                 gammamax1 = f0*kymax1
-               endif
-             else
-! the conditions f0<f1<f2 and xmin<xmax<1 are satisfied
-! use the quadratic fit to determine gammamax1 and kymax1
-               kymax1 = ky_mix(jmax1-1)+deltaky*xmax
-               gammamax1 = (a+b*xmax+c*xmax*xmax)*kymax1
-             endif !xmax tests
-           endif !f0 < f1
-       endif  ! jmax_mix > 1
-       vzf_mix = gammamax1/kymax1
-       kymax_mix = kymax1
-!      jmax_mix = jmax1
-!      write(*,*)"get_zonal_mxing"
-!      write(*,*)"xmax = ",xmax, "  xmin = ",xmin
-!      write(*,*)"gammamax1 = ",gammamax1," kymax1 = ",kymax1, "  kymin = ",kymin
- 
- END SUBROUTINE get_zonal_mixing
diff --git a/gftm/src/gftm_pkg.f90 b/gftm/src/gftm_pkg.f90
deleted file mode 100644
index 652da3623..000000000
--- a/gftm/src/gftm_pkg.f90
+++ /dev/null
@@ -1,72 +0,0 @@
-      MODULE gftm_pkg
-!
-      IMPLICIT NONE
-! output routines
-      REAL,EXTERNAL :: get_growthrate,get_frequency
-      REAL,EXTERNAL :: get_QL_particle_flux,get_QL_energy_flux
-      REAL,EXTERNAL :: get_QL_stress_par,get_QL_stress_tor
-      REAL,EXTERNAL :: get_QL_exchange
-      REAL,EXTERNAL :: get_QL_phi,get_QL_density,get_QL_temperature
-      REAL,EXTERNAL :: get_gaussian_width
-      REAl,EXTERNAL :: get_ft
-      REAL,EXTERNAL :: get_R_unit
-      REAL,EXTERNAL :: get_q_unit
-      REAL,EXTERNAL :: get_wd_bar
-      REAL,EXTERNAL :: get_b0_bar
-      REAL,EXTERNAL :: get_particle_flux
-      REAL,EXTERNAL :: get_energy_flux
-      REAL,EXTERNAL :: get_stress_par
-      REAL,EXTERNAL :: get_stress_tor
-      REAL,EXTERNAL :: get_exchange
-      REAL,EXTERNAL :: get_phi_bar
-      REAL,EXTERNAL :: get_kpar_bar
-      REAL,EXTERNAL :: get_v_bar
-      REAL,EXTERNAL :: get_n_bar
-      REAL,EXTERNAL :: get_t_bar
-      REAL,EXTERNAL :: get_n_bar_sum
-      REAL,EXTERNAL :: get_t_bar_sum
-      REAL,EXTERNAL :: get_Ne_Te_phase
-      REAL,EXTERNAL :: get_phi_bar_sum
-      REAL,EXTERNAL :: get_v_bar_sum
-      REAL,EXTERNAL :: get_q_low
-      REAL,EXTERNAL :: get_B_ave
-      REAL,EXTERNAL :: get_Bt_ave
-      REAL,EXTERNAL :: get_Bp0
-      REAL,EXTERNAL :: get_R2_ave
-      REAL,EXTERNAL :: get_B2_ave
-      REAL,EXTERNAL :: get_RBt_ave
-      INTEGER,EXTERNAL :: get_nky_out
-      REAL,EXTERNAL :: get_eigenvalue_spectrum_out
-      REAL,EXTERNAL :: get_field_spectrum_out
-      REAL,EXTERNAL :: get_intensity_spectrum_out
-      REAL,EXTERNAL :: get_flux_spectrum_out
-      REAL,EXTERNAL :: get_ky_spectrum_out
-      REAL,EXTERNAL :: get_DM
-      REAL,EXTERNAL :: get_DR
-!
-      CONTAINS
-!
-!
-      SUBROUTINE gftm_ky
-      USE gftm_dimensions
-      USE gftm_global
-      IMPLICIT NONE
-!
-      call gftm_startup
-!      write(*,*)"startup done"
-!
-      if(find_width_in)then
-        trace_path(1)=1
-        call gftm_max
-      else
-        call gftm_LS
-      endif
-!      write(*,*)"gftm done"
-      find_width_in=.FALSE.
-!
-      call gftm_shutdown
-!      write(*,*)"shutdown done"
-!
-      END SUBROUTINE gftm_ky
-!
-      END MODULE gftm_pkg
diff --git a/gftm/src/gftm_read_input.f90 b/gftm/src/gftm_read_input.f90
deleted file mode 100644
index dcbc1def8..000000000
--- a/gftm/src/gftm_read_input.f90
+++ /dev/null
@@ -1,200 +0,0 @@
-!--------------------------------------------------------------
-! gftm_read_input.f90
-!
-! PURPOSE:
-!  Complete read of gftm input parameters as specified by
-!  gftm_interface (but ignoring Fourier and ELITE geometry
-!  coefficients).
-!--------------------------------------------------------------
-
-subroutine gftm_read_input
-
-  use gftm_interface
-
-  implicit none
-
-  open(unit=1,file=trim(gftm_path_in)//'input.gftm.gen',status='old')
-
-  read(1,*) gftm_units_in
-  read(1,*) gftm_use_transport_model_in
-  read(1,*) gftm_geometry_flag_in
-  read(1,*) gftm_write_wavefunction_flag_in
-
-  ! Data passed to: put_signs
-  read(1,*) gftm_sign_bt_in
-  read(1,*) gftm_sign_it_in
-
-  ! Data passed to: put_rare_switches
-  read(1,*) gftm_theta_trapped_in
-  read(1,*) gftm_wdia_trapped_in
-  read(1,*) gftm_park_in
-  read(1,*) gftm_ghat_in
-  read(1,*) gftm_gchat_in
-  read(1,*) gftm_wd_zero_in
-  read(1,*) gftm_linsker_factor_in
-  read(1,*) gftm_gradb_factor_in
-  read(1,*) gftm_filter_in
-  read(1,*) gftm_damp_psi_in
-  read(1,*) gftm_damp_sig_in
-
-  ! Data passed to: put_switches
-  read(1,*) gftm_iflux_in
-  read(1,*) gftm_use_bper_in
-  read(1,*) gftm_use_bpar_in
-  read(1,*) gftm_use_mhd_rule_in
-  read(1,*) gftm_use_bisection_in
-  read(1,*) gftm_use_inboard_detrapped_in
-  read(1,*) gftm_ibranch_in
-  read(1,*) gftm_nmodes_in
-  read(1,*) gftm_nbasis_max_in
-  read(1,*) gftm_nbasis_min_in
-  read(1,*) gftm_nxgrid_in
-  read(1,*) gftm_nky_in
-  read(1,*) gftm_use_ave_ion_grid_in
-
-  ! Data passed to: put_model_parameters
-  read(1,*) gftm_adiabatic_elec_in
-  read(1,*) gftm_alpha_mach_in
-  read(1,*) gftm_alpha_e_in
-  read(1,*) gftm_alpha_p_in
-  read(1,*) gftm_alpha_quench_in
-  read(1,*) gftm_alpha_zf_in
-  read(1,*) gftm_xnu_factor_in
-  read(1,*) gftm_debye_factor_in
-  read(1,*) gftm_etg_factor_in
-  read(1,*) gftm_rlnp_cutoff_in
-  read(1,*) gftm_sat_rule_in
-  read(1,*) gftm_kygrid_model_in
-  read(1,*) gftm_xnu_model_in
-  read(1,*) gftm_vpar_model_in
-  read(1,*) gftm_vpar_shear_model_in
-
-  ! Data passed to: put_species
-  read(1,*) gftm_ns_in
-  read(1,*) gftm_mass_in(1)
-  read(1,*) gftm_mass_in(2)
-  read(1,*) gftm_mass_in(3)
-  read(1,*) gftm_mass_in(4)
-  read(1,*) gftm_mass_in(5)
-  read(1,*) gftm_mass_in(6)
-  read(1,*) gftm_mass_in(7)
-  read(1,*) gftm_zs_in(1)
-  read(1,*) gftm_zs_in(2)
-  read(1,*) gftm_zs_in(3)
-  read(1,*) gftm_zs_in(4)
-  read(1,*) gftm_zs_in(5)
-  read(1,*) gftm_zs_in(6)
-  read(1,*) gftm_zs_in(7)
-
-  ! Data passed to: put_kys
-  read(1,*) gftm_ky_in
-
-  ! Data passed to: put_gaussian_width
-  read(1,*) gftm_width_in
-  read(1,*) gftm_width_min_in
-  read(1,*) gftm_nwidth_in
-  read(1,*) gftm_find_width_in
-
-  ! Data passed to: put_gradients
-  read(1,*) gftm_rlns_in(1)
-  read(1,*) gftm_rlns_in(2)
-  read(1,*) gftm_rlns_in(3)
-  read(1,*) gftm_rlns_in(4)
-  read(1,*) gftm_rlns_in(5)
-  read(1,*) gftm_rlns_in(6)
-  read(1,*) gftm_rlns_in(7)
-  read(1,*) gftm_rlts_in(1)
-  read(1,*) gftm_rlts_in(2)
-  read(1,*) gftm_rlts_in(3)
-  read(1,*) gftm_rlts_in(4)
-  read(1,*) gftm_rlts_in(5)
-  read(1,*) gftm_rlts_in(6)
-  read(1,*) gftm_rlts_in(7)
-  read(1,*) gftm_vpar_shear_in(1)
-  read(1,*) gftm_vpar_shear_in(2)
-  read(1,*) gftm_vpar_shear_in(3)
-  read(1,*) gftm_vpar_shear_in(4)
-  read(1,*) gftm_vpar_shear_in(5)
-  read(1,*) gftm_vpar_shear_in(6)
-  read(1,*) gftm_vpar_shear_in(7)
-  read(1,*) gftm_vexb_shear_in
-
-  ! Data passed to: put_profile_shear
-  read(1,*) gftm_vns_shear_in(1)
-  read(1,*) gftm_vns_shear_in(2)
-  read(1,*) gftm_vns_shear_in(3)
-  read(1,*) gftm_vns_shear_in(4)
-  read(1,*) gftm_vns_shear_in(5)
-  read(1,*) gftm_vns_shear_in(6)
-  read(1,*) gftm_vns_shear_in(7)
-  read(1,*) gftm_vts_shear_in(1)
-  read(1,*) gftm_vts_shear_in(2)
-  read(1,*) gftm_vts_shear_in(3)
-  read(1,*) gftm_vts_shear_in(4)
-  read(1,*) gftm_vts_shear_in(5)
-  read(1,*) gftm_vts_shear_in(6)
-  read(1,*) gftm_vts_shear_in(7)
-
-  ! Data passed to: put_averages
-  read(1,*) gftm_taus_in(1)
-  read(1,*) gftm_taus_in(2)
-  read(1,*) gftm_taus_in(3)
-  read(1,*) gftm_taus_in(4)
-  read(1,*) gftm_taus_in(5)
-  read(1,*) gftm_taus_in(6)
-  read(1,*) gftm_taus_in(7)
-  read(1,*) gftm_as_in(1)
-  read(1,*) gftm_as_in(2)
-  read(1,*) gftm_as_in(3)
-  read(1,*) gftm_as_in(4)
-  read(1,*) gftm_as_in(5)
-  read(1,*) gftm_as_in(6)
-  read(1,*) gftm_as_in(7)
-  read(1,*) gftm_vpar_in(1)
-  read(1,*) gftm_vpar_in(2)
-  read(1,*) gftm_vpar_in(3)
-  read(1,*) gftm_vpar_in(4)
-  read(1,*) gftm_vpar_in(5)
-  read(1,*) gftm_vpar_in(6)
-  read(1,*) gftm_vpar_in(7)
-  read(1,*) gftm_vexb_in
-  read(1,*) gftm_betae_in
-  read(1,*) gftm_xnue_in
-  read(1,*) gftm_zeff_in
-  read(1,*) gftm_debye_in
-
-  ! Data passed to: put_eikonal
-  read(1,*) gftm_new_eikonal_in
-
-  ! Data passed to: put_s_alpha_geometry
-  read(1,*) gftm_rmin_sa_in
-  read(1,*) gftm_rmaj_sa_in
-  read(1,*) gftm_q_sa_in
-  read(1,*) gftm_shat_sa_in
-  read(1,*) gftm_alpha_sa_in
-  read(1,*) gftm_xwell_sa_in
-  read(1,*) gftm_theta0_sa_in
-  read(1,*) gftm_b_model_sa_in
-  read(1,*) gftm_ft_model_sa_in
-
-  ! Data passed to: put_Miller_geometry
-  read(1,*) gftm_rmin_loc_in
-  read(1,*) gftm_rmaj_loc_in
-  read(1,*) gftm_zmaj_loc_in
-  read(1,*) gftm_drmindx_loc_in
-  read(1,*) gftm_drmajdx_loc_in
-  read(1,*) gftm_dzmajdx_loc_in
-  read(1,*) gftm_kappa_loc_in
-  read(1,*) gftm_s_kappa_loc_in
-  read(1,*) gftm_delta_loc_in
-  read(1,*) gftm_s_delta_loc_in
-  read(1,*) gftm_zeta_loc_in
-  read(1,*) gftm_s_zeta_loc_in
-  read(1,*) gftm_q_loc_in
-  read(1,*) gftm_q_prime_loc_in
-  read(1,*) gftm_p_prime_loc_in
-  read(1,*) gftm_kx0_loc_in
-
-  close(1)
-
-end subroutine gftm_read_input
diff --git a/gftm/src/gftm_run.F90 b/gftm/src/gftm_run.F90
deleted file mode 100644
index c733f7170..000000000
--- a/gftm/src/gftm_run.F90
+++ /dev/null
@@ -1,227 +0,0 @@
-!---------------------------------------------------------
-! gftm_run_mpi.f90
-!
-! PURPOSE:
-!  Manage call to gftm simulation for both standalone and
-!  TGYRO usage.
-!---------------------------------------------------------
-
-#ifdef MPI_GFTM
-subroutine gftm_run_mpi()
-#else
-subroutine gftm_run()
-#endif
-
-  use gftm_pkg
-  use gftm_interface
-  use gftm_global
-
-#ifdef MPI_GFTM
-  use gftm_mpi
-#endif
-
-  implicit none
-
-  integer :: i_ion,n
-
-  call put_units(gftm_units_in)
-
-  call put_signs(gftm_sign_Bt_in,gftm_sign_It_in)
-
-  call put_species(gftm_ns_in, &
-       gftm_zs_in, &
-       gftm_mass_in)
-
-  call put_kys(gftm_ky_in)
-
-  call put_gaussian_width(gftm_width_in, &
-       gftm_width_min_in, &
-       gftm_nwidth_in, &
-       gftm_find_width_in)
-
-  call put_eikonal(gftm_new_eikonal_in)
-
-  call put_gradients(gftm_rlns_in, &
-       gftm_rlts_in, &
-       gftm_vpar_shear_in, &
-       gftm_vexb_shear_in)
-
-  call put_averages(gftm_taus_in, &
-       gftm_as_in, &
-       gftm_vpar_in, &
-       gftm_vexb_in, &
-       gftm_betae_in, &
-       gftm_xnue_in, &
-       gftm_zeff_in, &
-       gftm_debye_in)
-
-  call put_switches(gftm_iflux_in, &
-       gftm_use_bper_in, &
-       gftm_use_bpar_in, &
-       gftm_use_mhd_rule_in, &
-       gftm_use_bisection_in, &
-       gftm_use_inboard_detrapped_in, &
-       gftm_ibranch_in, &
-       gftm_nmodes_in, &
-       gftm_nbasis_max_in, &
-       gftm_nbasis_min_in, &
-       gftm_nxgrid_in, &
-       gftm_nky_in, &
-       gftm_use_ave_ion_grid_in)
-
-  call put_rare_switches(gftm_theta_trapped_in, &
-       gftm_wdia_trapped_in, &
-       gftm_park_in, &
-       gftm_ghat_in, &
-       gftm_gchat_in, &
-       gftm_wd_zero_in, &
-       gftm_linsker_factor_in, &
-       gftm_gradB_factor_in, &
-       gftm_filter_in, &
-       gftm_damp_psi_in, &
-       gftm_damp_sig_in)
-
-  call put_model_parameters(gftm_adiabatic_elec_in, &
-       gftm_alpha_e_in, &
-       gftm_alpha_p_in, &
-       gftm_alpha_mach_in, &
-       gftm_alpha_quench_in, &
-       gftm_alpha_zf_in, &
-       gftm_xnu_factor_in, &
-       gftm_debye_factor_in, &
-       gftm_etg_factor_in, &
-       gftm_rlnp_cutoff_in, &
-       gftm_sat_rule_in, &
-       gftm_kygrid_model_in, &
-       gftm_xnu_model_in, &
-       gftm_vpar_model_in, &
-       gftm_vpar_shear_model_in)
-
-  if (gftm_geometry_flag_in == 1 ) then
-
-     call put_miller_geometry(gftm_rmin_loc_in, &
-          gftm_rmaj_loc_in, &
-          gftm_zmaj_loc_in, &
-          gftm_drmindx_loc_in, &
-          gftm_drmajdx_loc_in, &
-          gftm_dzmajdx_loc_in, &
-          gftm_kappa_loc_in, &
-          gftm_s_kappa_loc_in, &
-          gftm_delta_loc_in, &
-          gftm_s_delta_loc_in, &
-          gftm_zeta_loc_in, &
-          gftm_s_zeta_loc_in, &
-          gftm_q_loc_in, &
-          gftm_q_prime_loc_in, &
-          gftm_p_prime_loc_in, &
-          gftm_kx0_loc_in)
-
-  elseif (gftm_geometry_flag_in == 2)then
-
-     call put_fourier_geometry(gftm_q_fourier_in,  &
-          gftm_q_prime_fourier_in, &
-          gftm_p_prime_fourier_in, &
-          gftm_nfourier_in, &
-          gftm_fourier_in)
-
-  else
-     write(*,*)"geometry_flag = ", gftm_geometry_flag_in
-     call put_s_alpha_geometry(gftm_rmin_sa_in, &
-          gftm_rmaj_sa_in, &
-          gftm_q_sa_in, &
-          gftm_shat_sa_in, &
-          gftm_alpha_sa_in, &
-          gftm_xwell_sa_in, &
-          gftm_theta0_sa_in, &
-          gftm_b_model_sa_in, &
-          gftm_ft_model_sa_in)
-
-  endif
-
-  ! Create parameter dump file
-  if (gftm_dump_flag_in .eqv. .true.) then
-     call gftm_dump_local
-     call gftm_dump_global
-     if (gftm_test_flag_in == 1) return
-  endif
-
-  if (gftm_use_transport_model_in) then
-
-#ifdef MPI_GFTM
-        call gftm_tm_mpi
-#else
-        call gftm_tm
-#endif
-
-     !---------------------------------------------
-     ! Output (normalized to Q_GB)
-     !
-     ! Electrons
-
-     ! Gammae/Gamma_GB
-     gftm_elec_pflux_out = get_particle_flux(1)
-
-     ! Qe/Q_GB
-     gftm_elec_eflux_low_out = get_q_low(1)
-     gftm_elec_eflux_out     = get_energy_flux(1)
-
-     ! Pi_e/Pi_GB
-     gftm_elec_mflux_out = get_stress_tor(1)
-
-     ! S_e/S_GB
-     gftm_elec_expwd_out = get_exchange(1)
-
-     ! Ions
-
-     do i_ion=1,ns_in
-
-             ! Gammai/Gamma_GB
-             gftm_ion_pflux_out(i_ion) = get_particle_flux(i_ion+1)
- 
-             ! Qi/Q_GB
-             gftm_ion_eflux_low_out(i_ion) = get_q_low(i_ion+1)
-             ! _low already included EM terms
-             gftm_ion_eflux_out(i_ion)     = get_energy_flux(i_ion+1)
-
-             ! Pi_i/Pi_GB
-             gftm_ion_mflux_out(i_ion) = get_stress_tor(i_ion+1)
-
-             ! S_i/S_GB
-             gftm_ion_expwd_out(i_ion) = get_exchange(i_ion+1)
-
-     enddo
-
-     call get_error_status(gftm_error_message,gftm_error_status)
-
-  else
-
-     ! Run single-ky linear stability
-     call gftm_ky
-
-     ! Collect linear eigenvalues
-     do n=1,gftm_nmodes_in
-        gftm_eigenvalue_out(n) = get_frequency(n) + xi*get_growthrate(n)
-     enddo
-
-     ! Print eigenfunction if flag set
-#ifdef MPI_GFTM
-     if (iProcgftm == iProc0gftm .and. gftm_write_wavefunction_flag_in == 1) then
-        call write_wavefunction_out(trim(gftm_path_in)//'out.gftm.wavefunction')
-     endif
-#else
-     if (gftm_write_wavefunction_flag_in == 1) then
-        call write_wavefunction_out(trim(gftm_path_in)//'out.gftm.wavefunction')
-     endif
-#endif
-
-  endif
-
-  ! Diagnostic output
-  interchange_DR = get_DR()
-  interchange_DM = get_DM()
-
-#ifdef MPI_GFTM
-end subroutine gftm_run_mpi
-#else
-end subroutine gftm_run
-#endif
diff --git a/gftm/src/gftm_setup_geometry.f90 b/gftm/src/gftm_setup_geometry.f90
deleted file mode 100644
index 9dafbad25..000000000
--- a/gftm/src/gftm_setup_geometry.f90
+++ /dev/null
@@ -1,86 +0,0 @@
-      SUBROUTINE gftm_setup_geometry
-!***********************************************************
-!  This routine is used to compute the geometric quantities
-!  needed by a transport code. It does not compute the linear
-!  eigenmodes. As a side effect the species and basis functions
-!  are defined so be sure that put_species and put_switches
-!  have been called if you don't want to use the defaults.
-!  R2_ave_out
-!  B2_ave_out
-!  others to be added later
-!***********************************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-!
-      new_geometry = .TRUE.
-!
-!
-! set global constants
-!
-      pi = atan2( 0.0, -1.0 )
-      pi_2 = 2.0*pi
-      sqrt_pi = SQRT(pi)
-      sqrt_two = SQRT(2.0)
-!
-      new_width=.TRUE.
-!
-!   load the xgrid and gauss-hermite weights
-!
-       if(gauher_uncalled)CALL gauher
-!
-! set ky in units of k_theta*rho_s  rho_s=C_s/omega_s
-! C_s=sqrt(Te/mi), omega_s=eB/(mi c)
-!
-     ky = ky_s
-!      write(*,*)"ky = ",ky
-!
-! check co-dependencies 
-!
-      if(new_geometry)new_width=.TRUE.
-      if(new_width)new_matrix=.TRUE.
-!      write(*,*)"new_start=",new_start
-!      write(*,*)"new_geometry=",new_geometry
-!      write(*,*)"new_width=",new_width
-!      write(*,*)"new_matrix=",new_matrix
-!      write(*,*)"width_in=",width_in
-!      write(*,*)"nbasis_max_in=",nbasis_max_in
-!      write(*,*)"new_eikonal_in=",new_eikonal_in
-!      write(*,*)"betae_in=",betae_in
-!      write(*,*)"debye_in=",debye_in
-!      write(*,*)"xnuei_in=",xnuei_in
-!      write(*,*)"zeff_in=",zeff_in
-!      write(*,*)"filter_in=",filter_in
-!      write(*,*)"park_in=",park_in
-!      write(*,*)"ghat_in=",ghat_in
-!      write(*,*)"wd_zero_in=",wd_zero_in
-!      write(*,*)"Linsker_factor_in=",Linsker_factor_in
-!      write(*,*)"gradB_factor_in=",gradB_factor_in
-!      write(*,*)"x_psi_in=",x_psi_in
-!      write(*,*)"xnu_factor_in=",xnu_factor_in
-!      write(*,*)"debye_factor_in=",debye_factor_in
-!      write(*,*)"theta_trapped_in=",theta_trapped_in
-!      write(*,*)"alpha_p_in=",alpha_p_in
-!      write(*,*)"alpha_e_in=",alpha_e_in
-!
-!
-       if(igeo.eq.1)then
-! set up MILLER geometry
-         call miller_geo
-       elseif(igeo.eq.2)then
-! set up Fourier geometry
-         call fourier_geo
-       elseif(igeo.eq.3)then
-! set up ELITE geometry
-         call ELITE_geo
-       endif
-!
-! compute the eikonal functions for general geometry (igeo > 0)
-!
-       if(igeo.gt.0)call mercier_luc 
-!
-       call get_xgrid_functions
-!
-       new_geometry=.FALSE.
-!
-      END SUBROUTINE gftm_setup_geometry
diff --git a/gftm/src/gftm_shutdown.f90 b/gftm/src/gftm_shutdown.f90
deleted file mode 100644
index 710302938..000000000
--- a/gftm/src/gftm_shutdown.f90
+++ /dev/null
@@ -1,9 +0,0 @@
-      SUBROUTINE gftm_shutdown
-!
-! save output and dealocate memory 
-!
-      IMPLICIT NONE
-
-      CALL gftm_deallocate
- 
-      END SUBROUTINE gftm_shutdown
diff --git a/gftm/src/gftm_startup.f90 b/gftm/src/gftm_startup.f90
deleted file mode 100644
index 3bd7142c9..000000000
--- a/gftm/src/gftm_startup.f90
+++ /dev/null
@@ -1,233 +0,0 @@
-       SUBROUTINE gftm_startup
-!*********************************************
-!
-!     initalization of gftm
-!
-!*********************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_velocity_matrix
-      USE gftm_gyro_average
-!
-      IMPLICIT NONE
-      INTEGER :: i,j
-      LOGICAL :: USE_PRESETS = .TRUE.
-!
-! initialized trace_path that records the flow of gftm internal calls
-!
-      do i=1,7
-        trace_path(i)=0
-      enddo
-!
-! set global constants
-!
-      pi = atan2( 0.0, -1.0 )
-      pi_2 = 2.0*pi
-      sqrt_pi = SQRT(pi)
-      sqrt_two = SQRT(2.0)
-!
-! set dimensions of allocatable arrays
-!
-      ns0 = 1
-      if(adiabatic_elec_in) then
-        ns0 = 2
-      endif
-      if(use_default_species)ns_in=2
-      ns = ns_in
-!      write(*,*)"ns = ",ns,"   ns0 = ",ns0
-      nx = 2*nxgrid_in-1
-      nbasis_max_in = 12
-      nbasis = nbasis_max_in
-      nbasis_max = nbasis
-! velocity space resolution
-      nu = 5
-      ne = 3
-!
-      nune = nu*ne
-      nphase = nu*ne*nbasis
-      ntot = (ns-ns0+1)*nu*ne*nbasis
-!
-      ! restrict user settings to three preset versions
-      ! SAT0 + GYRO + XNU 2
-      ! SAT1 + XNU 2
-      ! SAT2 + XNU 3 + UNITS != GYRO
-      if(USE_PRESETS)then
-        wdia_trapped_in=0.0
-        if(sat_rule_in.eq.2)then
-          xnu_model_in=3
-          wdia_trapped_in = 1.0
-          if(units_in.eq."GYRO")units_in = "CGYRO"
-          if(igeo .ne. 1)then
-            write(*,*)"SAT_RULE=2 requires Miller geometry, set GEOMETRY_FLAG=1"
-            STOP
-          endif
-        endif
-        if(sat_rule_in.eq.1)then
-          xnu_model_in = 2
-        endif
-        if(sat_rule_in.eq.0)then
-          units_in = 'GYRO'
-          xnu_model_in = 2
-        endif
-        if(use_bper_in)alpha_mach_in=0.0
-      endif
-! SAT_RULE=0 has different fits for nmodes=2 and nmodes=4
-      if(sat_rule_in.eq.0)then
-        if(nmodes_in.gt.2)nmodes_in=4
-      endif
-! debug
-!      write(*,*)"nx=",nx
-!      write(*,*)"nbasis =",nbasis    
-!      write(*,*)"ns0 = ",ns0
-!      write(*,*)"ns = ",ns
-!      write(*,*)"nxgrid_in=",nxgrid_in
-!      write(*,*)"nky_in=",nky_in
-!      write(*,*)"nmodes_in=",nmodes_in
-!      write(*,*)"nbasis_max_in=",nbasis_max_in
-!      write(*,*)"nbasis_min_in=",nbasis_min_in
-!      write(*,*)"nwidth_in=",nwidth_in
-!
-! allocate internal matricies
-!
-      CALL gftm_allocate
-!
-! fill species arrays
-!
-        trace_path(3)=1
-      CALL get_species
-!      write(*,*)"nxgrid_in=",nxgrid_in
-!      write(*,*)"nky_in=",nky_in
-!      write(*,*)"nmodes_in=",nmodes_in
-!      write(*,*)"nbasis_max_in=",nbasis_max_in
-!      write(*,*)"nbasis_min_in=",nbasis_min_in
-!      write(*,*)"nwidth_in=",nwidth_in
-!
-      if(new_start)then
-        trace_path(2)=1
-        new_width=.TRUE.
-      endif
-      new_start = .FALSE.
-!
-!   load the xgrid and gauss-hermite weights
-!
-      if(gauher_uncalled)CALL gauher
-!
-! load the hermite basis functions on the xgrid
-!  
-      if(gauss_hermite_uncalled)CALL gauss_hermite
-!
-      if(igeo.eq.1)grad_r0_out = 1.0/(1.0 + drmajdx_loc)
-!
-!debug
-      go to 10
-      call get_velocity_matrix
-      write(*,*)"mat_upar"
-      do i=1,num
-       write(*,*)(mat_upar(i,j),j=1,num)
-      enddo
-      write(*,*)"mat_dupar"
-      do i=1,num
-       write(*,*)(mat_dupar(i,j),j=1,num)
-      enddo
-      write(*,*)"mat_eper"
-      do i=1,nem
-       write(*,*)(mat_eper(i,j),j=1,nem)
-      enddo
-      write(*,*)"mat_deper"
-      do i=1,nem
-       write(*,*)(mat_deper(i,j),j=1,nem)
-      enddo
-      call get_gyro_average(1.0,nem)
-      write(*,*)"pe1j0",(pe1j0(j),j=1,nem)
-      write(*,*)"pe2j0",(pe2j0(j),j=1,nem)
-      write(*,*)"pe1j1",(pe1j1(j),j=1,nem)
-      write(*,*)"pe2j1",(pe2j1(j),j=1,nem)
- 10   continue
-! debug
-      END SUBROUTINE gftm_startup
-!
-!
-      SUBROUTINE get_species
-!******************************************************************************
-!  assign species arrays
-!******************************************************************************
-      USE gftm_dimensions
-      USE gftm_global
-      USE gftm_species
-!
-      IMPLICIT NONE
-      INTEGER :: is
-      REAL :: charge
-      REAL :: p_prime_factor
-
-! electrons=1, ions =2,...
-!
-      if(use_default_species)then
-       mass_in(1) = 0.0002723
-       mass_in(2) = 1.0
-       zs_in(1) = -1.0
-       zs_in(2) = 1.0
-       as_in(1) = 1.0
-       as_in(2) = 1.0
-       taus_in(1)=1.0
-       taus_in(2)=1.0
-       ns_in = 2
-       nstotal_in = 2
-      endif
-!
-      nfields_out = 1
-      if(use_bper_in)nfields_out = nfields_out + 1
-      if(use_bpar_in)nfields_out = nfields_out + 1
-!  inputs
-      ky_s = ky_in
-      vexb_shear_s = vexb_shear_in*sign_It_in
-      xnue_s = xnue_in
-      pol = 0.0
-      U0 = 0.0
-      charge = 0.0
-      rho_ion = 0.0
-!      do is=1,nstotal_in  ! include all species inputs
-      do is=1,ns
-        rlns(is) = rlns_in(is)
-        rlts(is) = rlts_in(is)
-        taus(is) = taus_in(is)
-        as(is) = as_in(is)
-        zs(is) = zs_in(is)
-        mass(is) = mass_in(is)
-        vpar_s(is) = alpha_mach_in*sign_It_in*vpar_in(is)
-        vpar_shear_s(is) = alpha_p_in*sign_It_in*vpar_shear_in(is)
-        vs(is) = SQRT(taus(is)/mass(is))
-        pol = pol +  zs(is)*zs(is)*as(is)/taus(is)
-        U0 = U0 + as(is)*vpar_s(is)*zs(is)*zs(is)/taus(is)
-        fts(is) = 0.0
-        if(is.gt.1.and.zs(is)*as(is)/ABS(as(1)*zs(1)).gt.0.1)then
-          charge = charge + zs(is)*as(is)
-          rho_ion = rho_ion + zs(is)*as(is)*SQRT(2.0*mass(is)*taus(is))/zs(is) ! charge weighted average ion gyroradius
-        endif
-        rho_e =SQRT(2.0*mass(1)*taus(1))/ABS(zs(1))
-!        write(*,*)"species",is
-!        write(*,*)" vs = ",vs(is)
-!        write(*,*)rlns(is),rlts(is)
-!        write(*,*)"taus = ",taus(is),"   mass = ",mass(is)
-!        write(*,*)zs(is),as(is)
-      enddo
-      if(charge.lt.0.001)call gftm_error(1,"total ion charge < 0.001")
-      rho_ion = rho_ion/charge
-      if(use_ave_ion_grid_in .eqv. .false.)then
-        rho_ion = SQRT(2.0*mass(2)*taus(2))/zs(2)
-      endif
-!      write(*,*)"rho_ion = ",rho_ion
-!      write(*,*)"rho_e = ",rho_e
-!      write(*,*)"charge = ",charge
-!
-!  p_prime like CGYRO
-!
-      if(betae_in.eq.0.0)betae_in=0.0005
-      p_prime_factor = -(q_loc/rmin_loc)*betae_in/(8.0*pi)
-      p_prime_loc = 0.0
-      do is=1,ns
-        p_prime_loc = p_prime_loc + p_prime_factor*as(is)*taus(is)*(rlns(is)+rlts(is))
-      enddo
-!      write(*,*)" p_prime_loc = ",p_prime_loc,"   betae_in = ",betae_in
-!
-      END SUBROUTINE get_species