From becdad2c35720aa4938f780994789835fe29397d Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 22 Aug 2024 14:41:30 +0200
Subject: [PATCH 01/47] PENTA: Added wrapper main function so PENTA can be
 called like a subroutine.

---
 PENTA/ObjectList           |   1 +
 PENTA/PENTA.dep            |   3 +
 PENTA/Sources/penta_imp.f  | 143 +++++++++----------------------------
 PENTA/Sources/penta_main.f | 126 ++++++++++++++++++++++++++++++++
 4 files changed, 163 insertions(+), 110 deletions(-)
 create mode 100644 PENTA/Sources/penta_main.f

diff --git a/PENTA/ObjectList b/PENTA/ObjectList
index 488576fbf..6a0b86914 100644
--- a/PENTA/ObjectList
+++ b/PENTA/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+penta_main.o \
 penta_functions_mod.o \
 penta_modules.o \
 quanc8.o \
diff --git a/PENTA/PENTA.dep b/PENTA/PENTA.dep
index db129c506..960e6f136 100644
--- a/PENTA/PENTA.dep
+++ b/PENTA/PENTA.dep
@@ -1,4 +1,7 @@
 # Microsoft Developer Studio Generated Dependency File, included by DKES.mak
+penta_main.o : \
+      penta_modules.o
+
 
 penta_imp.o : \
       read_input_file_mod.o \
diff --git a/PENTA/Sources/penta_imp.f b/PENTA/Sources/penta_imp.f
index b90c0b0bc..b4acb8633 100644
--- a/PENTA/Sources/penta_imp.f
+++ b/PENTA/Sources/penta_imp.f
@@ -1,90 +1,5 @@
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c
-c   -PENTA with Impurities-
-c
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c  To run,type: PENTA_imp [command line arguments]
-c
-c  where the command line arguments are:
-c
-c  1  unique identifier text on DKES database files
-c      i.e., for (m,l,n)star_lijs_***, this would be
-c      the text that replaces *** for the specific surface (ex: hsx_s10)
-c  2  Er,min
-c  3  Er,max  - args 2 and 3 specify the interval in Er over which
-c      the search is done for the ambipolar electric field root.
-c      Er,min and Er,max are dimensionless normalized electric
-c      field variables, i.e.: e<a>Er,min/max/kT_e
-c    - Note if the logical variable input_is_Er below is true then 
-c      the search interval is set by args 2 and 3 as Er (V/cm)
-c  4  flux surface number
-c  5  parameter that determines whether output data should be
-c      written into new files (=0) or appended to
-c      existing files (=1). Typically,when a script is run for a
-c      sequence of flux surfaces, this is set to 0 for the first
-c      surface and to 1 for subsequent surfaces
-c  6  extension of the profile_data_*** file (i.e., the *** text)
-c      that comes from extracting the appropriate profiles from
-c      the VMEC run using the profile_extractor.f code
-c  7  unique identifier on plasma profiles file, i.e., the ***
-c      text in the filename plasma_profiles***.dat. This allows
-c      multiple profiles to be run without having to rename files
-c  8  <B*E||> in T*V/m
-c
-c
-c  Required input files:
-c
-c   [l,m,n]star_lijs_***_s# - where *** is arg1 above and # arg 4.
-c       These files contain the values of efield and cmul and the
-c       corresponding normalized monoenergetic coefficients.  Note
-c       that L* should be L*/e**2 where e is the elementary charge.
-c
-c   ion_params - A file containing the namelist "ion_params" which
-c       defines the variables num_ion_species, Z_ion_init and 
-c       miomp_init which are the number of ion species (integer),
-c       the corresponding ion charge numbers (real, array) and 
-c       the ion to proton mass ratio (real, array) for each 
-c       non-electron species.
-c
-c   profile_data_*** - where *** is arg1 above.  Contains geometry
-c       variables, most likely from a VMEC run.
-c
-c   plasma_profilesXXX.dat - A file containing the plasma profile
-c       data, where XXX is arg8 above.  This file has the format:
-c       row 1: number of radial points for which data is specified.
-c       all other rows: r/a, ne, Te, Ti1, ni1, Ti2, ni2 ...
-c       where the densities are in units of 10**12/cc and the 
-c       temperatures in eV and i1, i2... are the ion species.
-c
-c	Utilde2_profile - Contains the quantity <U**2>, where U is the
-c		PS flow function as defined in Sugama and Nishimura.  The
-c		first row is the number of points, then r/a points and the
-c		corresponding <U**2> value.
-c   
-c  Output files:
-c
-c   "fluxes_vs_roa", "fluxes_vs_Er", "flows_vs_roa", "plasma_profiles_check"
-c
-c   
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c   NOTES
-c    - Be sure to check parameters below
-c    - based on Sugama, Nishimura PoP 9 4637 (2002) and 
-c         Sugama, Nishimura PoP 15, 042502 (2008)
-c    - Some code used from orignal PENTA code, written by Don Spong and 
-c        modified by Jeremy Lore
-c
-c  7/2009 JL
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c   PROGRAMMING NOTES
-c   -speed optimization
-c   -recursive ambipolar solver
-c     -fix numargs
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-    
-      program penta_imp
+      SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append, 
+     1               run_ident, pprof_char, B_Eprl_in)
       use penta_kind_mod
       use phys_const
       use read_input_file_mod
@@ -107,12 +22,21 @@ program penta_imp
       integer(iknd),parameter :: numKsteps_set = 1000_iknd  !Number of K points (linear) for convolution (used if use_quanc8_set=.false.)
       logical, parameter ::     log_interp_set = .true.     !If true, logarithmic interpolation of DKES coefficients is used
 
-      integer(iknd) :: num_species, iroot, js, i_append, 
+      character(100), intent(inout) :: coeff_ext
+      real(rknd), intent(inout) :: Er_min
+      real(rknd), intent(inout) :: Er_max
+      integer(iknd), intent(inout) :: js
+      integer(iknd), intent(inout) :: i_append
+      character(100), intent(inout) :: run_ident
+      character(10), intent(inout) :: pprof_char
+      real(rknd), intent(inout), OPTIONAL :: B_Eprl_in
+
+      integer(iknd) :: num_species, iroot, 
      1  num_ion_species, inv_err, nn_inv, j, ispec, tmp_ind, ie,
      2 ispec1, ispec2, spec1_ind, spec2_ind, numargs
 
       real(rknd) :: vth_e, loglambda, sigma_S, Er_test, U2,
-     1 lX_sum1, lX_sum2, J_E_tot, Er_min, Er_max, B_Eprl, J_E_cl, 
+     1 lX_sum1, lX_sum2, J_E_tot, J_E_cl, B_Eprl,
      2 eaEr_o_kTe
 
       real(rknd), dimension(:), allocatable :: Z_ion,ion_mass,vth_i,
@@ -130,9 +54,8 @@ program penta_imp
       real(rknd), dimension(num_ion_max) :: Z_ion_init,miomp_init  
 
       character(1)  :: tb = char(9)
-      character(10) :: pprof_char
       character(100) :: arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, 
-     1  arg9, coeff_ext, run_ident, format_tmp, str_num, fstatus, fpos
+     1  arg9, format_tmp, str_num, fstatus, fpos
 
       namelist / ion_params / num_ion_species,Z_ion_init,miomp_init
 
@@ -154,6 +77,7 @@ program penta_imp
 
       !default values
       B_Eprl=0._rknd
+      IF (PRESENT(B_Eprl_in)) B_Eprl= B_Eprl_in
      
       !Read namelist file for ion parameters
       open(iu_nl,file="ion_params",status="old",form="formatted")
@@ -162,25 +86,25 @@ program penta_imp
 
       !Get command line arguments
       !numargs = iargc()
-	numargs = 8
-      call getarg(1, arg1)
-      call getarg(2, arg2)
-      call getarg(3, arg3)
-      call getarg(4, arg4)
-      call getarg(5, arg5)
-      call getarg(6, arg6)
-      call getarg(7, arg7)
-      if (numargs .eq. 8) call getarg(8, arg8)
+!	numargs = 8
+!      call getarg(1, arg1)
+!      call getarg(2, arg2)
+!      call getarg(3, arg3)
+!      call getarg(4, arg4)
+!      call getarg(5, arg5)
+!      call getarg(6, arg6)
+!      call getarg(7, arg7)
+!      if (numargs .eq. 8) call getarg(8, arg8)
 
       !store command line args
-      coeff_ext = trim(adjustl(arg1))
-      read(arg2,*) Er_min
-      read(arg3,*) Er_max
-      read(arg4,*) js
-      read(arg5,*) i_append
-      run_ident = trim(adjustl(arg6))
-      pprof_char = trim(adjustl(arg7))
-      if (numargs .eq. 8) read(arg8,*) B_Eprl
+!      coeff_ext = trim(adjustl(arg1))
+!      read(arg2,*) Er_min
+!      read(arg3,*) Er_max
+!      read(arg4,*) js
+!      read(arg5,*) i_append
+!      run_ident = trim(adjustl(arg6))
+!      pprof_char = trim(adjustl(arg7))
+!      if (numargs .eq. 8) read(arg8,*) B_Eprl
   
       !allocate variables by number of species defined
       num_species=num_ion_species+1_iknd
@@ -509,5 +433,4 @@ program penta_imp
       close(iu_fvEr_out)
       close(iu_flows_out)
 
-      end program penta_imp
-
+      END SUBROUTINE penta_imp
\ No newline at end of file
diff --git a/PENTA/Sources/penta_main.f b/PENTA/Sources/penta_main.f
new file mode 100644
index 000000000..541f6a2dd
--- /dev/null
+++ b/PENTA/Sources/penta_main.f
@@ -0,0 +1,126 @@
+cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+c
+c   -PENTA with Impurities-
+c
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+c  To run,type: PENTA_imp [command line arguments]
+c
+c  where the command line arguments are:
+c
+c  1  unique identifier text on DKES database files
+c      i.e., for (m,l,n)star_lijs_***, this would be
+c      the text that replaces *** for the specific surface (ex: hsx_s10)
+c  2  Er,min
+c  3  Er,max  - args 2 and 3 specify the interval in Er over which
+c      the search is done for the ambipolar electric field root.
+c      Er,min and Er,max are dimensionless normalized electric
+c      field variables, i.e.: e<a>Er,min/max/kT_e
+c    - Note if the logical variable input_is_Er below is true then 
+c      the search interval is set by args 2 and 3 as Er (V/cm)
+c  4  flux surface number
+c  5  parameter that determines whether output data should be
+c      written into new files (=0) or appended to
+c      existing files (=1). Typically,when a script is run for a
+c      sequence of flux surfaces, this is set to 0 for the first
+c      surface and to 1 for subsequent surfaces
+c  6  extension of the profile_data_*** file (i.e., the *** text)
+c      that comes from extracting the appropriate profiles from
+c      the VMEC run using the profile_extractor.f code
+c  7  unique identifier on plasma profiles file, i.e., the ***
+c      text in the filename plasma_profiles***.dat. This allows
+c      multiple profiles to be run without having to rename files
+c  8  <B*E||> in T*V/m
+c
+c
+c  Required input files:
+c
+c   [l,m,n]star_lijs_***_s# - where *** is arg1 above and # arg 4.
+c       These files contain the values of efield and cmul and the
+c       corresponding normalized monoenergetic coefficients.  Note
+c       that L* should be L*/e**2 where e is the elementary charge.
+c
+c   ion_params - A file containing the namelist "ion_params" which
+c       defines the variables num_ion_species, Z_ion_init and 
+c       miomp_init which are the number of ion species (integer),
+c       the corresponding ion charge numbers (real, array) and 
+c       the ion to proton mass ratio (real, array) for each 
+c       non-electron species.
+c
+c   profile_data_*** - where *** is arg1 above.  Contains geometry
+c       variables, most likely from a VMEC run.
+c
+c   plasma_profilesXXX.dat - A file containing the plasma profile
+c       data, where XXX is arg8 above.  This file has the format:
+c       row 1: number of radial points for which data is specified.
+c       all other rows: r/a, ne, Te, Ti1, ni1, Ti2, ni2 ...
+c       where the densities are in units of 10**12/cc and the 
+c       temperatures in eV and i1, i2... are the ion species.
+c
+c	Utilde2_profile - Contains the quantity <U**2>, where U is the
+c		PS flow function as defined in Sugama and Nishimura.  The
+c		first row is the number of points, then r/a points and the
+c		corresponding <U**2> value.
+c   
+c  Output files:
+c
+c   "fluxes_vs_roa", "fluxes_vs_Er", "flows_vs_roa", "plasma_profiles_check"
+c
+c   
+cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+c   NOTES
+c    - Be sure to check parameters below
+c    - based on Sugama, Nishimura PoP 9 4637 (2002) and 
+c         Sugama, Nishimura PoP 15, 042502 (2008)
+c    - Some code used from orignal PENTA code, written by Don Spong and 
+c        modified by Jeremy Lore
+c
+c  7/2009 JL
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+      
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+c   PROGRAMMING NOTES
+c   -speed optimization
+c   -recursive ambipolar solver
+c     -fix numargs
+ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+
+cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+c   2024 Notes
+c    - Created PENTA_IMP_MAIN program and changed PENTA_IMP to a
+c      callable subroutine.
+c
+cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
+    
+      PROGRAM PENTA_MAIN
+      use penta_kind_mod
+      IMPLICIT NONE
+      integer(iknd) :: numargs, js, i_append
+      real(rknd) :: Er_min, Er_max, B_Eprl
+      character(100) :: arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8
+      character(100) :: coeff_ext, run_ident
+      character(10)  :: pprof_char
+      numargs = 8
+      call getarg(1, arg1)
+      call getarg(2, arg2)
+      call getarg(3, arg3)
+      call getarg(4, arg4)
+      call getarg(5, arg5)
+      call getarg(6, arg6)
+      call getarg(7, arg7)
+      if (numargs .eq. 8) call getarg(8, arg8)
+
+      !store command line args
+      coeff_ext = trim(adjustl(arg1))
+      read(arg2,*) Er_min
+      read(arg3,*) Er_max
+      read(arg4,*) js
+      read(arg5,*) i_append
+      run_ident = trim(adjustl(arg6))
+      pprof_char = trim(adjustl(arg7))
+      if (numargs .eq. 8) read(arg8,*) B_Eprl
+
+      ! Call subroutine
+      CALL PENTA_IMP(coeff_ext, Er_min, Er_max, js, i_append, 
+     1               run_ident, pprof_char, B_Eprl)
+      END PROGRAM PENTA_MAIN
+

From 8fbfe43a8290b1b0ca15c731205254a0c49caf73 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 22 Aug 2024 14:42:21 +0200
Subject: [PATCH 02/47] DKES: Added missing vimatrix dependency file.

---
 DKES/DKES.dep | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/DKES/DKES.dep b/DKES/DKES.dep
index 11eb0160e..29eba5665 100644
--- a/DKES/DKES.dep
+++ b/DKES/DKES.dep
@@ -73,6 +73,9 @@ residue_dkes.o : \
 
 vcmain.o : \
       ../../LIBSTELL/$(LOCTYPE)/stel_kinds.o 
+
+
+vimatrix.o : 
       
 
 vnamecl2.o : \
@@ -88,7 +91,7 @@ wrout.o : \
       dkes_input.o \
       dkes_realspace.o \
       vnamecl2.o 
-      
+
 
 dkes_input_prepare.o : \
       ../../LIBSTELL/$(LOCTYPE)/date_and_computer.o \

From 31a03cfb22ee9b1096d3179ecb385ff6fc12136c Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 22 Aug 2024 14:43:20 +0200
Subject: [PATCH 03/47] THRIFT: Added interface to DKES (for testing).

---
 SHARE/make_all.inc                  |  10 +
 THRIFT/ObjectList                   |   1 +
 THRIFT/Sources/thrift_dkes.f90      | 308 ++++++++++++++++++++++++++++
 THRIFT/Sources/thrift_input_mod.f90 |  11 +-
 THRIFT/Sources/thrift_vars.f90      |   8 +
 THRIFT/THRIFT.dep                   |  20 +-
 THRIFT/makethrift                   |   6 +-
 7 files changed, 360 insertions(+), 4 deletions(-)
 create mode 100644 THRIFT/Sources/thrift_dkes.f90

diff --git a/SHARE/make_all.inc b/SHARE/make_all.inc
index cb5dda4e8..730cf635c 100644
--- a/SHARE/make_all.inc
+++ b/SHARE/make_all.inc
@@ -111,6 +111,16 @@ else ifeq ($(MAKECMDGOALS),xthrift)
   $(BOOTSJ_DIR)/$(LOCTYPE)/$(LIB_BOOTSJ) \
   $(BOOZ_DIR)/$(LOCTYPE)/$(LIB_BOOZ) \
   $(DIAGNO_DIR)/$(LOCTYPE)/$(LIB_DIAGNO)
+  ifeq ($(LDKES),T)
+    DKES_DIR = ../../DKES
+    LIB_DKES = libdkes$(STATIC_EXT)
+    MOD_PATH += -I$(DKES_DIR)/$(LOCTYPE)
+    PRECOMP += -DDKES_OPT
+    LIB_LINK += $(DKES_DIR)/$(LOCTYPE)/$(LIB_DKES)
+  else
+    DKES_DIR = 
+    LIB_DKES = 
+  endif
   LGENE = F
   LCOILOPT = F
   LSFINCS = F
diff --git a/THRIFT/ObjectList b/THRIFT/ObjectList
index 983318595..634831d20 100644
--- a/THRIFT/ObjectList
+++ b/THRIFT/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+thrift_dkes.o \
 thrift_diagno.o \
 thrift_run_diagnostics.o \
 thrift_run_nbcd.o \
diff --git a/THRIFT/Sources/thrift_dkes.f90 b/THRIFT/Sources/thrift_dkes.f90
new file mode 100644
index 000000000..f55a45fb4
--- /dev/null
+++ b/THRIFT/Sources/thrift_dkes.f90
@@ -0,0 +1,308 @@
+!-----------------------------------------------------------------------
+!     Subroutine:    thrift_dkes
+!     Authors:       S. Lazerson (samuel.lazerson@gauss-fusion.com)
+!     Date:          08/22/2024
+!     Description:   This subroutine calculates the DKES coefficients.
+!                    see stellopt_dkes.f90 for more information.
+!-----------------------------------------------------------------------
+      SUBROUTINE thrift_dkes(lscreen,iflag)
+!-----------------------------------------------------------------------
+!     Libraries
+!-----------------------------------------------------------------------
+      USE thrift_runtime
+      USE thrift_input_mod
+      USE thrift_vars, nrho_thrift => nrho
+      USE thrift_profiles_mod
+      USE thrift_equil
+      USE thrift_funcs
+      USE mpi_params
+      USE mpi_inc
+      USE read_wout_mod, ONLY: read_wout_file, read_wout_deallocate
+      USE read_boozer_mod, ONLY: bcast_boozer_vars
+      ! DKES LIBRARIES
+#if defined(DKES_OPT)
+      USE Vimatrix
+      USE Vnamecl2
+      USE Vcmain
+      USE dkes_input, lscreen_dkes => lscreen
+      USE dkes_realspace
+#endif
+      
+!-----------------------------------------------------------------------
+!     Subroutine Parameters
+!        iflag         Error flag
+!----------------------------------------------------------------------
+      IMPLICIT NONE
+      LOGICAL, INTENT(in)    :: lscreen
+      INTEGER, INTENT(inout) :: iflag
+!-----------------------------------------------------------------------
+!     Local Variables
+!        ier         Error flag
+!        iunit       File unit number
+!----------------------------------------------------------------------
+      INTEGER :: i, j, k, l, istat, neqs, ier_phi, mystart, myend
+      INTEGER, DIMENSION(:), ALLOCATABLE :: ik_dkes
+      REAL(rprec), DIMENSION(:), ALLOCATABLE :: Earr_dkes, nuarr_dkes
+      REAL(rprec), DIMENSION(:), POINTER :: f0p1, f0p2, f0m1, f0m2
+      REAL(rprec) :: tcpu0, tcpu1, tcpui, tcput, tcpu, tcpua, dkes_efield,&
+                     phi_temp
+      CHARACTER :: tb*1           
+      CHARACTER*50 :: arg1(6)       
+      INTEGER :: numargs, iodata, iout_opt, idata, iout
+      INTEGER :: m, n ! nmax, mmax (revmoed due to conflict with dkes_realspace
+      CHARACTER :: output_file*64, opt_file*64, dkes_input_file*64, temp_str*64
+      LOGICAL :: lfirst_pass  
+
+!-----------------------------------------------
+!   E x t e r n a l   F u n c t i o n s
+!-----------------------------------------------
+!----------------------------------------------------------------------
+!     BEGIN SUBROUTINE
+!----------------------------------------------------------------------
+      IF (iflag < 0) RETURN
+      IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL CALCULATION USING DKES  -------------------'
+      IF (lvmec) THEN
+         ierr_mpi = 0
+         ! First we deallocate the old arrays and allocate new ones
+#if defined(MPI_OPT)
+         CALL MPI_BCAST(nruns_dkes,1,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
+#endif
+         IF (ALLOCATED(DKES_L11p)) DEALLOCATE(DKES_L11p)
+         IF (ALLOCATED(DKES_L33p)) DEALLOCATE(DKES_L33p)
+         IF (ALLOCATED(DKES_L31p)) DEALLOCATE(DKES_L31p)
+         IF (ALLOCATED(DKES_L11m)) DEALLOCATE(DKES_L11m)
+         IF (ALLOCATED(DKES_L33m)) DEALLOCATE(DKES_L33m)
+         IF (ALLOCATED(DKES_L31m)) DEALLOCATE(DKES_L31m)
+         IF (ALLOCATED(DKES_scal11)) DEALLOCATE(DKES_scal11)
+         IF (ALLOCATED(DKES_scal33)) DEALLOCATE(DKES_scal33)
+         IF (ALLOCATED(DKES_scal31)) DEALLOCATE(DKES_scal31)
+         ALLOCATE(DKES_L11p(nruns_dkes),DKES_L33p(nruns_dkes),DKES_L31p(nruns_dkes),&
+               DKES_L11m(nruns_dkes),DKES_L33m(nruns_dkes),DKES_L31m(nruns_dkes),&
+               DKES_scal11(nruns_dkes),DKES_scal33(nruns_dkes),DKES_scal31(nruns_dkes))
+         DKES_L11p=0.0; DKES_L33p=0.0; DKES_L31p=0.0
+         DKES_L11m=0.0; DKES_L33m=0.0; DKES_L31m=0.0
+         DKES_scal11=0.0; DKES_scal33=0.0; DKES_scal31=0.0
+         l = 1
+         ! Allocate Helper arrays to loop over dkes runs
+         ALLOCATE(ik_dkes(nruns_dkes),Earr_dkes(nruns_dkes),nuarr_dkes(nruns_dkes))
+         IF (myworkid == master) THEN
+            DO k = 1, DKES_NS_MAX
+               DO i = 1, DKES_NSTAR_MAX
+                  DO j = 1, DKES_NSTAR_MAX
+                     IF ((DKES_K(k) > 0) .AND. (DKES_Erstar(i)<1E10) .AND. (DKES_Nustar(j) < 1E10)) THEN
+                        ik_dkes(l) = DKES_K(k)
+                        Earr_dkes(l) = DKES_Erstar(i)
+                        nuarr_dkes(l) = DKES_Nustar(j)
+                        l = l + 1
+                     END IF
+                  END DO
+               END DO
+            END DO
+         ENDIF
+#if defined(MPI_OPT)
+         ierr_mpi = 0
+         CALL MPI_BCAST(ik_dkes,nruns_dkes,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(nuarr_dkes,nruns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(Earr_dkes,nruns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+#endif
+         ! Read the wout file
+         CALL read_wout_file(proc_string, ier)
+         ! Now bcast the boozer parameters
+         CALL bcast_boozer_vars(master, MPI_COMM_MYWORLD, ierr_mpi)
+         ! Breakup work
+         CALL MPI_CALC_MYRANGE(MPI_COMM_MYWORLD,1,nruns_dkes,mystart,myend)
+         !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+         !!!!!! Parallel Work block
+         !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+         ! Note there are multile file write statements which can
+         ! probably be removed so we only write what we need for PENTA
+         DO k = mystart,myend
+            ! Setup input
+            arg1(1) = TRIM(proc_string)
+            WRITE(arg1(2),'(i3)') ik_dkes(k)
+            WRITE(arg1(3),'(e20.10)') nuarr_dkes(k)
+            WRITE(arg1(4),'(e20.10)') dkes_efield
+            arg1(5) = 'F'
+            IF (lscreen .and. lfirst_pass) arg1(5) = 'T'
+            WRITE(temp_str,'(i3.3)') k
+            arg1(6) = '_s' // TRIM(temp_str)
+            ier_phi = 0 ! We don't read the boozmn or wout file we've done that already
+            CALL dkes_input_prepare(arg1,6,dkes_input_file,ier_phi)
+            output_file= 'dkesout.' // TRIM(proc_string) // '_s' // TRIM(temp_str)
+            opt_file= 'opt_dkes.' // TRIM(proc_string) // '_s' // TRIM(temp_str)       !DAS 2/21/2000  !Probably won't need
+            summary_file = 'results.' // TRIM(proc_string) //'_s' // TRIM(temp_str) !record file addition
+            !  OPEN INPUT AND OUTPUT FILES FOR READING (AND WRITING OUTPUT)
+            idata    = 7
+            iout     = 30
+            iout_opt = 14
+            iodata = idata
+            CALL safe_open(iodata, istat, dkes_input_file, 'old', 'formatted')
+            IF (istat .ne. 0) STOP 'Error reading input file in DKES'
+            ioout = iout
+            CALL safe_open(ioout, istat, output_file, 'replace', 'formatted')
+            IF (istat .ne. 0) STOP 'Error writing output file'
+            ioout_opt = iout_opt
+            CALL safe_open(ioout_opt, istat, opt_file, 'replace','formatted')
+            IF (istat .ne. 0) STOP 'Error writing opt_output file'
+            ! Read namelist (datain) input
+            lscreen_dkes = lscreen
+            nvalsb(1) = -bigint-1
+            idisk = 1
+            lfout = 0
+            ibbi = 1
+            borbi = 0
+            READ (iodata, nml=dkes_indata, iostat=istat)
+            IF (istat .ne. 0) STOP 'Error reading dkes_indata NAMELIST in DKES'
+            CLOSE (iodata)
+            ! Recompute ntorb, mpolb for new style input where
+            ! borbi is input with actual index value, borbi(n,m)
+            IF (nvalsb(1) <= -bigint) THEN
+               nmax = -bigint;  mmax = -bigint
+               DO n = -ntorbd, ntorbd
+                  DO m = 0, mpolbd
+                     IF (borbi(n,m) .ne. zero) THEN
+                        nmax = max (nmax, abs(n))
+                        mmax = max (mmax, abs(m))
+                     END IF
+                  END DO
+               END DO
+               ! User MAY input smaller values if he does not want to use entire array         
+               ntorb = min (abs(ntorb), nmax)
+               mpolb = min (abs(mpolb-1), mmax)
+            ELSE 
+               IF (ntorb > ntorbd) THEN
+                  WRITE (ioout, 45) ntorb, ntorbd
+                  STOP ' ntorb > ntorbd in DKES input'
+               END IF
+               IF (mpolb < 2) THEN
+                  WRITE (ioout, 20) mpolb
+                  STOP ' mpolb < 2 in DKES input'
+               ENDIF
+            END IF
+            IF (nzperiod .le. 0) nzperiod = 1
+            IF (ipmb<0 .or. ipmb>2) ipmb = 0
+            meshtz = MAX(0,meshtz)
+            !!!! END read_dkes_input
+            CALL set_mndim
+            neqs = mpnt*(lalpha + 1)
+            ALLOCATE (fzerop(2*neqs), fzerom(2*neqs), stat=istat)
+            !IF (istat .ne. 0) STOP 'allocation error(1) in dkes2!'
+            f0p1 => fzerop(1:neqs);   f0p2 => fzerop(neqs+1:)                  !+ functions
+            f0m1 => fzerom(1:neqs);   f0m2 => fzerom(neqs+1:)                  !- functions
+            CALL ftconv
+            CALL lcalc
+            CALL second0 (tcpu1); tcpui = tcpu1 - tcpu0
+            CALL header
+            CALL second0 (tcpu0); tcput = zero
+            ! Here things get a bit screwy
+            ! DKES allows for an array of nu/v and E/v to be evaluated
+            ! but dkes_input_prepare does not.  So nrun will always be 1 for stellopt
+            ! which is probably fine since we can parallelize over runs easier.
+            ! But in the future this logic could be improved.
+            nrun = MAX(nrun, 1)
+            nrun = MIN(nrun, krun)
+            DO i = 1, nrun
+               efield1 = efield(i)
+               cmul1 = cmul(i)
+               if(i .eq. 1) then
+                  call safe_open(itab_out, istat, summary_file,'unknown', &
+                 'formatted')
+                  write(itab_out,'("*",/,"cmul",a1,"efield",a1,"weov",a1,"wtov", &
+                                     & a1,"L11m",a1,"L11p",a1,"L31m",a1,"L31p",a1,"L33m",a1,"L33p", &
+                                     & a1,"scal11",a1,"scal13",a1,"scal33",a1,"max_residual", &
+                                     & a1,"chip",a1,"psip",a1,"btheta",a1,"bzeta",a1,"vp")') &
+                        tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb,tb
+               else if(i .gt. 1) then
+                  open(itab_out,file=summary_file,status='unknown',position='append',form='formatted')
+               endif
+               CALL cescale (srces0)
+               WRITE (ioout, 950) dashes, cmul1, efield1, weov, wtov, wcyclo, vthermi
+               IF (ipmb < 2) THEN
+                  iswpm = 1
+                  CALL blk5d (blk1, blk2, blk3, blk4, blk5, blk6, blk7, f0p1, f0p2, srces0)
+                  IF (ier .ne. 0) THEN
+                     WRITE (ioout, 1000) ier
+                     STOP
+                  ENDIF
+                  CALL residue_dkes (blk1, blk2, blk3, blk4, blk5, blk6,&
+                                f0p1, f0p2, srces0, rsd1p, rsd3p, g11p, g33p,&
+                                g31p, g13p, crs1p, crs3p)
+               ENDIF
+               IF (ipmb .ne. 1) THEN
+                  iswpm = 2
+                  CALL blk5d (blk1, blk2, blk3, blk4, blk5, blk6, blk7, f0m1, f0m2, srces0)
+                  IF (ier .ne. 0) THEN
+                     WRITE (ioout, 1050) ier
+                     STOP
+                  ENDIF
+                  CALL residue_dkes (blk1, blk2, blk3, blk4, blk5, blk6,&
+                       f0m1, f0m2, srces0, rsd1m, rsd3m, g11m, g33m,&
+                       g31m, g13m, crs1m, crs3m)
+               ENDIF
+               ! This is a trick to get the arrays corretly sorted
+               DKES_rad_dex = i
+               IF (.not. lfirst_pass) lscreen_dkes = .FALSE.
+               CALL dkes_printout (f0p1, f0m1, f0p2, f0m2, srces0)
+               DKES_rad_dex = ik_dkes(i)
+               ! End trick
+               CALL second0 (tcpu1); tcpu = tcpu1 - tcpu0; tcpu0 = tcpu1; tcput = tcput + tcpu; tcpua = tcput/i
+               WRITE (ioout, 1100) tcpu
+               CLOSE(unit=itab_out)
+            END DO
+            !IF (lfout .ne. 0) CALL wrout (f0p1, f0m1, f0p2, f0m2, srces0)  ! We don't need to do this
+            CALL free_mndim
+            DEALLOCATE (cols, al1, al2, al3, al4, bl1, bl2, bl3, bl4, cl1,&
+               cl2, cl3, cl4, cols0, omgl, al01, al02, al03, al04, bl01,&
+               bl02, bl03, bl04, cl01, cl02, cl03, cl04, fzerop, fzerom)
+            CLOSE(unit=ioout)
+            CLOSE(unit=ioout_opt)
+            lfirst_pass = .FALSE.
+         END DO
+         !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+         !!!!!! Parallel Work block Done
+         !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+#if defined(MPI_OPT)
+         CALL MPI_BARRIER(MPI_COMM_MYWORLD,ierr_mpi)
+         IF (myworkid == master) THEN
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_L11p, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_L11m, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_L33p, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_L33m, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_L31p, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_L31m, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_scal11, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_scal33, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE, DKES_scal31, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+         ELSE
+            CALL MPI_REDUCE(DKES_L11p,    DKES_L11p, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_L11m,    DKES_L11m, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_L33p,    DKES_L33p, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_L33m,    DKES_L33m, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_L31p,    DKES_L31p, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_L31m,    DKES_L31m, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_scal11,  DKES_scal11, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_scal33,  DKES_scal33, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+            CALL MPI_REDUCE(DKES_scal31,  DKES_scal31, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
+         END IF
+#endif
+         IF (lscreen) WRITE(6,'(a)') ' -----------------  DKES CALCULATION (DONE) ----------------'
+         IF (myworkid .ne. master) CALL read_wout_deallocate
+
+      END IF
+      IF (lscreen) WRITE(6,'(a)') ' -------------------  DKES NEOCLASSICAL CALCULATION DONE  ---------------------'
+      RETURN
+   90 format(5e16.8)
+  950 FORMAT(/9x,'CMUL',7x,'EFIELD',4x,'OMEGA-E/v',4x,'OMEGA-T/v',&
+               5x,'OMEGA-ci',3x,'VI-THERMAL'/&
+               7x,'(nu/v)',7x,'(Es/v)',2x,'(ExB drift)',4x,'(transit)',&
+               3x, '(H+, B=B00)',2x,'(H+, Ti=1keV)'/,131a,/&
+               1p,6e13.4/)
+   20 FORMAT(' mpolb = ',i5,'  is less than 2')
+   45 FORMAT(' ntorb = ',i5,'  is greater than ntorbd = ',i5)
+ 1000 FORMAT(/' blk5d error in block = ',i5)
+ 1050 FORMAT(/' blk5d error : ierm = ',i5)
+ 1100 FORMAT(/' time used:    tcpu =',1p,e10.2,'  sec'/)
+!----------------------------------------------------------------------
+!     END SUBROUTINE
+!----------------------------------------------------------------------
+      END SUBROUTINE thrift_dkes
diff --git a/THRIFT/Sources/thrift_input_mod.f90 b/THRIFT/Sources/thrift_input_mod.f90
index 05e4862a5..d52d86b2d 100644
--- a/THRIFT/Sources/thrift_input_mod.f90
+++ b/THRIFT/Sources/thrift_input_mod.f90
@@ -35,7 +35,8 @@ MODULE thrift_input_mod
                               targetposition_ecrh, rbeam_ecrh, &
                               rfocus_ecrh, nra_ecrh, nphi_ecrh, &
                               freq_ecrh, power_ecrh, &
-                              pecrh_aux_t, pecrh_aux_f, ecrh_rc, ecrh_w
+                              pecrh_aux_t, pecrh_aux_f, ecrh_rc, ecrh_w, &
+                              dkes_k, dkes_Erstar, dkes_Nustar
       
 !-----------------------------------------------------------------------
 !     Subroutines
@@ -84,6 +85,10 @@ SUBROUTINE init_thrift_input
       rfocus_ecrh = 0
       nra_ecrh = 0
       nphi_ecrh = 8
+      ! DKES Vars
+      dkes_k = -1
+      dkes_Erstar = 1E10
+      dkes_Nustar = 1E10
       RETURN
       END SUBROUTINE init_thrift_input
       
@@ -115,7 +120,8 @@ SUBROUTINE read_thrift_input(filename, istat)
       CALL tolower(bootstrap_type)
       CALL tolower(eccd_type)
       leccd = eccd_type .ne. ''
-      nsj = nrho;
+      nsj = nrho
+      nruns_dkes = COUNT(dkes_k>0)*COUNT(dkes_Erstar<1E10)*COUNT(dkes_Nustar<1E10)
       RETURN
       END SUBROUTINE read_thrift_input
 
@@ -150,6 +156,7 @@ SUBROUTINE write_thrift_namelist(iunit_out, istat)
       WRITE(iunit_out,outint) 'MBOZ',nboz
       WRITE(iunit_out,'(A)') '!---------- ECCD PARAMETERS ------------'
       WRITE(iunit_out,outstr) 'ECCD_TYPE',eccd_type
+      WRITE(iunit_out,'(A)') '!---------- DKES PARAMETERS ------------'
       WRITE(iunit_out,'(A)') '/'
       RETURN
       END SUBROUTINE write_thrift_namelist
diff --git a/THRIFT/Sources/thrift_vars.f90 b/THRIFT/Sources/thrift_vars.f90
index c6d820fc1..21290a09c 100644
--- a/THRIFT/Sources/thrift_vars.f90
+++ b/THRIFT/Sources/thrift_vars.f90
@@ -110,5 +110,13 @@ MODULE thrift_vars
     REAL(rprec), DIMENSION(nsys,3)     :: antennaposition_ecrh, &
                  targetposition_ecrh,rbeam_ecrh,rfocus_ecrh
 
+    ! For DKES
+    INTEGER, PARAMETER :: DKES_NS_MAX = 64
+    INTEGER, PARAMETER :: DKES_NSTAR_MAX = 32
+    INTEGER :: nruns_dkes
+    INTEGER, DIMENSION(:), POINTER :: DKES_rundex
+    INTEGER, DIMENSION(DKES_NS_MAX) :: DKES_K
+    REAL(rprec), DIMENSION(DKES_NSTAR_MAX) :: DKES_Erstar, DKES_Nustar
+
 
 END MODULE thrift_vars
diff --git a/THRIFT/THRIFT.dep b/THRIFT/THRIFT.dep
index f93470d1c..38ac7e9a9 100644
--- a/THRIFT/THRIFT.dep
+++ b/THRIFT/THRIFT.dep
@@ -22,7 +22,25 @@ thrift_boozer.o : \
       $(BOOZ_DIR)/$(LOCTYPE)/booz_persistent.o \
       $(LIB_DIR)/$(LOCTYPE)/read_boozer_mod.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
-      $(LIB_DIR)/$(LOCTYPE)/mpi_params.o  
+      $(LIB_DIR)/$(LOCTYPE)/mpi_params.o
+
+thrift_dkes.o : \
+      thrift_runtime.o \
+      thrift_vars.o \
+      thrift_input_mod.o \
+      thrift_profiles_mod.o \
+      thrift_equil.o \
+      thrift_funcs.o \
+      $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
+      $(LIB_DIR)/$(LOCTYPE)/mpi_params.o  \
+      $(LIB_DIR)/$(LOCTYPE)/bootsj_input.o \
+      $(DKES_DIR)/$(LOCTYPE)/vimatrix.o \
+      $(DKES_DIR)/$(LOCTYPE)/vnamecl2.o \
+      $(DKES_DIR)/$(LOCTYPE)/vcmain.o \
+      $(DKES_DIR)/$(LOCTYPE)/dkes_input.o \
+      $(DKES_DIR)/$(LOCTYPE)/dkes_realspace.o \
+      $(LIB_DIR)/$(LOCTYPE)/read_wout_mod.o \
+      $(LIB_DIR)/$(LOCTYPE)/read_boozer_mod.o 
 
 thrift_diagno.o : \
       thrift_runtime.o \
diff --git a/THRIFT/makethrift b/THRIFT/makethrift
index 0e3442056..fd2ad7315 100644
--- a/THRIFT/makethrift
+++ b/THRIFT/makethrift
@@ -15,7 +15,7 @@ VPATH = $(SPATH)
 
 .SUFFIXES :
 .SUFFIXES : .f .f90 .o
-xthrift: $(LIB) $(LIB_VMEC) $(LIB_BOOTSJ) $(LIB_BOOZ) $(LIB_DIAGNO) $(ObjectFiles)
+xthrift: $(LIB) $(LIB_VMEC) $(LIB_BOOTSJ) $(LIB_BOOZ) $(LIB_DIAGNO) $(LIB_DKES) $(ObjectFiles)
 	$(LINK) $@ $(ObjectFiles) $(LIB_LINK)
 ifdef VMEC_DIR 
 #	@rm $(VMEC_DIR)/$(LOCTYPE)/$(LIB_VMEC) 
@@ -89,3 +89,7 @@ $(LIB_BOOZ) :
 #Construct diagno library. 
 $(LIB_DIAGNO) :
 	@cd $(DIAGNO_DIR); make $(TYPE); cd $(LOCTYPE); ar -cruv $(LIB_DIAGNO) *.o
+   
+#Construct DKES library. 
+$(LIB_DKES) :
+	@cd $(DKES_DIR); make $(TYPE); cd $(LOCTYPE); ar -cruv $(LIB_DKES) *.o

From fcd45a15e92025fe0e4a90b27630edffb464e6a5 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sat, 24 Aug 2024 10:45:15 +0900
Subject: [PATCH 04/47] PENTA: Make possible to read namelist from input.ext
 file.

---
 PENTA/Sources/penta_imp.f     | 50 ++++++++++++++++++++++++++++++++---
 PENTA/Sources/penta_modules.f |  3 ++-
 2 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/PENTA/Sources/penta_imp.f b/PENTA/Sources/penta_imp.f
index b4acb8633..b37fb7632 100644
--- a/PENTA/Sources/penta_imp.f
+++ b/PENTA/Sources/penta_imp.f
@@ -9,6 +9,7 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
       use Er_roots_pass
       use io_unit_spec
       use parameter_pass
+      USE safe_open_mod
       implicit none
 
       logical,       parameter ::  input_is_Er = .true.       !If true, Er range is (V/cm) otherwise e<a>Er/kT_e
@@ -33,7 +34,7 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
 
       integer(iknd) :: num_species, iroot, 
      1  num_ion_species, inv_err, nn_inv, j, ispec, tmp_ind, ie,
-     2 ispec1, ispec2, spec1_ind, spec2_ind, numargs
+     2 ispec1, ispec2, spec1_ind, spec2_ind, numargs, istat
 
       real(rknd) :: vth_e, loglambda, sigma_S, Er_test, U2,
      1 lX_sum1, lX_sum2, J_E_tot, J_E_cl, B_Eprl,
@@ -57,6 +58,8 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
       character(100) :: arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, 
      1  arg9, format_tmp, str_num, fstatus, fpos
 
+      LOGICAL :: lexist
+
       namelist / ion_params / num_ion_species,Z_ion_init,miomp_init
 
       !external functions
@@ -80,9 +83,50 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
       IF (PRESENT(B_Eprl_in)) B_Eprl= B_Eprl_in
      
       !Read namelist file for ion parameters
-      open(iu_nl,file="ion_params",status="old",form="formatted")
-      read(iu_nl,nml=ion_params)
+      INQUIRE(FILE='input.'//TRIM(run_ident),EXIST=lexist)
+      IF (lexist) THEN
+         CALL safe_open(iu_nl,istat,'input.'//TRIM(run_ident),'old',
+     1                  'formatted')
+      ELSE
+         CALL safe_open(iu_nl,istat,'ion_params','old','formatted')
+         WRITE(6,*) 
+     1     '   -Reading ion_params namelist from ion_params file'
+      END IF
+      READ(iu_nl,NML=ion_params,IOSTAT=istat)
+      IF (istat /= 0) THEN
+         CLOSE(iu_nl)
+!         IF (lverb) THEN
+!            WRITE(6,*) 
+!     1          '   -Could not find ion_params namelist in input.'//
+!     2          TRIM(run_ident)//' file'
+!            WRITE(6,*) 
+!     1 '   -Attempting to read ion_params namelist from ion_params file'
+!         END IF
+         iu_nl = 25
+         istat = 0
+         CALL safe_open(iu_nl,istat,'ion_params','old','formatted')
+         IF (istat /= 0) THEN
+            WRITE(6,*) '   -Could not open ion_params file'
+            !WRITE(6,*) '   -Dumping ion_params to screen'
+            stop
+         END IF
+         istat = 0
+         READ(iu_nl,NML=ion_params,IOSTAT=istat)
+         IF (istat /= 0) THEN
+            WRITE(6,*) 
+     1        '   -Could not read ion_params from ion_params file'
+            !WRITE(6,*) '   -Dumping ion_params to screen'
+            !CALL write_diagno_input(6,istat)
+            !backspace(iu_nl)
+            !read(iu_nl,fmt='(A)') line
+            !write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
+            stop
+         END IF
       close(iu_nl)
+      END IF
+      !open(iu_nl,file="ion_params",status="old",form="formatted")
+      !read(iu_nl,nml=ion_params)
+      !close(iu_nl)
 
       !Get command line arguments
       !numargs = iargc()
diff --git a/PENTA/Sources/penta_modules.f b/PENTA/Sources/penta_modules.f
index b0daba464..f38b958f7 100644
--- a/PENTA/Sources/penta_modules.f
+++ b/PENTA/Sources/penta_modules.f
@@ -27,7 +27,8 @@ end module phys_const
 c-----------------------------------------------------------------
 c
       module io_unit_spec
-      integer, parameter :: iu_nl=21, iu_vmec=22, iu_pprof=23, 
+      INTEGER :: iu_nl = 21
+      integer, parameter :: iu_vmec=22, iu_pprof=23, 
      1  iu_coeff=24, iu_Ufile=25, iu_flux_out=10, iu_pprof_out=11,
      2  iu_fvEr_out=12, iu_flows_out=13
       end module io_unit_spec

From 3f2aff746bef2fa675cb3abe28efefe4949734d7 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sat, 24 Aug 2024 10:45:45 +0900
Subject: [PATCH 05/47] THRIFT: Now links to PENTA sources

---
 SHARE/make_all.inc | 8 ++++++--
 THRIFT/makethrift  | 9 ++++++++-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/SHARE/make_all.inc b/SHARE/make_all.inc
index 730cf635c..cd26367da 100644
--- a/SHARE/make_all.inc
+++ b/SHARE/make_all.inc
@@ -72,7 +72,7 @@ ifeq ($(MAKECMDGOALS),xstelloptv2)
 	$(DIAGNO_DIR)/$(LOCTYPE)/$(LIB_DIAGNO) \
 	$(FIELDLINES_DIR)/$(LOCTYPE)/$(LIB_FIELDLINES) \
 	$(JINV_DIR)/$(LOCTYPE)/$(LIB_JINV) \
-	$(MGRID_DIR)/$(LOCTYPE)/$(LIB_MGRID) 
+  $(MGRID_DIR)/$(LOCTYPE)/$(LIB_MGRID)
   ifeq ($(LDKES),T)
     DKES_DIR = ../../DKES
     LIB_DKES = libdkes$(STATIC_EXT)
@@ -107,10 +107,14 @@ else ifeq ($(MAKECMDGOALS),xthrift)
   DIAGNO_DIR = ../../DIAGNO
   LIB_DIAGNO= libdiagno$(STATIC_EXT)
   MOD_PATH+= -I$(DIAGNO_DIR)/$(LOCTYPE)
+  PENTA_DIR= ../../PENTA
+  LIB_PENTA= libpenta$(STATIC_EXT)
+  MOD_PATH+= -I$(PENTA_DIR)/$(LOCTYPE)
   LIB_LINK=  $(VMEC_DIR)/$(LOCTYPE)/$(LIB_VMEC)  \
   $(BOOTSJ_DIR)/$(LOCTYPE)/$(LIB_BOOTSJ) \
   $(BOOZ_DIR)/$(LOCTYPE)/$(LIB_BOOZ) \
-  $(DIAGNO_DIR)/$(LOCTYPE)/$(LIB_DIAGNO)
+  $(DIAGNO_DIR)/$(LOCTYPE)/$(LIB_DIAGNO) \
+  $(PENTA_DIR)/$(LOCTYPE)/$(LIB_PENTA) 
   ifeq ($(LDKES),T)
     DKES_DIR = ../../DKES
     LIB_DKES = libdkes$(STATIC_EXT)
diff --git a/THRIFT/makethrift b/THRIFT/makethrift
index fd2ad7315..b221d5249 100644
--- a/THRIFT/makethrift
+++ b/THRIFT/makethrift
@@ -15,7 +15,7 @@ VPATH = $(SPATH)
 
 .SUFFIXES :
 .SUFFIXES : .f .f90 .o
-xthrift: $(LIB) $(LIB_VMEC) $(LIB_BOOTSJ) $(LIB_BOOZ) $(LIB_DIAGNO) $(LIB_DKES) $(ObjectFiles)
+xthrift: $(LIB) $(LIB_VMEC) $(LIB_BOOTSJ) $(LIB_BOOZ) $(LIB_DIAGNO) $(LIB_DKES) $(LIB_PENTA) $(ObjectFiles)
 	$(LINK) $@ $(ObjectFiles) $(LIB_LINK)
 ifdef VMEC_DIR 
 #	@rm $(VMEC_DIR)/$(LOCTYPE)/$(LIB_VMEC) 
@@ -29,6 +29,9 @@ endif
 ifdef DIAGNO_DIR
 	@rm $(DIAGNO_DIR)/$(LOCTYPE)/$(LIB_DIAGNO)
 endif
+ifdef PENTA_DIR
+	@rm $(PENTA_DIR)/$(LOCTYPE)/$(LIB_PENTA)
+endif
 
 #Compile object files defined in OBJLIST.
 .f.o :
@@ -93,3 +96,7 @@ $(LIB_DIAGNO) :
 #Construct DKES library. 
 $(LIB_DKES) :
 	@cd $(DKES_DIR); make $(TYPE); cd $(LOCTYPE); ar -cruv $(LIB_DKES) *.o
+   
+#Construct PENTA library. 
+$(LIB_PENTA) :
+	@cd $(PENTA_DIR); make $(TYPE); cd $(LOCTYPE); ar -cruv $(LIB_PENTA) *.o

From 96ef2082aaf0baa6e0d95c7379f4441cda0cbaac Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 26 Aug 2024 10:08:35 +0900
Subject: [PATCH 06/47] PENTA: Fixed call to vmec_2 routine.

---
 PENTA/Sources/penta_imp.f | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/PENTA/Sources/penta_imp.f b/PENTA/Sources/penta_imp.f
index b37fb7632..7553a7c5b 100644
--- a/PENTA/Sources/penta_imp.f
+++ b/PENTA/Sources/penta_imp.f
@@ -173,7 +173,8 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
       allocate(u_theta(num_species),u_zeta(num_species))
 
       !read input files
-      call read_vmec_file(js,run_ident)
+      !call read_vmec_file(js,run_ident)
+      call read_vmec_file_2(js,run_ident)
       call read_pprof_file(js,pprof_char,num_ion_species,roa_surf,arad)
       call read_lmn_star_files(coeff_ext)
       call read_Utilde2_file(roa_surf,U2)

From e7aca022fa09f1f10273a8f588e196ce4181add0 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 26 Aug 2024 10:08:56 +0900
Subject: [PATCH 07/47] PENTA: Added routine to set profiles via subroutine
 call.

---
 PENTA/Sources/read_input_file_mod.f | 97 ++++++++++++++++++++++++++++-
 1 file changed, 94 insertions(+), 3 deletions(-)

diff --git a/PENTA/Sources/read_input_file_mod.f b/PENTA/Sources/read_input_file_mod.f
index 3b00accf8..bf9509ad6 100644
--- a/PENTA/Sources/read_input_file_mod.f
+++ b/PENTA/Sources/read_input_file_mod.f
@@ -70,8 +70,8 @@ subroutine read_vmec_file(js,run_ident)
       integer(iknd) :: js
       character(60) :: run_ident
       !local variables
-      integer(iknd) :: j, js_min, js_max
-	integer(iknd), dimension(:), allocatable :: js_vmec
+      integer(iknd) :: j, js_min, js_max 
+      integer(iknd), dimension(:), allocatable :: js_vmec
       real(rknd), dimension(:), allocatable :: r_vmec, roa_vmec
      1 ,chip_vmec, psip_vmec, btheta_vmec, bzeta_vmec, vp_vmec, bsq_vmec
      2 ,iota_vmec
@@ -125,7 +125,7 @@ subroutine read_vmec_file_2(js,run_ident)
       character(60) :: run_ident
       !local variables
       integer(iknd) :: j, js_min, js_max, ierr, u, v, mn
-	integer(iknd), dimension(:), allocatable :: js_vmec
+      integer(iknd), dimension(:), allocatable :: js_vmec
 !      real(rknd), dimension(:), allocatable :: r_vmec, roa_vmec
 !     1 ,chip_vmec, psip_vmec, btheta_vmec, bzeta_vmec, vp_vmec, bsq_vmec
 !     2 ,iota_vmec
@@ -284,6 +284,97 @@ subroutine read_pprof_file(js,pprof_char,nis,roa_surf,arad)
       end subroutine read_pprof_file
 c
 c----------------------------------------------------------------------------
+c   Reads the file "plasma_profiles*.dat" and assigns plasma parameters for the
+c     current surface.  Variables are passed using module pprof_pass
+c----------------------------------------------------------------------------
+c
+      subroutine set_pprof(np_prof,nis,roa_prof,ne_prof,Te_prof,
+     1                     ni_local,Ti_local,roa_surf,arad)
+      use penta_kind_mod
+      use pprof_pass
+      use bspline
+      use io_unit_spec
+      implicit none
+      ! Input Parameters
+      INTEGER(iknd) :: np_prof
+      INTEGER(iknd) :: nis
+      REAL(rknd), DIMENSION(np_prof) :: roa_prof
+      REAL(rknd), DIMENSION(np_prof) :: ne_prof
+      REAL(rknd), DIMENSION(np_prof) :: Te_prof
+      REAL(rknd), DIMENSION(np_prof,nis) :: ni_local
+      REAL(rknd), DIMENSION(np_prof,nis) :: Ti_local
+      INTEGER(iknd) :: js
+      REAL(rknd) :: roa_surf
+      REAL(rknd) :: arad
+      integer(iknd) :: ispec, kord_prof
+      real(rknd), dimension(:), allocatable ::  
+     1 Te_knot_array, spl_Te,  ne_knot_array,
+     2 spl_ne, ni_knot_array, spl_ni, Ti_knot_array, spl_Ti
+
+      ! Some global helpers for ions (Not sure these are really needed)
+      IF (ALLOCATED(ni_prof)) DEALLOCATE(ni_prof)
+      IF (ALLOCATED(Ti_prof)) DEALLOCATE(Ti_prof)
+      ALLOCATE(ni_prof(np_prof,nis),Ti_prof(np_prof,nis))
+      ni_prof = ni_local
+      Ti_prof = Ti_local
+
+      !spline fit ne,Te,Ti,ni profiles and evaluate at r/a of current surface
+      kord_prof = 3 !spline order for profile fitting
+      allocate(ne_knot_array(np_prof+kord_prof),spl_ne(np_prof))
+      allocate(Te_knot_array(np_prof+kord_prof),spl_Te(np_prof))
+      allocate(ni_knot_array(np_prof+kord_prof),spl_ni(np_prof))
+      allocate(Ti_knot_array(np_prof+kord_prof),spl_Ti(np_prof))
+
+      !fit electron profiles
+      call dbsnak(np_prof,roa_prof,kord_prof,ne_knot_array)
+      call dbsnak(np_prof,roa_prof,kord_prof,Te_knot_array)   
+      call dbsint(np_prof,roa_prof,ne_prof,kord_prof,
+     1            ne_knot_array,spl_ne)
+      call dbsint(np_prof,roa_prof,te_prof,kord_prof,
+     1            Te_knot_array,spl_Te)
+    
+      !loop over ion species, fit profiles and assign values
+      do ispec=1,nis
+        call dbsnak(np_prof,roa_prof,kord_prof,ti_knot_array)
+        call dbsnak(np_prof,roa_prof,kord_prof,ni_knot_array)
+        call dbsint(np_prof,roa_prof,ni_prof(:,ispec),kord_prof,
+     1            ni_knot_array,spl_ni)
+        call dbsint(np_prof,roa_prof,Ti_prof(:,ispec),kord_prof,
+     1            Ti_knot_array,spl_ti)
+        !evaluate spline fit at r/a of the test surface
+        ni(ispec) = dbsval(roa_surf,kord_prof,ni_knot_array,np_prof,
+     1    spl_ni)
+        Ti(ispec) = dbsval(roa_surf,kord_prof,ti_knot_array,np_prof,
+     1    spl_ti)
+        !evaluate derivatives (d/dr) at r/a
+        dnidr(ispec) = dbsder(1,roa_surf,kord_prof,ni_knot_array,
+     1                   np_prof,spl_ni)/arad
+        dTidr(ispec) = dbsder(1,roa_surf,kord_prof,Ti_knot_array,
+     1                   np_prof,spl_Ti)/arad
+      enddo
+ 
+      !evaluate spline fit at r/a of the test surface for electrons
+      ne = dbsval(roa_surf,kord_prof,ne_knot_array,np_prof,spl_ne)
+      Te = dbsval(roa_surf,kord_prof,te_knot_array,np_prof,spl_te)
+      !evaluate derivatives (d/dr) at r/a for electrons
+      dnedr = dbsder(1,roa_surf,kord_prof,ne_knot_array,
+     1                   np_prof,spl_ne)/arad
+      dTedr = dbsder(1,roa_surf,kord_prof,Te_knot_array,
+     1                   np_prof,spl_Te)/arad
+      !convert units to mks
+      ne=ne*1.e18_rknd
+      ni=ni*1.e18_rknd
+      dnedr=dnedr*1.e18_rknd
+      dnidr=dnidr*1.e18_rknd
+
+      !deallocate variables
+      deallocate(Te_knot_array,spl_Te)
+      deallocate(ne_knot_array,spl_ne)
+      deallocate(ni_knot_array,spl_ni)
+      deallocate(Ti_knot_array, spl_Ti)
+      end subroutine set_pprof
+c
+c----------------------------------------------------------------------------
 c   Reads the file *star_lijs_*** files and assigns variables for passing
 c     using module coeff_var_pass
 c----------------------------------------------------------------------------

From 7cd76c88b47efea6b9e599e2fc4f235ae8ed5e27 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 28 Aug 2024 10:34:34 +0900
Subject: [PATCH 08/47] PENTA: Added routine to set LMNIJ coefficients.

---
 PENTA/Sources/read_input_file_mod.f | 48 +++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/PENTA/Sources/read_input_file_mod.f b/PENTA/Sources/read_input_file_mod.f
index bf9509ad6..22e652943 100644
--- a/PENTA/Sources/read_input_file_mod.f
+++ b/PENTA/Sources/read_input_file_mod.f
@@ -465,5 +465,53 @@ subroutine read_lmn_star_files(coeff_ext)
       num_cm=size(cmul_ms); num_em=size(efield_ms)
       num_cn=size(cmul_ns); num_en=size(efield_ns)
       end subroutine read_lmn_star_files
+c
+c----------------------------------------------------------------------------
+c   Assigns variables for passing using module coeff_var_pass
+c----------------------------------------------------------------------------
+c
+      subroutine set_lmn_star_files(nc,ne,ifile,cmul_vec,efield_vec,
+     1                              coef2d)
+      use penta_kind_mod
+      use coeff_var_pass
+      use io_unit_spec
+      implicit none
+      ! Input parameters
+      INTEGER, INTENT(IN) :: nc
+      INTEGER, INTENT(IN) :: ne
+      INTEGER, INTENT(IN) :: ifile ! 1=L; 2=M; 3=N
+      REAL(rknd), DIMENSION(nc), INTENT(IN) :: cmul_vec
+      REAL(rknd), DIMENSION(ne), INTENT(IN) :: efield_vec
+      REAL(rknd), DIMENSION(nc,ne), INTENT(IN) :: coef2d
+
+      IF (ifile == 1) THEN
+         allocate(cmul_ls(nc))
+         allocate(efield_ls(ne))
+         allocate(coef2d_ls(nc,ne))
+         cmul_ls=cmul_vec
+         efield_ls=efield_vec
+         coef2d_ls=coef2d
+         num_cl=size(cmul_ls); num_el=size(efield_ls)
+      ELSEIF (ifile == 2) THEN
+         allocate(cmul_ms(nc))
+         allocate(efield_ms(ne))
+         allocate(coef2d_ms(nc,ne))
+         cmul_ms=cmul_vec
+         efield_ms=efield_vec
+         coef2d_ms=coef2d
+         num_cm=size(cmul_ms); num_em=size(efield_ms)
+      ELSEIF (ifile == 3) THEN
+         allocate(cmul_ns(nc))
+         allocate(efield_ns(ne))
+         allocate(coef2d_ns(nc,ne))
+         cmul_ns=cmul_vec
+         efield_ns=efield_vec
+         coef2d_ns=coef2d
+         num_cn=size(cmul_ns); num_en=size(efield_ns)
+      ELSE
+         WRITE(6,*) 'set_lmn_star_files: Unknown ifile=',ifile
+      END IF
+      RETURN
+      end subroutine set_lmn_star_files
 
       end module read_input_file_mod
\ No newline at end of file

From 9a3974457d5e5778b1448d7173a1a1bb45f7b13f Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 28 Aug 2024 10:35:26 +0900
Subject: [PATCH 09/47] PENTA: Cleanup of routine a bit.

---
 PENTA/Sources/penta_imp.f | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/PENTA/Sources/penta_imp.f b/PENTA/Sources/penta_imp.f
index 7553a7c5b..31477113b 100644
--- a/PENTA/Sources/penta_imp.f
+++ b/PENTA/Sources/penta_imp.f
@@ -339,7 +339,6 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
 
         !write fluxes vs Er
         write(str_num,*) num_ion_species*2+3
-	!write(str_num,'(i)') num_ion_species*2+3
         format_tmp='(f7.4,' // trim(adjustl(str_num)) // '(" ",e15.7))'
         write(iu_fvEr_out,format_tmp) roa_surf,Er_test/100._rknd,
      1      gamma_e(ie),gamma_i(:,ie),q_e(ie),q_i(:,ie)
@@ -430,7 +429,6 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
 
         !write fluxes to file "flux_vs_roa"
         write(str_num,*) 2*num_ion_species+5
-	 !write(str_num,'(i)') 2*num_ion_species+5
         format_tmp='(f7.4,' // trim(adjustl(str_num)) // '(" ",e15.7))'
         write(iu_flux_out,format_tmp) roa_surf,Er_test/100._rknd,
      1    eaEr_o_kTe,gamma_e_ambi(iroot),q_e_ambi(iroot),
@@ -438,7 +436,6 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
 
         !write flows to file "flows_vs_roa"
         write(str_num,*) 4*num_ion_species+6
-	!write(str_num,'(i)') 4*num_ion_species+6
         format_tmp='(f7.4,' // trim(adjustl(str_num)) // '(" ",e15.7))'
         write(iu_flows_out,format_tmp) roa_surf,Er_test/100._rknd,
      1    eaEr_o_kTe,B_uprle(iroot),B_uprli(:,iroot),B_qprle(iroot),
@@ -447,16 +444,13 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
 
 
       !write output files
-      !"plasma_profiles_check"
-      !write(str_num,'(i)') 4*num_ion_species+5
-	write(str_num,*) 4*num_ion_species+5
+      write(str_num,*) 4*num_ion_species+5
       format_tmp='(' // trim(adjustl(str_num)) // '(" ",e15.7))'
       write(iu_pprof_out,format_tmp) roa_surf,Te,ne,dnedr,dTedr,
      1  Ti,ni,dnidr,dTidr
 
       !write to screen
-      !write(str_num,'(i)') num_roots
-	write(str_num,*) num_roots
+      write(str_num,*) num_roots
       format_tmp='(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.4))'
       write(*,format_tmp) roa_surf,er_roots/100._rknd
 

From 0c45d24cdf16182f5d5d47a6ac847af76a201fca Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 28 Aug 2024 11:01:51 +0900
Subject: [PATCH 10/47] PENTA: Changed name for VMEC reading routine.

---
 PENTA/Sources/penta_imp.f | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PENTA/Sources/penta_imp.f b/PENTA/Sources/penta_imp.f
index 31477113b..b88025e37 100644
--- a/PENTA/Sources/penta_imp.f
+++ b/PENTA/Sources/penta_imp.f
@@ -174,7 +174,7 @@ SUBROUTINE penta_imp(coeff_ext, Er_min, Er_max, js, i_append,
 
       !read input files
       !call read_vmec_file(js,run_ident)
-      call read_vmec_file_2(js,run_ident)
+      call read_vmec_file_wout(js,run_ident)
       call read_pprof_file(js,pprof_char,num_ion_species,roa_surf,arad)
       call read_lmn_star_files(coeff_ext)
       call read_Utilde2_file(roa_surf,U2)

From a4cb861007488e7ad016c23c5f9eaf750c8d82bd Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 28 Aug 2024 11:02:29 +0900
Subject: [PATCH 11/47] PENTA: Changed VMEC reading routine name and added
 Utilde2 setting routine.

---
 PENTA/Sources/penta_main.f          |  9 ++++
 PENTA/Sources/read_input_file_mod.f | 83 ++++++++++++++++++-----------
 2 files changed, 60 insertions(+), 32 deletions(-)

diff --git a/PENTA/Sources/penta_main.f b/PENTA/Sources/penta_main.f
index 541f6a2dd..e49aa383a 100644
--- a/PENTA/Sources/penta_main.f
+++ b/PENTA/Sources/penta_main.f
@@ -88,11 +88,16 @@
 c   2024 Notes
 c    - Created PENTA_IMP_MAIN program and changed PENTA_IMP to a
 c      callable subroutine.
+c    - Can read wout files instead of profile_data_****
+c    - Routine to set profiles instead of reading plasma_profiles_****
+c    - Routine to set L/M/NIJ coefficients instead of reading them.
+c    - Routine to set Utilde2 value instead of reading from file.
 c
 cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
     
       PROGRAM PENTA_MAIN
       use penta_kind_mod
+      USE read_wout_mod, ONLY: read_wout_deallocate
       IMPLICIT NONE
       integer(iknd) :: numargs, js, i_append
       real(rknd) :: Er_min, Er_max, B_Eprl
@@ -122,5 +127,9 @@ PROGRAM PENTA_MAIN
       ! Call subroutine
       CALL PENTA_IMP(coeff_ext, Er_min, Er_max, js, i_append, 
      1               run_ident, pprof_char, B_Eprl)
+
+      ! DEALLOCATE VMEC DATA
+      CALL read_wout_deallocate
+
       END PROGRAM PENTA_MAIN
 
diff --git a/PENTA/Sources/read_input_file_mod.f b/PENTA/Sources/read_input_file_mod.f
index 22e652943..bc204c093 100644
--- a/PENTA/Sources/read_input_file_mod.f
+++ b/PENTA/Sources/read_input_file_mod.f
@@ -57,6 +57,40 @@ subroutine read_Utilde2_file(roa_test,U2)
       end subroutine read_Utilde2_file
 c
 c----------------------------------------------------------------------------
+c   Sets the file "Utilde2_profile" and returns <U**2> for the run surface
+c----------------------------------------------------------------------------
+c
+      subroutine set_Utilde2_file(num_pts,roa_Utilde,U_tilde2,
+     1                            roa_test,U2)
+      use penta_kind_mod
+      use io_unit_spec
+      implicit none
+      ! Input parameters
+      INTEGER(iknd), INTENT(IN) :: num_pts
+      REAL(rknd), DIMENSION(num_pts), INTENT(IN) :: roa_Utilde
+      REAL(rknd), DIMENSION(num_pts), INTENT(IN) :: U_tilde2
+      REAL(rknd), INTENT(IN) :: roa_test
+      REAL(rknd), INTENT(OUT) :: U2
+      !dummy variables
+      !local varibles
+      integer(iknd) :: j, js_surf, num_pts, kord_prof
+      real(rknd), dimension(:), allocatable :: U2_knot_array, spl_U2
+
+      !spline fit profile and evaluate at r/a of current surface
+      kord_prof = 3 !spline order
+      allocate(U2_knot_array(num_pts+kord_prof))
+      allocate(spl_U2(num_pts))
+      call dbsnak(num_pts,roa_Utilde,kord_prof,U2_knot_array)
+      call dbsint(num_pts,roa_Utilde,U_tilde2,kord_prof,
+     1            U2_knot_array,spl_U2)
+      U2 = dbsval(roa_test,kord_prof,U2_knot_array,num_pts,
+     1    spl_U2)
+
+      !deallocate variables
+      deallocate(U2_knot_array,spl_U2)
+      end subroutine set_Utilde2_file
+c
+c----------------------------------------------------------------------------
 c   Reads the file "profile_data_***" and assigns VMEC variables, passed
 c     using module vmec_var_pass
 c----------------------------------------------------------------------------
@@ -108,7 +142,7 @@ end subroutine read_vmec_file
 c   Reads the wout file for vmec information (SAL 05/30/13)
 c----------------------------------------------------------------------------
 c
-      subroutine read_vmec_file_2(js,run_ident)
+      subroutine read_vmec_file_wout(js,run_ident)
       use vmec_var_pass
       use penta_kind_mod
       use io_unit_spec
@@ -118,7 +152,8 @@ subroutine read_vmec_file_2(js,run_ident)
      3                          Rmajor_vmec => Rmajor,
      4                          Aminor_vmec => Aminor,
      5                          phi_vmec => phi, bmnc, mnmax_nyq, gmnc,
-     6                          xm_nyq, xn_nyq, ns_vmec => ns
+     6                          xm_nyq, xn_nyq, ns_vmec => ns,
+     7                          lwout_opened
       implicit none
       !dummy variables
       integer(iknd) :: js
@@ -126,37 +161,23 @@ subroutine read_vmec_file_2(js,run_ident)
       !local variables
       integer(iknd) :: j, js_min, js_max, ierr, u, v, mn
       integer(iknd), dimension(:), allocatable :: js_vmec
-!      real(rknd), dimension(:), allocatable :: r_vmec, roa_vmec
-!     1 ,chip_vmec, psip_vmec, btheta_vmec, bzeta_vmec, vp_vmec, bsq_vmec
-!     2 ,iota_vmec
       REAL(rknd) :: TWOPI, top, bottom, theta, zeta, arg, cs_arg,
      1              jacob_vmec, bbf
       character(60) :: vmec_fname, ch_dum, tb = char(9)
+      INTEGER(iknd), PARAMETER :: nu_int = 360
+      INTEGER(iknd), PARAMETER :: nv_int = 360
 
+      ! Initializations
       TWOPI = 8*ATAN(1.0_rknd)
-      !Read VMEC profile data file 
-!      vmec_fname = "profile_data_" // run_ident
-!      open(unit=iu_vmec,file=vmec_fname,status="old")
-      CALL read_wout_file(TRIM(run_ident),ierr)
-      
-!      read(iu_vmec,*) js_min, js_max
-!      allocate(js_vmec(js_max),r_vmec(js_max),roa_vmec(js_max))
-!      allocate(chip_vmec(js_max),psip_vmec(js_max),btheta_vmec(js_max))
-!      allocate(bzeta_vmec(js_max),vp_vmec(js_max),bsq_vmec(js_max))
-!      allocate(iota_vmec(js_max))
-!      read(iu_vmec,*) arad, Rmajor
-!      read(iu_vmec,'(a10)') ch_dum
-!      do j = js_min,js_max
-!        read(iu_vmec,'(i4,9(a1,e15.7))') js_vmec(j),tb,r_vmec(j),tb,
-!     1  roa_vmec(j),tb,chip_vmec(j),tb,psip_vmec(j),tb,btheta_vmec(j),
-!     2    tb,bzeta_vmec(j),tb,vp_vmec(j),tb,bsq_vmec(j),tb,iota_vmec(j)
-!      end do
-!      close(iu_vmec)
+      top = 0.0
+      bottom = 0.0
+
+      !Read VMEC wout data file 
+      IF (.not. lwout_opened) CALL read_wout_file(TRIM(run_ident),ierr)
 
       ! Assign variables for the current surface
       chip = iota_vmec(js)*phipf_vmec(js);  !note this only works for non-RFP
-      psip = phipf_vmec(js)  
-      ! bsq = bsq_vmec(js)
+      psip = phipf_vmec(js)
       btheta = btheta_vmec(js); bzeta = bzeta_vmec(js)
       iota = iota_vmec(js);
       roa_surf = sqrt(phi_vmec(js)/phi_vmec(ns_vmec))
@@ -164,11 +185,12 @@ subroutine read_vmec_file_2(js,run_ident)
       vol_p = vp_vmec(js)
       Rmajor = Rmajor_vmec
       arad = Aminor_vmec
-      ! Now calc Bsq
+
+      ! Now calc <Bsq> = int(B*B*sqrt(g)/sqrt(g))
       bsq = 0.0
-      DO v = 1, 360
+      DO v = 1, nv_int
          zeta = TWOPI*REAL(v-1)/359.
-         DO u = 1, 360
+         DO u = 1, nu_int
             theta = TWOPI*REAL(u-1)/359.
             bbf = 0.0; jacob_vmec = 0.0;
             DO mn = 1, mnmax_nyq
@@ -182,10 +204,7 @@ subroutine read_vmec_file_2(js,run_ident)
          END DO
       END DO
       bsq = top/bottom
-      !deallocate variables
-!      deallocate(js_vmec, r_vmec, roa_vmec, chip_vmec, psip_vmec)
-!      deallocate(btheta_vmec, bzeta_vmec, vp_vmec, bsq_vmec,iota_vmec)
-      end subroutine read_vmec_file_2
+      end subroutine read_vmec_file_wout
 c
 c----------------------------------------------------------------------------
 c   Reads the file "plasma_profiles*.dat" and assigns plasma parameters for the

From 308d4ac5c500fcd4e45927bbddcbf8209eb3d238 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 28 Aug 2024 11:04:16 +0900
Subject: [PATCH 12/47] PENTA: Fixed bug

---
 PENTA/Sources/read_input_file_mod.f | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PENTA/Sources/read_input_file_mod.f b/PENTA/Sources/read_input_file_mod.f
index bc204c093..c6394c73e 100644
--- a/PENTA/Sources/read_input_file_mod.f
+++ b/PENTA/Sources/read_input_file_mod.f
@@ -73,7 +73,7 @@ subroutine set_Utilde2_file(num_pts,roa_Utilde,U_tilde2,
       REAL(rknd), INTENT(OUT) :: U2
       !dummy variables
       !local varibles
-      integer(iknd) :: j, js_surf, num_pts, kord_prof
+      integer(iknd) :: kord_prof
       real(rknd), dimension(:), allocatable :: U2_knot_array, spl_U2
 
       !spline fit profile and evaluate at r/a of current surface

From 536471ce8ff5e2c2fc115db1e4ff9d85512e0953 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 2 Sep 2024 14:04:32 +0900
Subject: [PATCH 13/47] PENTA: Added PENTA input module.

---
 PENTA/ObjectList                    |   1 +
 PENTA/PENTA.dep                     |   5 ++
 PENTA/Sources/penta_functions_mod.f |   6 +-
 PENTA/Sources/penta_input_mod.f     | 103 ++++++++++++++++++++++++++++
 4 files changed, 112 insertions(+), 3 deletions(-)
 create mode 100644 PENTA/Sources/penta_input_mod.f

diff --git a/PENTA/ObjectList b/PENTA/ObjectList
index 6a0b86914..7b008d112 100644
--- a/PENTA/ObjectList
+++ b/PENTA/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+penta_input_mod.o \
 penta_main.o \
 penta_functions_mod.o \
 penta_modules.o \
diff --git a/PENTA/PENTA.dep b/PENTA/PENTA.dep
index 960e6f136..04320ae86 100644
--- a/PENTA/PENTA.dep
+++ b/PENTA/PENTA.dep
@@ -13,6 +13,11 @@ read_input_file_mod.o : \
       bspline90_22.o \
       penta_modules.o \
       ../../LIBSTELL/$(LOCTYPE)/read_wout_mod.o
+
+
+penta_input_mod.o : \
+      penta_modules.o \
+      ../../LIBSTELL/$(LOCTYPE)/safe_open_mod.o
       
 
 penta_subroutines.o : \
diff --git a/PENTA/Sources/penta_functions_mod.f b/PENTA/Sources/penta_functions_mod.f
index 962270338..f94632a24 100644
--- a/PENTA/Sources/penta_functions_mod.f
+++ b/PENTA/Sources/penta_functions_mod.f
@@ -1,7 +1,7 @@
       module penta_functions_mod
-	use penta_kind_mod
-	implicit none
-	contains
+      use penta_kind_mod
+      implicit none
+      contains
 
 
 cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
diff --git a/PENTA/Sources/penta_input_mod.f b/PENTA/Sources/penta_input_mod.f
new file mode 100644
index 000000000..e4640084d
--- /dev/null
+++ b/PENTA/Sources/penta_input_mod.f
@@ -0,0 +1,103 @@
+      module penta_input_mod
+      use penta_kind_mod
+      implicit none      
+      INTEGER(iknd), parameter ::  num_ion_max = 20_iknd    !Maximum number of ion species to be read from namelist file
+      INTEGER(iknd) :: num_ion_species ! Number of ion species
+      REAL(rknd), DIMENSION(num_ion_max) :: Z_ion_init,miomp_init  
+
+      namelist / ion_params / num_ion_species,Z_ion_init,miomp_init
+      contains
+
+      SUBROUTINE init_ion_params_nml
+      IMPLICIT NONE
+      num_ion_species = 1
+      Z_ion_init = 1.0_rknd
+      miomp_init = 1.0_rknd
+      END SUBROUTINE init_ion_params_nml
+
+      SUBROUTINE read_ion_params_nml(filename,istat)
+      USE safe_open_mod
+      IMPLICIT NONE
+      ! Subroutine parameters
+      CHARACTER(256), INTENT(INOUT) :: filename
+      INTEGER(iknd), INTENT(INOUT) :: istat
+      ! Local Variables
+      LOGICAL :: lexist
+      INTEGER(iknd) :: iunit
+      CHARACTER(256) :: filename_local
+
+      ! Handle filename
+      filename_local = TRIM(filename)
+
+      !Check which file is available
+      INQUIRE(FILE=TRIM(filename_local),EXIST=lexist)
+      IF (.not. lexist) THEN
+         WRITE(6,*) '   -Could not open input file trying ion_params'
+         filename_local = 'ion_params'
+         INQUIRE(FILE=TRIM(filename_local),EXIST=lexist)
+         IF (.not. lexist) THEN
+            WRITE(6,*) '   -Could not open ion_params file'
+            istat = -1
+            RETURN
+         ENDIF
+      ENDIF
+
+      ! Open and read the file
+      CALL safe_open(iunit,istat,TRIM(filename_local),'old',
+     1                  'formatted')
+      IF (istat /= 0) THEN
+         WRITE(6,*) 'ERROR: Could no open: ',TRIM(filename_local)
+         RETURN
+      ENDIF
+      READ(iunit,NML=ion_params,IOSTAT=istat)
+      IF (istat /= 0) THEN
+         WRITE(6,*) 'ERROR: ion_params in ',TRIM(filename_local)
+         !backspace(iu_nl)
+         !read(iu_nl,fmt='(A)') line
+         !write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
+         RETURN
+      ENDIF
+      CLOSE(iunit)
+      RETURN
+      END SUBROUTINE read_ion_params_nml
+
+      SUBROUTINE write_ion_params_nml(iunit)
+      IMPLICIT NONE
+      INTEGER(iknd), INTENT(inout) :: iunit
+      CHARACTER(LEN=*), PARAMETER :: outint  = "(2X,A,1X,'=',1X,I0)"
+      INTEGER(iknd) :: k
+      WRITE(iunit,'(A)') '&ION_PARAMS'
+      WRITE(iunit,'(A)') 
+     1'----------------------------------------------------------------'
+      WRITE(iunit,outint) 'NUM_ION_SPECIES',num_ion_species
+      WRITE(iunit,"(2X,A,1X,'=',4(1X,ES22.12E3))") 
+     1'Z_ION_INIT',(Z_ion_init(k), k=1,num_ion_species)
+      WRITE(iunit,"(2X,A,1X,'=',4(1X,ES22.12E3))") 
+     1'MIOMP_INIT',(miomp_init(k), k=1,num_ion_species)
+      WRITE(iunit,'(A)') '/\n'
+      END SUBROUTINE write_ion_params_nml
+
+      SUBROUTINE write_ion_params_namelist_byfile(filename)
+      USE safe_open_mod
+      IMPLICIT NONE
+      CHARACTER(LEN=*), INTENT(in) :: filename
+      INTEGER(iknd) :: iunit, istat
+      LOGICAL :: lexists
+      
+      iunit = 100
+      istat = 0
+      INQUIRE(FILE=TRIM(filename),exist=lexists)
+      IF (lexists) THEN
+         OPEN(unit=iunit, file=TRIM(filename), 
+     1        iostat=istat, status="old", position="append")
+      ELSE
+         OPEN(unit=iunit, file=TRIM(filename), 
+     1        iostat=istat, status="new")
+      END IF
+      IF (istat .ne. 0) RETURN
+      CALL write_ion_params_nml(iunit)
+      CLOSE(iunit)
+
+      RETURN
+      END SUBROUTINE write_ion_params_namelist_byfile
+      end module penta_input_mod
\ No newline at end of file

From 9b7a5fb7b8c70bd8af9eeb266317ff356ad9e41c Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 16 Oct 2024 13:48:57 +0200
Subject: [PATCH 14/47] LIBSTELL: Added thrift_globals.f90 for future python
 interfacing.

---
 LIBSTELL/LIBSTELL.dep                       |  3 +
 LIBSTELL/ObjectList                         |  1 +
 LIBSTELL/Sources/Modules/thrift_globals.f90 | 75 +++++++++++++++++++++
 3 files changed, 79 insertions(+)
 create mode 100644 LIBSTELL/Sources/Modules/thrift_globals.f90

diff --git a/LIBSTELL/LIBSTELL.dep b/LIBSTELL/LIBSTELL.dep
index 5b09cc036..f7016a4b2 100644
--- a/LIBSTELL/LIBSTELL.dep
+++ b/LIBSTELL/LIBSTELL.dep
@@ -52,6 +52,9 @@ beams3d_input_mod.o: \
 beams3d_globals.o :  \
       stel_kinds.o 
 
+thrift_globals.o : \
+      stel_kinds.o
+
 diagno_runtime.o :  \
       ezspline.o \
       stel_kinds.o 
diff --git a/LIBSTELL/ObjectList b/LIBSTELL/ObjectList
index a04acd792..79b36ba5c 100644
--- a/LIBSTELL/ObjectList
+++ b/LIBSTELL/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+thrift_globals.o \
 read_nescoil_mod.o \
 stellopt_targets.o \
 stellopt_vars.o \
diff --git a/LIBSTELL/Sources/Modules/thrift_globals.f90 b/LIBSTELL/Sources/Modules/thrift_globals.f90
new file mode 100644
index 000000000..5c252bc0f
--- /dev/null
+++ b/LIBSTELL/Sources/Modules/thrift_globals.f90
@@ -0,0 +1,75 @@
+!-----------------------------------------------------------------------
+!     Module:        thrift_globals
+!     Authors:       S. Lazerson (samuel.lazerson@gauss-fusion.com)
+!     Date:          10/16/2024
+!     Description:   This module contains the THRIFT global variables
+!                    needed by the input namelist.
+!-----------------------------------------------------------------------
+      MODULE thrift_globals
+!-----------------------------------------------------------------------
+!     Libraries
+!-----------------------------------------------------------------------
+      USE stel_kinds, ONLY: rprec
+      
+!-----------------------------------------------------------------------
+!     Module Variables
+!-----------------------------------------------------------------------
+      IMPLICIT NONE
+
+      ! Moved from thrift_vars
+      LOGICAL ::  lverbj
+      INTEGER ::  nrho, ntimesteps, n_eq, npicard
+      REAL(rprec) :: tstart, tend, jtol, picard_factor, boot_factor
+
+      ! Moved from thrift_vars (For ECCD in general)
+      INTEGER, PARAMETER :: ntime_ecrh = 200
+      REAL(rprec), DIMENSION(ntime_ecrh) :: PECRH_AUX_T, PECRH_AUX_F
+      REAL(rprec) :: ecrh_rc, ecrh_w
+
+      ! Moved from thrift_vars (for TRAVIS)
+      INTEGER, PARAMETER :: nsys   = 16
+      INTEGER :: nra_ecrh, nphi_ecrh
+      INTEGER, DIMENSION(nsys)     :: wmode_ecrh
+      REAL(rprec), DIMENSION(nsys) :: freq_ecrh, power_ecrh
+      REAL(rprec), DIMENSION(nsys,3)     :: antennaposition_ecrh, &
+                 targetposition_ecrh, rbeam_ecrh, rfocus_ecrh
+
+      ! Moved from thrift_vars (For DKES)
+      INTEGER, PARAMETER :: DKES_NS_MAX = 64
+      INTEGER, PARAMETER :: DKES_NSTAR_MAX = 32
+      INTEGER :: nruns_dkes
+      INTEGER, DIMENSION(:), POINTER :: DKES_rundex
+      INTEGER, DIMENSION(DKES_NS_MAX) :: DKES_K
+      REAL(rprec), DIMENSION(DKES_NSTAR_MAX) :: DKES_Erstar, DKES_Nustar
+
+      ! Moved from thrift_runtime
+      INTEGER :: nparallel_runs, mboz, nboz
+      CHARACTER(256) :: bootstrap_type, eccd_type, vessel_ecrh, &
+                        mirror_ecrh, targettype_ecrh, antennatype_ecrh
+
+
+
+      CONTAINS
+
+      ! These expose the global variables through ctypes
+      INTEGER FUNCTION getmaxtimeecrh()
+      IMPLICIT NONE
+      getmaxtimeecrh = ntime_ecrh
+      END FUNCTION getmaxtimeecrh
+      
+      INTEGER FUNCTION getmaxsys()
+      IMPLICIT NONE
+      getmaxsys = nsys
+      END FUNCTION getmaxsys
+      
+      INTEGER FUNCTION getmaxns()
+      IMPLICIT NONE
+      getmaxns = DKES_NS_MAX
+      END FUNCTION getmaxns
+      
+      INTEGER FUNCTION getmaxnstar()
+      IMPLICIT NONE
+      getmaxnstar =DKES_NSTAR_MAX
+      END FUNCTION getmaxnstar
+
+      END MODULE thrift_globals

From 81901ab1d98309ccb1bbf9ed89b3fc0c25d1cb1c Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 16 Oct 2024 13:56:24 +0200
Subject: [PATCH 15/47] LIBSTELL: Added thrift_input_mod.f90 to LIBSTELL

---
 LIBSTELL/LIBSTELL.dep                              |  5 +++++
 LIBSTELL/ObjectList                                |  1 +
 LIBSTELL/Sources/Modules/thrift_globals.f90        |  4 ++--
 .../Sources/Modules}/thrift_input_mod.f90          | 14 ++++++++++----
 4 files changed, 18 insertions(+), 6 deletions(-)
 rename {THRIFT/Sources => LIBSTELL/Sources/Modules}/thrift_input_mod.f90 (95%)

diff --git a/LIBSTELL/LIBSTELL.dep b/LIBSTELL/LIBSTELL.dep
index f7016a4b2..ddd059785 100644
--- a/LIBSTELL/LIBSTELL.dep
+++ b/LIBSTELL/LIBSTELL.dep
@@ -55,6 +55,11 @@ beams3d_globals.o :  \
 thrift_globals.o : \
       stel_kinds.o
 
+thrift_input_mod.o: \
+      stel_kinds.o \
+      safe_open_mod.o \
+      thrift_globals.o 
+
 diagno_runtime.o :  \
       ezspline.o \
       stel_kinds.o 
diff --git a/LIBSTELL/ObjectList b/LIBSTELL/ObjectList
index 79b36ba5c..829936646 100644
--- a/LIBSTELL/ObjectList
+++ b/LIBSTELL/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+thrift_input_mod.o \
 thrift_globals.o \
 read_nescoil_mod.o \
 stellopt_targets.o \
diff --git a/LIBSTELL/Sources/Modules/thrift_globals.f90 b/LIBSTELL/Sources/Modules/thrift_globals.f90
index 5c252bc0f..d60bbf5db 100644
--- a/LIBSTELL/Sources/Modules/thrift_globals.f90
+++ b/LIBSTELL/Sources/Modules/thrift_globals.f90
@@ -17,8 +17,8 @@ MODULE thrift_globals
       IMPLICIT NONE
 
       ! Moved from thrift_vars
-      LOGICAL ::  lverbj
-      INTEGER ::  nrho, ntimesteps, n_eq, npicard
+      LOGICAL ::  lverbj, leccd, lnbcd, lohmic
+      INTEGER ::  nrho, ntimesteps, n_eq, npicard, nsj
       REAL(rprec) :: tstart, tend, jtol, picard_factor, boot_factor
 
       ! Moved from thrift_vars (For ECCD in general)
diff --git a/THRIFT/Sources/thrift_input_mod.f90 b/LIBSTELL/Sources/Modules/thrift_input_mod.f90
similarity index 95%
rename from THRIFT/Sources/thrift_input_mod.f90
rename to LIBSTELL/Sources/Modules/thrift_input_mod.f90
index d52d86b2d..383214588 100644
--- a/THRIFT/Sources/thrift_input_mod.f90
+++ b/LIBSTELL/Sources/Modules/thrift_input_mod.f90
@@ -11,8 +11,7 @@ MODULE thrift_input_mod
 !     Libraries
 !-----------------------------------------------------------------------
       USE stel_kinds, ONLY: rprec
-      USE thrift_vars
-      USE thrift_runtime
+      USE thrift_globals
       USE safe_open_mod
 
 !-----------------------------------------------------------------------
@@ -107,16 +106,23 @@ SUBROUTINE read_thrift_input(filename, istat)
          INQUIRE(FILE=TRIM(filename),EXIST=lexist)
          IF (.not.lexist) stop 'Could not find input file'
          CALL safe_open(iunit,istat,TRIM(filename),'old','formatted')
-         IF (istat /= 0) CALL handle_err(NAMELIST_READ_ERR,'thrift_input in: '//TRIM(filename),istat)
+         IF (istat /= 0) THEN
+            WRITE(6,'(A)') 'ERROR opening file: ',TRIM(filename)
+            CALL FLUSH(6)
+            STOP
+         END IF
          READ(iunit,NML=thrift_input,IOSTAT=istat)
          IF (istat /= 0) THEN
+            WRITE(6,'(A)') 'ERROR reading namelist THRIFT_INPUT from file: ',TRIM(filename)
             backspace(iunit)
             read(iunit,fmt='(A)') line
             write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
-            CALL handle_err(NAMELIST_READ_ERR,'thrift_input in: '//TRIM(filename),istat)
+            CALL FLUSH(6)
+            STOP
          END IF
          CLOSE(iunit)
       END IF
+      
       CALL tolower(bootstrap_type)
       CALL tolower(eccd_type)
       leccd = eccd_type .ne. ''

From 41ff46d66222b8dfff3d3d7f66f089ff50070e3d Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 16 Oct 2024 14:17:40 +0200
Subject: [PATCH 16/47] THRIFT: Cleanup after creating thrift_globals.f90 in
 LIBSTELL

---
 THRIFT/ObjectList                 |  1 -
 THRIFT/Sources/thrift_runtime.f90 | 25 +++++++++++-----------
 THRIFT/Sources/thrift_vars.f90    | 35 +++++++++----------------------
 THRIFT/THRIFT.dep                 | 14 ++-----------
 4 files changed, 25 insertions(+), 50 deletions(-)

diff --git a/THRIFT/ObjectList b/THRIFT/ObjectList
index 634831d20..1da248bf7 100644
--- a/THRIFT/ObjectList
+++ b/THRIFT/ObjectList
@@ -21,7 +21,6 @@ thrift_vars.o \
 thrift_init.o \
 thrift_init_mpisubgroup.o \
 thrift_paraexe.o \
-thrift_input_mod.o \
 thrift_profiles_mod.o \
 thrift_interface_mod.o \
 thrift_funcs.o \
diff --git a/THRIFT/Sources/thrift_runtime.f90 b/THRIFT/Sources/thrift_runtime.f90
index 67c737160..c6a4eab77 100644
--- a/THRIFT/Sources/thrift_runtime.f90
+++ b/THRIFT/Sources/thrift_runtime.f90
@@ -8,16 +8,20 @@
 !     v0.00 11/XX/22 - Generally used to track major version information
 !-----------------------------------------------------------------------
 MODULE thrift_runtime
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     !     Libraries
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     USE stel_kinds, ONLY: rprec
+    USE thrift_globals, ONLY:   nparallel_runs, mboz, nboz, &
+                                bootstrap_type, eccd_type, vessel_ecrh, &
+                                mirror_ecrh, targettype_ecrh, &
+                                antennatype_ecrh
     USE mpi_params
     USE EZspline
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     !     Module Variables
     !          lverb         Logical to control screen output
-    !----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     IMPLICIT NONE
 
     INTEGER, PARAMETER :: MPI_CHECK = 0
@@ -68,20 +72,17 @@ MODULE thrift_runtime
     DOUBLE PRECISION, PARAMETER :: e_charge      = 1.60217662E-19 !e_c
 
     LOGICAL :: lverb, lvmec, lread_input, limas
-    INTEGER :: nprocs_thrift, nparallel_runs, mboz, nboz, ier_paraexe, &
+    INTEGER :: nprocs_thrift, ier_paraexe, &
                mytimestep, nsubsteps
     REAL(rprec) :: pi, pi2, invpi2, mu0, to3
-    CHARACTER(256) :: id_string, prof_string, bootstrap_type, &
-                      eccd_type, nbcd_type, &
-                      proc_string, vessel_ecrh, mirror_ecrh, &
-                      targettype_ecrh, antennatype_ecrh, &
-                      magdiag_coil
+    CHARACTER(256) :: id_string, prof_string, &
+                      nbcd_type, proc_string, magdiag_coil
 
     REAL(rprec), PARAMETER :: THRIFT_VERSION = 0.50 
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     !     Subroutines
     !          handle_err  Controls Program Termination
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
 CONTAINS
 
     SUBROUTINE handle_err(error_num, string_val, ierr)
diff --git a/THRIFT/Sources/thrift_vars.f90 b/THRIFT/Sources/thrift_vars.f90
index 21290a09c..f78663517 100644
--- a/THRIFT/Sources/thrift_vars.f90
+++ b/THRIFT/Sources/thrift_vars.f90
@@ -10,6 +10,14 @@ MODULE thrift_vars
     !     Libraries
     !-------------------------------------------------------------------
     USE stel_kinds, ONLY: rprec
+    USE thrift_globals, ONLY: lverbj, nrho, ntimesteps, n_eq, npicard, &
+        tstart, tend, jtol, picard_factor, boot_factor, ntime_ecrh, &
+        pecrh_aux_t, pecrh_aux_f, ecrh_rc, ecrh_w, nsys, nra_ecrh, &
+        nphi_ecrh, wmode_ecrh, freq_ecrh, power_ecrh, &
+        antennaposition_ecrh, targetposition_ecrh, rbeam_ecrh, &
+        rfocus_ecrh, DKES_NS_MAX, DKES_NSTAR_MAX, nruns_dkes, &
+        DKES_rundex, DKES_K, dkes_Erstar, dkes_Nustar, nsj, leccd, &
+        lnbcd, lohmic
     !-------------------------------------------------------------------
     !     Module Variables
     !          leccd            Calc Elec. Cyclo. Current Drive
@@ -56,10 +64,9 @@ MODULE thrift_vars
     !-------------------------------------------------------------------
     IMPLICIT NONE
 
-    LOGICAL :: leccd, lnbcd, lohmic, ldiagno, lscreen_subcodes, lverbj
+    LOGICAL :: ldiagno, lscreen_subcodes
     LOGICAL, DIMENSION(:), ALLOCATABLE :: lbooz
-    INTEGER :: ntimesteps, nrho, nsj,  npicard, n_eq,&
-             win_thrift_j,win_thrift_i,win_thrift_ugrid, &
+    INTEGER :: win_thrift_j,win_thrift_i,win_thrift_ugrid, &
              win_thrift_jplasma, win_thrift_iplasma, &
              win_thrift_jboot,   win_thrift_iboot,   &
              win_thrift_jeccd,   win_thrift_ieccd,   &
@@ -77,7 +84,6 @@ MODULE thrift_vars
              win_thrift_alpha1,  win_thrift_alpha2,   win_thrift_alpha3,   win_thrift_alpha4,   &
              win_thrift_matld,   win_thrift_matmd,    win_thrift_matud,    win_thrift_matrhs,   &
              win_thrift_bvav
-    REAL(rprec) :: tstart, tend, jtol, picard_factor, boot_factor
     REAL(rprec), DIMENSION(:), POINTER :: THRIFT_RHO(:), THRIFT_RHOFULL(:), THRIFT_PHIEDGE(:), &
                                           THRIFT_S(:),   THRIFT_SNOB(:),  THRIFT_T(:)
     REAL(rprec), DIMENSION(:,:), POINTER :: &
@@ -97,26 +103,5 @@ MODULE thrift_vars
                  THRIFT_MATLD,   THRIFT_MATMD,   THRIFT_MATUD,   THRIFT_MATRHS,  &
                  THRIFT_BVAV
 
-    ! For ECCD in general
-    INTEGER, PARAMETER :: ntime_ecrh = 200
-    REAL(rprec), DIMENSION(ntime_ecrh) :: PECRH_AUX_T, PECRH_AUX_F
-    REAL(rprec) :: ecrh_rc, ecrh_w
-
-    ! For TRAVIS
-    INTEGER, PARAMETER :: nsys   = 16
-    INTEGER :: nra_ecrh, nphi_ecrh
-    INTEGER, DIMENSION(nsys)     :: wmode_ecrh
-    REAL(rprec), DIMENSION(nsys) :: freq_ecrh, power_ecrh
-    REAL(rprec), DIMENSION(nsys,3)     :: antennaposition_ecrh, &
-                 targetposition_ecrh,rbeam_ecrh,rfocus_ecrh
-
-    ! For DKES
-    INTEGER, PARAMETER :: DKES_NS_MAX = 64
-    INTEGER, PARAMETER :: DKES_NSTAR_MAX = 32
-    INTEGER :: nruns_dkes
-    INTEGER, DIMENSION(:), POINTER :: DKES_rundex
-    INTEGER, DIMENSION(DKES_NS_MAX) :: DKES_K
-    REAL(rprec), DIMENSION(DKES_NSTAR_MAX) :: DKES_Erstar, DKES_Nustar
-
 
 END MODULE thrift_vars
diff --git a/THRIFT/THRIFT.dep b/THRIFT/THRIFT.dep
index 38ac7e9a9..018053f37 100644
--- a/THRIFT/THRIFT.dep
+++ b/THRIFT/THRIFT.dep
@@ -1,7 +1,6 @@
 thrift_bootsj.o : \
       thrift_runtime.o \
       thrift_vars.o \
-      thrift_input_mod.o \
       thrift_profiles_mod.o \
       thrift_equil.o \
       thrift_funcs.o \
@@ -27,7 +26,6 @@ thrift_boozer.o : \
 thrift_dkes.o : \
       thrift_runtime.o \
       thrift_vars.o \
-      thrift_input_mod.o \
       thrift_profiles_mod.o \
       thrift_equil.o \
       thrift_funcs.o \
@@ -78,7 +76,6 @@ thrift_evolve.o : \
 
 thrift_init.o : \
       thrift_runtime.o \
-      thrift_input_mod.o \
       thrift_vars.o \
       thrift_profiles_mod.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
@@ -88,17 +85,10 @@ thrift_init.o : \
 
 thrift_init_mpisubgroup.o : \
       thrift_runtime.o \
-      thrift_input_mod.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_params.o \
       $(LIB_DIR)/$(LOCTYPE)/safe_open_mod.o 
 
-thrift_input_mod.o : \
-      thrift_runtime.o \
-      thrift_vars.o \
-      $(LIB_DIR)/$(LOCTYPE)/stel_kinds.o \
-      $(LIB_DIR)/$(LOCTYPE)/safe_open_mod.o 
-
 thrift_interface_mod.o : \
       thrift_runtime.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
@@ -139,7 +129,6 @@ thrift_main.o : \
 
 thrift_paraexe.o : \
       thrift_runtime.o \
-      thrift_input_mod.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_params.o \
       $(LIB_DIR)/$(LOCTYPE)/vmec_input.o \
@@ -166,6 +155,7 @@ thrift_reinit_vmec.o : \
 
 thrift_runtime.o : \
       $(LIB_DIR)/$(LOCTYPE)/stel_kinds.o \
+      $(LIB_DIR)/$(LOCTYPE)/thrift_globals.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_params.o 
 
@@ -200,7 +190,6 @@ thrift_run_nbcd.o : \
 
 thrift_travis.o : \
       thrift_runtime.o \
-      thrift_input_mod.o \
       thrift_vars.o \
       thrift_equil.o \
       thrift_profiles_mod.o \
@@ -210,6 +199,7 @@ thrift_travis.o : \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o
 
 thrift_vars.o : \
+      $(LIB_DIR)/$(LOCTYPE)/thrift_globals.o \
       $(LIB_DIR)/$(LOCTYPE)/stel_kinds.o 
 
 thrift_write.o : \

From 1871667c038bbe17a9999c7a5b0aa781d24d7291 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 16 Oct 2024 14:18:04 +0200
Subject: [PATCH 17/47] THRIFT: Added cleanup routines from STELLOPT.

---
 THRIFT/Sources/thrift_interface_mod.f90 | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/THRIFT/Sources/thrift_interface_mod.f90 b/THRIFT/Sources/thrift_interface_mod.f90
index 13416ede5..89d0e272a 100644
--- a/THRIFT/Sources/thrift_interface_mod.f90
+++ b/THRIFT/Sources/thrift_interface_mod.f90
@@ -77,8 +77,26 @@ END SUBROUTINE thrift_init_mpi_split
 
       SUBROUTINE thrift_cleanup
       IMPLICIT NONE
+      CHARACTER(200) :: cmdtxt = ""
       ! Clean up
       ierr_mpi = 0
+      ! Remove files and cleanup directory
+!DEC$ IF DEFINED (STELZIP)
+      IF (myid == master) THEN
+      ! Remove the *_opt* files
+         WRITE(6,*) ' Cleaning up files'; CALL FLUSH(6); ier = 0; ierr_mpi = 0; cmdtxt=''
+         CALL EXECUTE_COMMAND_LINE("rm -rf dcon* jxbout* mercier*",WAIT=.TRUE.,EXITSTAT=ier,CMDSTAT=ierr_mpi,CMDMSG=cmdtxt)
+         WRITE(6,*) ' rm: EXITSTAT=',ier,' CMDSTAT=',ierr_mpi; CALL FLUSH(6)
+         WRITE(6,*) '     MESSAGE: ',TRIM(cmdtxt); CALL FLUSH(6)
+         ! Zip up the results
+         WRITE(6,*) ' Zipping files'; CALL FLUSH(6); ier = 0; ierr_mpi = 0; cmdtxt=''
+         CALL EXECUTE_COMMAND_LINE("zip -r thrift_files.zip *",WAIT=.TRUE.,EXITSTAT=ier,CMDSTAT=ierr_mpi,CMDMSG=cmdtxt)
+         WRITE(6,*) ' zip: EXITSTAT=',ier,' CMDSTAT=',ierr_mpi; CALL FLUSH(6)
+         WRITE(6,*) '     MESSAGE: ',TRIM(cmdtxt); CALL FLUSH(6)
+         ier = 0; ierr_mpi=0
+      END IF
+!DEC$ ENDIF
+
       !CALL thrift_free(MPI_COMM_SHARMEM)
 #if defined(MPI_OPT)
       !CALL MPI_BARRIER(MPI_COMM_MYWORLD,ierr_mpi)

From 2bc3ba67e0969231fd82950a38ebddbc7e9416aa Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 10:29:04 +0200
Subject: [PATCH 18/47] PENTA: Added interface module to simplify interfacing
 to other codes.

---
 PENTA/ObjectList                      |   1 +
 PENTA/PENTA.dep                       |  12 +
 PENTA/Sources/penta_interface_mod.f90 | 877 ++++++++++++++++++++++++++
 3 files changed, 890 insertions(+)
 create mode 100644 PENTA/Sources/penta_interface_mod.f90

diff --git a/PENTA/ObjectList b/PENTA/ObjectList
index ddd055cf3..c74604b38 100644
--- a/PENTA/ObjectList
+++ b/PENTA/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+penta_interface_mod.o \
 bspline.o \
 coeff_var_pass.o \
 io_unit_spec.o \
diff --git a/PENTA/PENTA.dep b/PENTA/PENTA.dep
index 322013ea5..80b076008 100644
--- a/PENTA/PENTA.dep
+++ b/PENTA/PENTA.dep
@@ -20,6 +20,18 @@ penta.o : \
       penta_math_routines_mod.o \
       penta_subroutines.o
 
+penta_interface_mod.o : \
+      penta_kind_mod.o \
+      io_unit_spec.o \
+      read_input_file_mod.o \
+      vmec_var_pass.o \
+      pprof_pass.o \
+      coeff_var_pass.o \
+      phys_const.o \
+      penta_functions_mod.o \
+      penta_math_routines_mod.o \
+      penta_subroutines.o
+
 penta_functions_mod.o : \
       penta_kind_mod.o \
       phys_const.o \
diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
new file mode 100644
index 000000000..ca80e2055
--- /dev/null
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -0,0 +1,877 @@
+!-----------------------------------------------------------------------
+!     Module:        PENTA_INTERFACE_MOD
+!     Authors:       S. Lazerson
+!     Date:          10/16/2022
+!     Description:   Module provides a subroutine based interface to
+!                    the PENTA code.
+!-----------------------------------------------------------------------
+MODULE PENTA_INTERFACE_MOD
+!-----------------------------------------------------------------------
+!     Libraries
+!-----------------------------------------------------------------------
+   USE penta_kind_mod
+
+!-----------------------------------------------------------------------
+!     Module Variables
+!-----------------------------------------------------------------------
+   IMPLICIT NONE
+
+   INTEGER(iknd), PARAMETER :: NUM_ROOTS_MAX = 10_iknd
+   INTEGER(iknd), PARAMETER :: NUM_ION_MAX = 20_iknd
+
+   LOGICAL ::  input_is_Er, log_interp, use_quanc8, read_U2_file, &
+      flux_cap, output_QoT_vs_Er, Add_Spitzer_to_D33, use_beam
+   INTEGER(iknd) ::  num_Er_test, numKsteps, kord_pprof, keord, kcord, &
+      numargs, js, i_append, num_species, num_ion_species, Smax, &
+      iocheck, ie, ind_X, ind_A, ispec1, min_ind, iroot, num_roots
+   REAL(rknd) ::  Kmin, Kmax, epsabs, epsrel, Er_min, Er_max, B_Eprl, &
+      U2, vth_e, loglambda, Er_test, abs_Er, min_Er, eaEr_o_kTe, cmin, &
+      cmax, emin, emax, sigma_par, sigma_par_Spitzer, J_BS
+   REAL(rknd), DIMENSION(NUM_ION_MAX) ::  Z_ion_init, miomp_init
+   REAL(rknd), DIMENSION(NUM_ROOTS_MAX) ::  Er_roots
+   REAL(rknd), DIMENSION(:), ALLOCATABLE :: ion_mass, Z_ion, vth_i, &
+      charges, dens, masses, temps, vths, dTdrs, dndrs, Xvec, Avec, &
+      Flows, Gammas, QoTs, xt_c, xt_e, Gamma_e_vs_Er, QoT_e_vs_Er, &
+      Er_test_vals, Jprl_ambi, sigma_par_ambi, sigma_par_Spitzer_ambi, &
+      J_BS_ambi
+   REAL(rknd), DIMENSION(:,:), ALLOCATABLE :: lmat, Dspl_D11, Dspl_D13, &
+      Dspl_D31, Dspl_D33, Dspl_Dex, Dspl_Dua, Dspl_Drat, Dspl_Drat2, &
+      Dspl_logD11, Dspl_logD33, cmesh, gamma_i_vs_er, QoT_i_vs_Er, &
+      Flows_ambi, gammas_ambi, QoTs_ambi, Jprl_parts, upol, utor
+   CHARACTER(LEN=10) :: Method
+   CHARACTER(LEN=100) :: arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, &
+      arg9, coeff_ext, run_ident, pprof_char, fpos, fstatus, str_num
+
+!-----------------------------------------------------------------------
+!     Module Namelists
+!-----------------------------------------------------------------------
+   NAMELIST /ion_params/ num_ion_species, Z_ion_init, miomp_init
+   NAMELIST /run_params/ input_is_Er, log_interp, use_quanc8, &
+      read_U2_file, Add_Spitzer_to_D33, num_Er_test, numKsteps, &
+      kord_pprof, keord, kcord, Kmin, Kmax, epsabs, epsrel, Method, &
+      flux_cap, output_QoT_vs_Er, use_beam
+
+!-----------------------------------------------------------------------
+!     SUBROUTINES
+!-----------------------------------------------------------------------
+   CONTAINS
+
+   SUBROUTINE init_penta_input
+      IMPLICIT NONE
+      input_is_Er          = .TRUE.
+      log_interp           = .TRUE.
+      use_quanc8           = .FALSE.
+      read_U2_file         = .TRUE.
+      flux_cap             = .TRUE.
+      output_QoT_vs_Er     = .FALSE.
+      Add_Spitzer_to_D33   = .TRUE.
+      use_beam             = .FALSE.
+      num_Er_test          = 50_iknd
+      numKsteps            = 10000_iknd
+      kord_pprof           = 3_iknd
+      keord                = 2_iknd
+      kcord                = 2_iknd
+      Kmin                 = 1.0E-5_rknd
+      Kmax                 = 2.0E+1_rknd
+      epsabs               = 1.0E-8_rknd
+      epsrel               = 1.0E-6_rknd
+      sigma_par            = 0.0E+0_rknd
+      sigma_par_Spitzer    = 0.0E+0_rknd
+      J_BS                 = 0.0E+0_rknd
+      method               = 'DKES'
+      RETURN
+   END SUBROUTINE init_penta_input
+
+   SUBROUTINE read_penta_ion_params_namelist(filename,istat)
+      USE safe_open_mod
+      IMPLICIT NONE
+      CHARACTER(*), INTENT(in) :: filename
+      INTEGER, INTENT(inout) :: istat
+      LOGICAL :: lexist
+      INTEGER :: iunit
+      CHARACTER(LEN=1000) :: line
+      istat = 0; iunit = 12
+      INQUIRE(FILE=TRIM(filename),EXIST=lexist)
+      IF (.not.lexist) stop 'Could not find input file'
+      CALL safe_open(iunit,istat,TRIM(filename),'old','formatted')
+      IF (istat /= 0) THEN
+         WRITE(6,'(A)') 'ERROR opening file: ',TRIM(filename)
+         CALL FLUSH(6)
+         STOP
+      END IF
+      READ(iunit,NML=ion_params,IOSTAT=istat)
+      IF (istat /= 0) THEN
+         WRITE(6,'(A)') 'ERROR reading PENTA ion_params namelist from file: ',TRIM(filename)
+         backspace(iunit)
+         read(iunit,fmt='(A)') line
+         write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
+         CALL FLUSH(6)
+         STOP
+      END IF
+      CLOSE(iunit)
+      ! Electrons + ions
+      num_species = num_ion_species + 1_iknd
+      RETURN
+   END SUBROUTINE read_penta_ion_params_namelist
+
+   SUBROUTINE read_penta_run_params_namelist(filename,istat)
+      USE safe_open_mod
+      IMPLICIT NONE
+      CHARACTER(*), INTENT(in) :: filename
+      INTEGER, INTENT(inout) :: istat
+      LOGICAL :: lexist
+      INTEGER :: iunit
+      CHARACTER(LEN=1000) :: line
+      istat = 0; iunit = 12
+      INQUIRE(FILE=TRIM(filename),EXIST=lexist)
+      IF (.not.lexist) stop 'Could not find input file'
+      CALL safe_open(iunit,istat,TRIM(filename),'old','formatted')
+      IF (istat /= 0) THEN
+         WRITE(6,'(A)') 'ERROR opening file: ',TRIM(filename)
+         CALL FLUSH(6)
+         STOP
+      END IF
+      READ(iunit,NML=run_params,IOSTAT=istat)
+      IF (istat /= 0) THEN
+         WRITE(6,'(A)') 'ERROR reading PENTA ion_params namelist from file: ',TRIM(filename)
+         backspace(iunit)
+         read(iunit,fmt='(A)') line
+         write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
+         CALL FLUSH(6)
+         STOP
+      END IF
+      CLOSE(iunit)
+      RETURN
+   END SUBROUTINE read_penta_run_params_namelist
+
+   SUBROUTINE penta_init_commandline
+      IMPLICIT NONE
+      CALL GETCARG(1, arg1, numargs)
+      IF (numargs .NE. 9) THEN
+         Write(6,'(A)') 'ERROR Incorrect number of input arguments, see penta.f90 for details'
+         CALL FLUSH(6)
+         STOP
+      END IF
+      CALL GETCARG(2, arg2, numargs)
+      CALL GETCARG(3, arg3, numargs)
+      CALL GETCARG(4, arg4, numargs)
+      CALL GETCARG(5, arg5, numargs)
+      CALL GETCARG(6, arg6, numargs)
+      CALL GETCARG(7, arg7, numargs)
+      CALL GETCARG(8, arg8, numargs)
+      CALL GETCARG(9, arg9, numargs)
+
+      READ(arg2,*) Er_min
+      READ(arg3,*) Er_max
+      READ(arg4,*) js
+      READ(arg5,*) i_append
+      READ(arg8,*) B_Eprl
+      READ(arg9,*) Smax
+      coeff_ext  = TRIM(ADJUSTL(arg1))
+      run_ident  = TRIM(ADJUSTL(arg6))
+      pprof_char = TRIM(ADJUSTL(arg7))
+      RETURN
+   END SUBROUTINE penta_init_commandline
+
+   SUBROUTINE penta_allocate_species
+      USE pprof_pass, ONLY: ni, Ti, dnidr, dTidr
+      IMPLICIT NONE
+      ALLOCATE(ni(num_ion_species))
+      ALLOCATE(Ti(num_ion_species))          ! Ion profile info
+      ALLOCATE(dnidr(num_ion_species))
+      ALLOCATE(dTidr(num_ion_species))
+      ALLOCATE(Z_ion(num_ion_species))
+      ALLOCATE(ion_mass(num_ion_species)) ! Ion parameters
+      ALLOCATE(vth_i(num_ion_species))
+      ALLOCATE(charges(num_species))                             ! Parameters for
+      ALLOCATE(dens(num_species))                                !  all species
+      ALLOCATE(vths(num_species)) 
+      ALLOCATE(masses(num_species))
+      ALLOCATE(Temps(num_species))
+      ALLOCATE(dTdrs(num_species))
+      ALLOCATE(dndrs(num_species))
+      ALLOCATE(lmat((Smax+1)*num_species,(Smax+1)*num_species))  ! Clas. fric.coeffs
+      ALLOCATE(Xvec(num_species*2+1))
+      ALLOCATE(Avec(num_species*3))        ! Thermo. Force vecs.
+      ALLOCATE(Flows((Smax+1)*num_species))                      ! Prl flow moments
+      ALLOCATE(Gammas(num_species))                              ! Rad fluxes
+      ALLOCATE(QoTs(num_species))                                ! Rad energy fluxes
+      ALLOCATE(Gamma_i_vs_Er(num_Er_test,num_ion_species))       ! Ion flux vs Er
+      ALLOCATE(Gamma_e_vs_Er(num_Er_test))                       ! Electron flux vs Er
+      ALLOCATE(Er_test_vals(num_Er_test))                        ! Er to loop over
+      IF ( output_QoT_vs_Er ) THEN
+        ALLOCATE(QoT_i_vs_Er(num_Er_test,num_ion_species))       ! Ion flux vs Er
+        ALLOCATE(QoT_e_vs_Er(num_Er_test))                       ! Electron flux vs Er
+      ENDIF
+      RETURN
+   END SUBROUTINE penta_allocate_species
+
+   SUBROUTINE penta_allocate_dkescoeff
+      USE coeff_var_pass, ONLY: num_c, num_e
+      IMPLICIT NONE
+      ALLOCATE(xt_c(num_c + kcord))
+      ALLOCATE(xt_e(num_e + keord))
+      ALLOCATE(Dspl_D11(num_c,num_e))
+      ALLOCATE(Dspl_D13(num_c,num_e))
+      ALLOCATE(Dspl_D31(num_c,num_e))
+      ALLOCATE(Dspl_D33(num_c,num_e))
+      ALLOCATE(Dspl_Dex(num_c,num_e))
+      ALLOCATE(Dspl_Drat(num_c,num_e)) 
+      ALLOCATE(Dspl_Drat2(num_c,num_e)) 
+      ALLOCATE(Dspl_DUa(num_c,num_e))  
+      ALLOCATE(Dspl_logD11(num_c,num_e))
+      ALLOCATE(Dspl_logD33(num_c,num_e))
+      ALLOCATE(cmesh(num_c,num_e))
+      RETURN
+   END SUBROUTINE penta_allocate_dkescoeff
+
+   SUBROUTINE penta_deallocate_species
+      USE pprof_pass, ONLY: ni, Ti, dnidr, dTidr
+      IMPLICIT NONE
+      IF (ALLOCATED(ni)) DEALLOCATE(ni)
+      IF (ALLOCATED(ti)) DEALLOCATE(ti)
+      IF (ALLOCATED(dnidr)) DEALLOCATE(dnidr)
+      IF (ALLOCATED(dTidr)) DEALLOCATE(dTidr)
+      IF (ALLOCATED(Z_ion)) DEALLOCATE(Z_ion)
+      IF (ALLOCATED(ion_mass)) DEALLOCATE(ion_mass)
+      IF (ALLOCATED(vth_i)) DEALLOCATE(vth_i)
+      IF (ALLOCATED(charges)) DEALLOCATE(charges)
+      IF (ALLOCATED(dens)) DEALLOCATE(dens)
+      IF (ALLOCATED(vths)) DEALLOCATE(vths)
+      IF (ALLOCATED(masses)) DEALLOCATE(masses)
+      IF (ALLOCATED(Temps)) DEALLOCATE(Temps)
+      IF (ALLOCATED(dTdrs)) DEALLOCATE(dTdrs)
+      IF (ALLOCATED(dndrs)) DEALLOCATE(dndrs)
+      IF (ALLOCATED(lmat)) DEALLOCATE(lmat)
+      IF (ALLOCATED(Xvec)) DEALLOCATE(Xvec)
+      IF (ALLOCATED(Avec)) DEALLOCATE(Avec)
+      IF (ALLOCATED(Flows)) DEALLOCATE(Flows)
+      IF (ALLOCATED(Gammas)) DEALLOCATE(Gammas)
+      IF (ALLOCATED(QoTs)) DEALLOCATE(QoTs)
+      IF (ALLOCATED(Gamma_i_vs_Er)) DEALLOCATE(Gamma_i_vs_Er)
+      IF (ALLOCATED(Gamma_e_vs_Er)) DEALLOCATE(Gamma_e_vs_Er)
+      IF (ALLOCATED(Er_test_vals)) DEALLOCATE(Er_test_vals)
+      IF (ALLOCATED(QoT_i_vs_Er)) DEALLOCATE(QoT_i_vs_Er)
+      IF (ALLOCATED(QoT_e_vs_Er)) DEALLOCATE(QoT_e_vs_Er)
+      RETURN
+   END SUBROUTINE penta_deallocate_species
+
+   SUBROUTINE penta_deallocate_dkescoeff
+      IMPLICIT NONE
+      IF (ALLOCATED(xt_c)) DEALLOCATE(xt_c)
+      IF (ALLOCATED(xt_e)) DEALLOCATE(xt_e)
+      IF (ALLOCATED(Dspl_D11)) DEALLOCATE(Dspl_D11)
+      IF (ALLOCATED(Dspl_D13)) DEALLOCATE(Dspl_D13)
+      IF (ALLOCATED(Dspl_D31)) DEALLOCATE(Dspl_D31)
+      IF (ALLOCATED(Dspl_D33)) DEALLOCATE(Dspl_D33)
+      IF (ALLOCATED(Dspl_Dex)) DEALLOCATE(Dspl_Dex)
+      IF (ALLOCATED(Dspl_Drat)) DEALLOCATE(Dspl_Drat)
+      IF (ALLOCATED(Dspl_Drat2)) DEALLOCATE(Dspl_Drat2)
+      IF (ALLOCATED(Dspl_DUa)) DEALLOCATE(Dspl_DUa)
+      IF (ALLOCATED(Dspl_logD11)) DEALLOCATE(Dspl_logD11)
+      IF (ALLOCATED(Dspl_logD33)) DEALLOCATE(Dspl_logD33)
+      IF (ALLOCATED(cmesh)) DEALLOCATE(cmesh)
+      RETURN
+   END SUBROUTINE penta_deallocate_dkescoeff
+
+   SUBROUTINE penta_read_input_files
+      USE vmec_var_pass, ONLY: roa_surf, arad, Bsq
+      USE pprof_pass
+      USE coeff_var_pass, ONLY: D11_mat, cmul, num_c
+      USE phys_const, ONLY: p_mass, elem_charge, e_mass
+      USE read_input_file_mod
+      USE PENTA_subroutines, ONLY : define_friction_coeffs
+      IMPLICIT NONE
+      CALL read_vmec_file_2(js,run_ident)
+      CALL read_pprof_file(pprof_char,num_ion_species,roa_surf,arad,kord_pprof)
+      CALL read_dkes_star_files(coeff_ext,Add_Spitzer_to_D33,Bsq)
+      IF (use_beam) THEN
+         CALL read_beam_file(roa_surf,kord_pprof)
+      ELSE
+         beam_force = 0._rknd
+      ENDIF
+      ! Optionally read file containing <U**2> info.  Else this is 
+      ! calculated from the D11* coefficient at high nu/v and Er=0.
+      IF ( read_U2_file ) THEN
+         CALL read_Utilde2_file(roa_surf,U2,kord_pprof)
+      ELSE
+         U2=1.5d0*D11_mat(num_c,1)/cmul(num_c);
+      ENDIF
+      ! Change Er test range to V/cm if necessary
+      IF ( input_is_Er) THEN
+         Er_min = Er_min * Te / arad
+         Er_max = Er_max * Te / arad
+      ENDIF
+      ! Assign ion parameters
+      Z_ion    = Z_ion_init(1:num_ion_species)
+      ion_mass = miomp_init(1:num_ion_species) * p_mass
+      ! Calculate thermal velocities 
+      vth_i = Dsqrt(2._rknd*Ti*elem_charge/ion_mass)
+      vth_e = Dsqrt(2._rknd*Te*elem_charge/e_mass)
+      ! Calculate Coulomb logarithm
+      IF ( Te > 50._rknd ) THEN
+        loglambda = 25.3_rknd - 1.15_rknd*Dlog10(ne/1.e6_rknd) + 2.3_rknd*Dlog10(Te)
+      ELSE
+        loglambda = 23.4_rknd - 1.15_rknd*Dlog10(ne/1.e6_rknd) + 3.45_rknd*Dlog10(Te)
+      ENDIF
+      ! Assign arrays of parameters for all species (charge, mass, n, T, v_th, dTdr)
+      charges=elem_charge*(/-1._rknd,Z_ion/)
+      dens=(/ne, ni/)
+      masses=(/e_mass, ion_mass/)
+      Temps=(/Te,Ti/)
+      vths=(/vth_e,vth_i/)
+      dTdrs=(/dTedr,dTidr/)
+      dndrs=(/dnedr,dnidr/)
+      ! Define matrix of friction coefficients (lmat)
+      Call define_friction_coeffs(masses,charges,vths,Temps,dens,loglambda, &
+                            num_species,Smax,lmat)
+      RETURN
+   END SUBROUTINE penta_read_input_files
+
+   SUBROUTINE penta_fit_DXX_coef
+      USE coeff_var_pass
+      USE PENTA_subroutines, ONLY : fit_coeffs
+      IMPLICIT NONE
+
+      ! Calculate fitting parameters to the D##* coefficients
+      Call fit_coeffs(cmul,efield,num_c,num_e,D11_mat,log_interp, &
+         kcord,keord,xt_c,xt_e,Dspl_D11,cmin,cmax,emin,emax)
+      Call fit_coeffs(cmul,efield,num_c,num_e,D13_mat,log_interp, &
+         kcord,keord,xt_c,xt_e,Dspl_D13,cmin,cmax,emin,emax)
+      Call fit_coeffs(cmul,efield,num_c,num_e,D31_mat,log_interp, &
+         kcord,keord,xt_c,xt_e,Dspl_D31,cmin,cmax,emin,emax)
+      Call fit_coeffs(cmul,efield,num_c,num_e,D33_mat,log_interp, &
+         kcord,keord,xt_c,xt_e,Dspl_D33,cmin,cmax,emin,emax)
+
+      ! Fit log(D*) for D11 and D33
+      Call fit_coeffs(cmul,efield,num_c,num_e,LOG(D11_mat),log_interp, &
+         kcord,keord,xt_c,xt_e,Dspl_logD11,cmin,cmax,emin,emax)
+      Call fit_coeffs(cmul,efield,num_c,num_e,LOG(D33_mat),log_interp, &
+         kcord,keord,xt_c,xt_e,Dspl_logD33,cmin,cmax,emin,emax)
+      RETURN
+   END SUBROUTINE penta_fit_DXX_coef
+
+   SUBROUTINE penta_screen_info
+      IMPLICIT NONE
+      If ( i_append == 0 ) Then
+         WRITE(6,'(A)') ""
+         WRITE(6,'(A)') "Welcome to PENTA3, please note the following settings:"
+         WRITE(6,'(A)')
+         WRITE(6,'(A,I3)') ' Number of ion species: ',num_ion_species
+         IF ( input_is_Er ) THEN
+            WRITE(6,'(A)') 'Interpreting input range as Er (V/cm)'
+         ELSE
+            WRITE(6,'(A)') 'Interpreting input range as e<a>Er/kTe'
+         ENDIF
+         IF ( log_interp ) THEN
+            WRITE(6,'(A)') 'Performing logarithmic interpolation in Er, cmul'
+         ELSE
+            WRITE(6,'(A)') 'Performing linear interpolation in Er,cmul'
+         ENDIF
+         IF ( use_quanc8 ) THEN
+            WRITE(6,'(A,2(A,E10.4))')                           &
+               ' Using quanc8 integrator with tolerances: ',     &
+               'abs: ',epsabs,' rel: ', epsrel
+         ELSE
+            WRITE(6,'(A,i6,A)') ' Using ',numKsteps,            &
+               ' point integral approximation'
+         ENDIF
+         WRITE(6,'(a,2(" ",e15.4))') ' K range on convolution integral: ', &
+            Kmin, Kmax
+         IF ( Add_Spitzer_to_D33) &
+            WRITE(6,'(A)') 'Adding collisional (Spitzer) portion to D33 coefficient'
+         IF ( flux_cap ) &
+            WRITE(6,'(A)') 'Enforcing minimum radial diffusion coefficient = 0'
+         WRITE(6,'(A,I2)') ' Number of terms in Sonine expansion: ', Smax+1
+         SELECT CASE (Method)
+            CASE ('T')
+               WRITE(6,'(A)') 'Using Taguchi Method'
+            CASE ('SN')
+               WRITE(6,'(A)') 'Using Sugama-Nishimura Method'
+            CASE ('MBT')
+               WRITE(6,'(A)') 'Using Maassberg-Beidler-Turkin Method'
+            CASE ('DKES')
+               WRITE(6,'(A)') 'Using DKES Method'
+            CASE DEFAULT
+               Write(6,'(3A)') ' Error: ''', Trim(Adjustl(Method)), &
+                  ''' is not a valid Method'
+               STOP 'Error: Exiting, method select error in penta.f90 (1)'
+         END SELECT  
+         WRITE(6,'(A)') ""
+         WRITE(6,'(A)') " <r>/<a>","   Er root(s) (V/cm)"
+      ENDIF
+      RETURN
+   END SUBROUTINE penta_screen_info
+
+   SUBROUTINE penta_open_output
+      USE safe_open_mod
+      USE io_unit_spec
+      IMPLICIT NONE
+      INTEGER :: istat
+      istat = 0
+      ! Set write status
+      IF (i_append == 0) THEN
+         fstatus = "unknown"
+         fpos = "asis"
+      ELSEIF (i_append == 1) THEN
+         fstatus = "old"
+         fpos = "append"
+      ELSE
+         Write(6,'(A)') 'PENTA: Bad value for i_append (0 or 1 expected)'
+         CALL FLUSH(6)
+         STOP 'Error: Exiting, i_append error in penta.f90'
+      END IF
+      ! Open files
+      !Open(unit=iu_flux_out, file="fluxes_vs_roa", position=Trim(Adjustl(fpos)),status=Trim(Adjustl(fstatus)))
+      CALL safe_open(iu_flux_out, istat, "fluxes_vs_roa", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      CALL safe_open(iu_pprof_out, istat, "plasma_profiles_check", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      CALL safe_open(iu_fvEr_out, istat, "fluxes_vs_Er", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      CALL safe_open(iu_flows_out, istat, "flows_vs_roa", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      CALL safe_open(iu_flowvEr_out, istat, "flows_vs_Er", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      CALL safe_open(iu_Jprl_out, istat, "Jprl_vs_roa", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      CALL safe_open(iu_contraflows_out, istat, "ucontra_vs_roa", &
+         Trim(Adjustl(fstatus)), 'formatted',&
+         access_in=Trim(Adjustl(fpos)))
+      IF (method == 'SN') &
+         CALL safe_open(iu_sigmas_out, istat, "sigmas_vs_roa", &
+            Trim(Adjustl(fstatus)), 'formatted',&
+            access_in=Trim(Adjustl(fpos)))
+      IF (output_QoT_vs_Er) THEN
+         CALL safe_open(iu_QoTvEr_out, istat, "QoTs_vs_Er", &
+            Trim(Adjustl(fstatus)), 'formatted',&
+            access_in=Trim(Adjustl(fpos)))
+         Write(iu_QoTvEr_out,'("*",/,"r/a   Er[V/cm]   Q_e/T_e [m**-2s**-1] ",&
+                               "   Q_i/T_i [m**-2s**-1]")')
+      END IF
+      ! WRITE Headers
+      IF (i_append == 0) THEN
+         ! Fluxes vs r/a
+         Write(iu_flux_out,'("*",/,"r/a    Er[V/cm]    e<a>Er/kTe    ",  &
+            "Gamma_e [m**-2s**-1]   Q_e/T_e [m**-2s**-1]     ",         &
+            "Gamma_i [m**-2s**-1]   Q_i/T_i [m**-2s**-1]")')
+         ! Flows vs r/a
+         Write(iu_flows_out,'("*",/,"r/a   Er[V/cm]    e<a>Er/kTe    ",  &
+            " <B*u_||ke>/<B**2> [m/sT]   <B*u_||ki>/<B**2> [m/sT]")')
+         ! Plasma profile check
+         Write(iu_pprof_out,'("*",/,"r/a    Te [eV]   ne [m**-3]     ",  & 
+            "dnedr [m**-4]   dTedr [eV/m]  Ti [eV]   ni [m**-3]     ",  &
+            "dnidr [m**-4]   dTidr [eV/m]")')
+         Write(iu_Jprl_out,'("*",/,"r/a    Er [V/cm]    e<a>Er/kTe    ",  &
+            "Jprl_e [A/m**2]    Jprli [A/m**2]    Jprl [A/m**2]    J_BS [A/m**2]")')
+         Write(iu_contraflows_out,'("*",/,"r/a    Er [V/cm]    e<a>Er/kTe    ",  &
+            "<ue^pol_contra> [1/s]     <ue^tor_contra> [1/s]       ",  &
+            " <ui^pol_contra> [1/s]     <ui^tor_contra> [1/s]")')
+         ! Sigmas vs r/a
+         IF (Method == 'SN') &
+            Write(iu_sigmas_out,'("*",/,"r/a   Er[V/cm]    sigma_par [1/Ohm.m]    ",  &
+               " sigma_par_Spitzer [1/Ohm.m]")')
+         ! Legend for fluxes vs Er 
+         Write(iu_fvEr_out,'("*",/,"r/a   Er[V/cm]   Gamma_e [m**-2s**-1] ",&
+            "   Gamma_i [m**-2s**-1]")')
+         ! Legend for flows vs Er
+         Write(iu_flowvEr_out,'("*",/,"r/a   Er[V/cm]  ", &
+            "    <B*u_||ke>/<B**2> [m/sT]  <B*u_||ki>/<B**2> [m/sT]")')
+      END IF
+      RETURN
+   END SUBROUTINE penta_open_output
+
+   SUBROUTINE penta_fit_rad_trans
+      USE coeff_var_pass
+      USE vmec_var_pass
+      USE PENTA_subroutines, ONLY : fit_coeffs
+      IMPLICIT NONE
+      ! Fit radial transport coefficients specific to different methods
+      SELECT CASE (Method)
+         CASE ('T', 'MBT')
+            cmesh = Spread(cmul,2,num_e)
+            ! Calculate the D11 coefficient minus the P-S contribution  (Dex)
+            ! Also, do not allow for negative coefficients
+            CALL fit_coeffs(cmul,efield,num_c,num_e, &
+               Max(D11_mat-(2._rknd/3._rknd)*cmesh*U2,0._rknd), &
+               log_interp,kcord,keord,xt_c,xt_e,Dspl_Dex,     &
+               cmin,cmax,emin,emax)
+         CASE ('SN')
+            ! Calculate fits to D31*/D33*  (Drat)
+            CALL fit_coeffs(cmul,efield,num_c,num_e, &
+               D31_mat/D33_mat, &
+               log_interp,kcord,keord,xt_c,xt_e,Dspl_Drat,     &
+               cmin,cmax,emin,emax)
+            ! Calculate fits to (D31*)**2/D33*   (Drat2)
+            CALL fit_coeffs(cmul,efield,num_c,num_e, &
+               D31_mat*D31_mat/D33_mat, &
+               log_interp,kcord,keord,xt_c,xt_e,Dspl_Drat2,     &
+               cmin,cmax,emin,emax)
+            cmesh = Spread(cmul,2,num_e)
+            ! Calculate coefficient for Ua term  (DUa)
+            CALL fit_coeffs(cmul,efield,num_c,num_e, &
+               (2._rknd*Bsq/(3._rknd*D33_mat) - cmesh), &
+               log_interp,kcord,keord,xt_c,xt_e,Dspl_DUa,     &
+               cmin,cmax,emin,emax)
+            ! Calculate coefficient for radial flux  (Capped term)  (Dex)
+            ! Also, do not allow for negative coefficients
+            CALL fit_coeffs(cmul,efield,num_c,num_e, &
+               Max(D11_mat-(2._rknd/3._rknd)*cmesh*U2+D31_mat*D31_mat/D33_mat, &
+               0._rknd),log_interp,kcord,keord,xt_c,xt_e,Dspl_Dex,     &
+               cmin,cmax,emin,emax)
+        CASE ('DKES')
+        CASE DEFAULT
+          WRITE(6,'(3a)') ' Error: ''', Trim(Adjustl(Method)), &
+            ''' is not a valid Method'
+          STOP 'Error: Exiting, method select error in penta.f90 (2)'
+      ENDSELECT
+      RETURN
+   END SUBROUTINE penta_fit_rad_trans
+
+   SUBROUTINE penta_run_1_init
+      IMPLICIT NONE
+      INTEGER :: istat
+      istat = 0
+      CALL read_penta_ion_params_namelist('ion_params',istat)
+      istat = 0
+      CALL read_penta_run_params_namelist('run_params',istat)
+      CALL penta_init_commandline
+      CALL penta_allocate_species
+      CALL penta_read_input_files
+      CALL penta_screen_info
+      CALL penta_allocate_dkescoeff
+      CALL penta_fit_DXX_coef
+      CALL penta_open_output
+      CALL penta_fit_rad_trans
+      RETURN
+   END SUBROUTINE penta_run_1_init
+
+   SUBROUTINE penta_run_2_efield
+      USE vmec_var_pass
+      USE pprof_pass
+      USE phys_const
+      USE io_unit_spec
+      USE coeff_var_pass
+      USE penta_math_routines_mod, ONLY: rlinspace
+      USE penta_functions_mod
+      USE PENTA_subroutines, ONLY: form_xvec
+      IMPLICIT NONE
+      ! Define array of Er values to test [V/m]
+      Er_test_vals = rlinspace(Er_min,Er_max,num_Er_test)*100._rknd
+
+      ! Check for Er=0, doesn't work for log interpolation
+      min_Er = Minval(Dabs(Er_test_vals),DIM=1) 
+      If ((log_interp .EQV. .true. ) .AND. ( Dabs(min_Er) <= elem_charge ))  Then
+         min_ind = Minloc(Dabs(Er_test_vals),DIM=1)
+         If ( min_ind == Num_Er_test ) Then 
+            Er_test_vals(min_ind) = Er_test_vals(min_ind - 1)/2._rknd
+         Else
+            Er_test_vals(min_ind) = Er_test_vals(min_ind + 1)/2._rknd
+         EndIf
+         Write(*,'(a,i4,a,f10.3)') 'Cannot use Er=0 with log_interp, using Er(',  &
+            min_ind, ') = ', Er_test_vals(min_ind)
+      EndIf
+      ! Loop over Er to get fluxes as a function of Er
+      Do ie = 1,num_Er_test
+         Er_test = Er_test_vals(ie)
+         abs_Er = Abs(Er_test)
+
+         ! Form thermodynamic force vector (Xvec)
+         Call form_Xvec(Er_test,Z_ion,B_Eprl,num_ion_species,Xvec)
+
+         ! Form alternate thermodynamic force vector (Avec)
+         Do ispec1 = 1,num_species
+            ind_X = (ispec1-1)*2 + 1
+            ind_A = (ispec1-1)*3 + 1
+
+            Avec(ind_A)   = -Xvec(ind_X) / (Temps(ispec1)*elem_charge) &
+               - 2.5_rknd*dTdrs(ispec1)/Temps(ispec1)
+            Avec(ind_A+1)   = -Xvec(ind_X+1) / (Temps(ispec1)*elem_charge)
+            Avec(ind_A+2)   = Xvec(num_species*2+1)*charges(ispec1) &
+               * B0/(Temps(ispec1)*elem_charge*Sqrt(Bsq)) + &
+               beam_force/(Temps(ispec1)*elem_charge*dens(ispec1))
+         Enddo
+
+         ! Select the appropriate algorithm and calculate the flows and fluxes
+         SELECT CASE (Method)
+            Case ('T', 'MBT')
+               ! Calculate array of parallel flow moments
+               Flows = calc_flows_T(num_species,Smax,abs_Er,Temps,dens,vths,charges,   &
+                 masses,loglambda,B0,use_quanc8,Kmin,Kmax,numKsteps,log_interp,cmin,   &
+                 cmax,emin,emax,xt_c,xt_e,Dspl_D31,Dspl_logD33,num_c,num_e,kcord,      &
+                 keord,Avec,Bsq,lmat,J_BS)
+               Gammas = calc_fluxes_MBT(num_species,Smax,abs_Er,Temps,dens,vths,       &
+                 charges,masses,dTdrs,dndrs,loglambda,use_quanc8,Kmin,Kmax,numKsteps,  &
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_logD11,Dspl_D31,        &
+                 Dspl_Dex,num_c,num_e,kcord,keord,Avec,lmat,Flows,U2,B0,flux_cap)   
+               If ( output_QoT_vs_Er .EQV. .true. ) Then
+                  QoTs = calc_QoTs_MBT(num_species,Smax,abs_Er,Temps,dens,vths,charges, &
+                   masses,dTdrs,dndrs,loglambda,use_quanc8,Kmin,Kmax,numKsteps,        &
+                   log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_logD11,Dspl_D31,      &
+                   Dspl_Dex,num_c,num_e,kcord,keord,Avec,lmat,Flows,U2,B0,flux_cap)   
+               Endif    
+            Case ('SN')                    
+               Flows = calc_flows_SN(num_species,Smax,abs_Er,Temps,dens,vths,charges,  &
+                  masses,loglambda,B0,use_quanc8,Kmin,Kmax,numKsteps,log_interp,       &
+                  cmin,cmax,emin,emax,xt_c,xt_e,Dspl_Drat,Dspl_DUa,num_c,num_e,kcord,  &
+                  keord,Avec,lmat,sigma_par,sigma_par_Spitzer,J_BS)                                                
+               Gammas = calc_fluxes_SN(num_species,Smax,abs_Er,Temps,dens,vths,charges,&
+                 masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,log_interp,cmin,cmax, &
+                 emin,emax,xt_c,xt_e,Dspl_Drat,Dspl_Drat2,Dspl_Dex,Dspl_logD11,        &
+                 Dspl_D31,num_c,num_e,kcord,keord,Avec,Bsq,lmat,Flows,U2,dTdrs,        &
+                 dndrs,flux_cap)  
+               If ( output_QoT_vs_Er .EQV. .true. ) Then
+                  QoTs = calc_QoTs_SN(num_species,Smax,abs_Er,Temps,dens,vths,charges,  &
+                     masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,log_interp,cmin,    &
+                     cmax,emin,emax,xt_c,xt_e,Dspl_Drat,Dspl_Drat2,Dspl_Dex,Dspl_logD11, &
+                     Dspl_D31,num_c,num_e,kcord,keord,Avec,Bsq,lmat,Flows,U2,dTdrs,      &
+                     dndrs,flux_cap)  
+               Endif    
+            Case ('DKES')
+               Flows = calc_flows_DKES(num_species,Smax,abs_Er,Temps,dens,vths,charges,&
+                  masses,loglambda,B0,use_quanc8,Kmin,Kmax,numKsteps,log_interp,cmin,  &
+                  cmax,emin,emax,xt_c,xt_e,Dspl_D31,Dspl_logD33,num_c,num_e,kcord,     &
+                  keord,Avec,J_BS)
+               Gammas = calc_fluxes_DKES(num_species,abs_Er,Temps,dens,vths,charges,   &
+                  masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,log_interp,cmin,cmax, &
+                  emin,emax,xt_c,xt_e,Dspl_logD11,Dspl_D31,num_c,num_e,kcord,keord,     &
+                  Avec,B0)   
+               If ( output_QoT_vs_Er .EQV. .true. ) Then
+                  QoTs = calc_QoTs_DKES(num_species,abs_Er,Temps,dens,vths,charges,     &
+                     masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,log_interp,cmin,    &
+                     cmax,emin,emax,xt_c,xt_e,Dspl_logD11,Dspl_D31,num_c,num_e,kcord,    &
+                     keord,Avec,B0)  
+               Endif
+            Case Default
+               Write(6,'(3a)') ' Error: ''', Trim(Adjustl(Method)), &
+              ''' is not a valid Method'
+               Stop 'Error: Exiting, method select error in penta.f90 (3)'
+         END SELECT
+
+         Gamma_e_vs_Er(ie)   = Gammas(1)
+         Gamma_i_vs_Er(ie,:) = Gammas(2:num_species)
+
+         ! Write fluxes vs Er
+         Write(str_num,*) num_ion_species + 2  ! Convert num to string
+         Write(iu_fvEr_out,'(f7.4,' // trim(adjustl(str_num)) // '(" ",e15.7))') &
+            roa_surf,Er_test/100._rknd,Gamma_e_vs_Er(ie),Gamma_i_vs_Er(ie,:)
+
+         If ( output_QoT_vs_Er .EQV. .true. ) Then
+            QoT_e_vs_Er(ie)   = QoTs(1)
+            QoT_i_vs_Er(ie,:) = QoTs(2:num_species)
+            Write(iu_QoTvEr_out,'(f7.4,' // trim(adjustl(str_num)) // '(" ",e15.7))') &
+               roa_surf,Er_test/100._rknd,QoT_e_vs_Er(ie),QoT_i_vs_Er(ie,:)
+         Endif
+
+         ! Write flows vs Er
+         Write(str_num,*) (Smax+1)*num_species + 2  ! Convert num to string
+         Write(iu_flowvEr_out,'(f7.4,' // trim(adjustl(str_num)) // '(" ",e15.7))') &
+          roa_surf,Er_test/100._rknd,Flows
+
+      Enddo !efield loop
+      RETURN
+   END SUBROUTINE penta_run_2_efield
+
+   SUBROUTINE penta_run_3_ambipolar
+      USE vmec_var_pass
+      USE phys_const
+      USE coeff_var_pass
+      USE penta_functions_mod
+      USE PENTA_subroutines, ONLY: form_xvec, find_Er_roots
+      IMPLICIT NONE
+      ! Check for only one Er test value -- this is then used to evaluate the ambipolar fluxes QQ
+      !If ( num_Er_test  == 1 ) Then
+      !  Er_roots = Er_test_vals
+
+      ! Find the ambipolar root(s) from gamma_e = sum(Z*gamma_i)
+      Call find_Er_roots(gamma_e_vs_Er,gamma_i_vs_Er,Er_test_vals,Z_ion, &
+         num_Er_test,num_ion_species,Er_roots,num_roots)
+
+      ! Allocate arrays according to number of ambipolar roots
+      Allocate(Flows_ambi((Smax+1)*num_species,num_roots)) ! Parallel flow moments
+      Allocate(Gammas_ambi(num_species,num_roots))         ! Rad. particle fluxes
+      Allocate(QoTs_ambi(num_species,num_roots))           ! Rad. energy fluxes
+      Allocate(Jprl_ambi(num_roots))                       ! Parallel current density
+      Allocate(J_BS_ambi(num_roots))                       ! BS current density
+      Allocate(sigma_par_ambi(num_roots))                  ! Parallel conductivity
+      Allocate(sigma_par_Spitzer_ambi(num_roots))          ! Spitzer Parallel conductivity
+      Allocate(Jprl_parts(num_species,num_roots))          ! Par. curr. dens. per spec.
+      Allocate(upol(num_species,num_roots))                ! fsa contra pol flow
+      Allocate(utor(num_species,num_roots))                ! fsa contra tor flow
+
+      ! Evaluate fluxes and flows at the ambipolar Er
+      Do iroot = 1_iknd, num_roots
+
+         Er_test = Er_roots(iroot)
+         abs_Er = Dabs(Er_test)
+
+         ! Form thermodynamic force vector (Xvec)
+         Call form_Xvec(Er_test,Z_ion,B_Eprl,num_ion_species,Xvec)
+
+         ! Form alternate thermodynamic force vector (Avec)
+         Do ispec1 = 1,num_species
+            ind_X = (ispec1-1)*2 + 1
+            ind_A = (ispec1-1)*3 + 1
+
+            Avec(ind_A)   = -Xvec(ind_X) / (Temps(ispec1)*elem_charge) &
+               - 2.5_rknd*dTdrs(ispec1)/Temps(ispec1)
+            Avec(ind_A+1)   = -Xvec(ind_X+1) / (Temps(ispec1)*elem_charge)
+            Avec(ind_A+2)   = Xvec(num_species*2+1)*charges(ispec1) &
+               * B0/(Temps(ispec1)*elem_charge*Sqrt(Bsq))
+         Enddo
+
+         ! Select the appropriate algorithm and calculate the flows and fluxes
+         SELECT CASE (Method)
+            Case ('T', 'MBT')
+               ! Calculate array of parallel flow moments 
+                 ! Note: Flow methods are the same for T and MBT
+               Flows_ambi(:,iroot) = calc_flows_T(num_species,Smax,abs_Er,Temps,dens, &
+                 vths,charges,masses,loglambda,B0,use_quanc8,Kmin,Kmax,numKsteps,     &
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_D31,Dspl_logD33,num_c, &
+                 num_e,kcord,keord,Avec,Bsq,lmat,J_BS)
+               ! Calculate array of radial particle fluxes
+               Gammas_ambi(:,iroot) = calc_fluxes_MBT(num_species,Smax,abs_Er,Temps,  &
+                 dens,vths,charges,masses,dTdrs,dndrs,loglambda,use_quanc8,Kmin,Kmax, &
+                 numKsteps,log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_logD11,      &
+                 Dspl_D31,Dspl_Dex,num_c,num_e,kcord,keord,Avec,lmat,                 &
+                 Flows_ambi(:,iroot),U2,B0,flux_cap)   
+               ! Calculate array of radial energy fluxes
+               QoTs_ambi(:,iroot) = calc_QoTs_MBT(num_species,Smax,abs_Er,Temps,dens, &
+                 vths,charges,masses,dTdrs,dndrs,loglambda,use_quanc8,Kmin,Kmax,      &
+                 numKsteps,log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_logD11,      &
+                 Dspl_D31,Dspl_Dex,num_c,num_e,kcord,keord,Avec,lmat,                 &
+                 Flows_ambi(:,iroot),U2,B0,flux_cap)
+
+               J_BS_ambi(iroot) = J_BS
+            Case ('SN')
+               ! Calculate array of parallel flow moments
+                                                       
+               Flows_ambi(:,iroot) = calc_flows_SN(num_species,Smax,abs_Er,Temps,dens,&
+                  vths,charges,masses,loglambda,B0,use_quanc8,Kmin,Kmax,numKsteps,    &
+                  log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_Drat,Dspl_DUa,num_c,  &
+                  num_e,kcord,keord,Avec,lmat,sigma_par,sigma_par_Spitzer,J_BS)                                                
+               ! Calculate array of radial particle fluxes
+               Gammas_ambi(:,iroot) = calc_fluxes_SN(num_species,Smax,abs_Er,Temps,   &
+                 dens,vths,charges,masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,   &
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_Drat,Dspl_Drat2,       &
+                 Dspl_Dex,Dspl_logD11,Dspl_D31,num_c,num_e,kcord,keord,Avec,Bsq,      &
+                 lmat,Flows_ambi(:,iroot),U2,dTdrs,dndrs,flux_cap)  
+               ! Calculate array of radial energy fluxes
+               QoTs_ambi(:,iroot) = calc_QoTs_SN(num_species,Smax,abs_Er,Temps,dens,  &
+                 vths,charges,masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,        &
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_Drat,Dspl_Drat2,       &
+                 Dspl_Dex,Dspl_logD11,Dspl_D31,num_c,num_e,kcord,keord,Avec,Bsq,      &
+                 lmat,Flows_ambi(:,iroot),U2,dTdrs,dndrs,flux_cap)
+
+               sigma_par_ambi(iroot) = sigma_par
+               sigma_par_Spitzer_ambi(iroot) = sigma_par_Spitzer
+               J_BS_ambi(iroot) = J_BS
+            Case ('DKES')
+               ! Calculate array of parallel flow moments 
+               Flows_ambi(:,iroot) = calc_flows_DKES(num_species,Smax,abs_Er,Temps,   &
+                 dens,vths,charges,masses,loglambda,B0,use_quanc8,Kmin,Kmax,numKsteps,&
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_D31,Dspl_logD33,num_c, &
+                 num_e,kcord,keord,Avec,J_BS)
+               ! Calculate array of radial particle fluxes
+               Gammas_ambi(:,iroot) = calc_fluxes_DKES(num_species,abs_Er,Temps,dens, &
+                 vths,charges,masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,        &
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_logD11,Dspl_D31,num_c, &
+                 num_e,kcord,keord,Avec,B0)  
+               ! Calculate array of radial energy fluxes
+               QoTs_ambi(:,iroot) = calc_QoTs_DKES(num_species,abs_Er,Temps,dens,     &
+                 vths,charges,masses,loglambda,use_quanc8,Kmin,Kmax,numKsteps,        &
+                 log_interp,cmin,cmax,emin,emax,xt_c,xt_e,Dspl_logD11,Dspl_D31,num_c, &
+                 num_e,kcord,keord,Avec,B0)
+               
+               J_BS_ambi(iroot) = J_BS                
+            Case Default
+               Write(*,'(3a)') ' Error: ''', Trim(Adjustl(Method)), &
+                  ''' is not a valid Method'
+               Stop 'Error: Exiting, method select error in penta.f90 (4)'
+         ENDSELECT
+
+         ! Calculate parallel current density
+         Jprl_parts(:,iroot) = dens*charges*Sqrt(Bsq) *         &
+            Flows_ambi(1:(num_species-1)*(Smax+1)+1:Smax+1,iroot)
+         Jprl_ambi(iroot) = Sum(Jprl_parts(:,iroot))
+
+         ! Calculate flow components
+         upol(:,iroot) = chip*(4._rknd*pi*pi/vol_p)*(                 &
+            Flows_ambi(1:(num_species-1)*(Smax+1)+1:Smax+1,iroot) - &
+            bzeta*Xvec(1:(num_species-1)*2+1:2)/(charges*chip*Bsq))
+         utor(:,iroot) = psip*(4._rknd*pi*pi/vol_p)*(                 &
+            Flows_ambi(1:(num_species-1)*(Smax+1)+1:Smax+1,iroot) + &
+            btheta*Xvec(1:(num_species-1)*2+1:2)/(charges*psip*Bsq))
+
+      END DO ! Ambipolar root loop
+      RETURN
+   END SUBROUTINE penta_run_3_ambipolar
+
+   SUBROUTINE penta_run_4_cleanup
+      USE io_unit_spec
+      USE pprof_pass
+      USE vmec_var_pass
+      IMPLICIT NONE
+      ! First write output files
+      ! Loop over ambipolar Er for writing output files
+      Do iroot = 1_iknd, num_roots
+
+         Er_test = Er_roots(iroot)
+         eaEr_o_kTe = arad*Er_test/Te
+
+         ! Write fluxes to file "fluxes_vs_roa"
+         Write(str_num,*) 2*num_species + 2
+         Write(iu_flux_out,'(f7.3,' // Trim(Adjustl(str_num)) // '(" ",e15.7))') &
+          roa_surf,Er_test/100._rknd,eaEr_o_kTe,Gammas_ambi(1,iroot),  &
+          QoTs_ambi(1,iroot),Gammas_ambi(2:num_species,iroot),  &
+          QoTs_ambi(2:num_species,iroot)
+
+         ! Write flows to file "flows_vs_roa"
+         Write(str_num,*) (Smax+1)*num_species + 2
+         Write(iu_flows_out,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.7))') &
+          roa_surf,Er_test/100._rknd,eaEr_o_kTe,Flows_ambi(:,iroot)
+
+         ! Write current densities to file "Jprl_vs_roa"
+         Write(str_num,*) num_species + 4 
+         Write(iu_Jprl_out,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.7))')  & 
+          roa_surf,Er_test/100._rknd,eaEr_o_kTe,Jprl_parts(:,iroot),Jprl_ambi(iroot),J_BS_ambi(iroot)
+
+         ! Write contravariant flows to file "ucontra_vs_roa"
+         Write(str_num,*) 2*num_species + 2
+         Write(iu_contraflows_out,'(f7.3,' // trim(adjustl(str_num))//'(" ",e15.7))') & 
+          roa_surf,Er_test/100._rknd,eaEr_o_kTe,upol(1,iroot),utor(1,iroot),         &
+          upol(2:num_species,iroot),utor(2:num_species,iroot)
+
+         ! Write sigmas to file "sigmas_vs_roa"
+         If( Method == 'SN') then
+          Write(str_num,*) 3
+          Write(iu_sigmas_out,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.7))') &
+            roa_surf,Er_test/100._rknd,sigma_par_ambi(iroot),sigma_par_Spitzer_ambi(iroot)
+         Endif
+      EndDo ! Ambipolar root loop
+
+      ! Write plasma profile information to "plasma_profiles_check"
+      Write(str_num,*) 4*num_species
+      Write(iu_pprof_out,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.7))') & 
+        roa_surf,Te,ne,dnedr,dTedr,Ti,ni,dnidr,dTidr
+
+      ! QQ write file with number of roots per surface!
+
+      ! Write screen output
+      write(str_num,*) num_roots
+      write(*,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.4))') & 
+        roa_surf,er_roots(1:num_roots)/100._rknd
+      ! DEALLOCATE
+      CALL penta_deallocate_species
+      CALL penta_deallocate_dkescoeff
+   END SUBROUTINE penta_run_4_cleanup
+
+
+
+END MODULE PENTA_INTERFACE_MOD
\ No newline at end of file

From 9b8e4c5b6c8628be2536adfb68860c687d81c750 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 10:29:43 +0200
Subject: [PATCH 19/47] PENTA: Change unit numbers from parameters to
 variables.

---
 PENTA/Sources/io_unit_spec.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PENTA/Sources/io_unit_spec.f90 b/PENTA/Sources/io_unit_spec.f90
index 375ee6115..061f5c107 100644
--- a/PENTA/Sources/io_unit_spec.f90
+++ b/PENTA/Sources/io_unit_spec.f90
@@ -21,7 +21,7 @@ Module io_unit_spec
 
   Implicit none
   
-  Integer, parameter ::   &
+  Integer ::   &
     iu_nl=21,             &   ! Ion parameter namelist file (input)
     iu_vmec=22,           &   ! VMEC data file (input)
     iu_pprof=23,          &   ! Plasma profile file (input)

From cd12712f7e79d86cd5f8c22fa1d259b111eaf11d Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 13:46:49 +0200
Subject: [PATCH 20/47] PENTA: Subroutine interface checked.

---
 PENTA/Sources/penta_interface_mod.f90 | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index ca80e2055..07b86cb6c 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -133,7 +133,7 @@ SUBROUTINE read_penta_run_params_namelist(filename,istat)
       END IF
       READ(iunit,NML=run_params,IOSTAT=istat)
       IF (istat /= 0) THEN
-         WRITE(6,'(A)') 'ERROR reading PENTA ion_params namelist from file: ',TRIM(filename)
+         WRITE(6,'(A)') 'ERROR reading PENTA run_params namelist from file: ',TRIM(filename)
          backspace(iunit)
          read(iunit,fmt='(A)') line
          write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
@@ -280,7 +280,6 @@ SUBROUTINE penta_read_input_files
       USE coeff_var_pass, ONLY: D11_mat, cmul, num_c
       USE phys_const, ONLY: p_mass, elem_charge, e_mass
       USE read_input_file_mod
-      USE PENTA_subroutines, ONLY : define_friction_coeffs
       IMPLICIT NONE
       CALL read_vmec_file_2(js,run_ident)
       CALL read_pprof_file(pprof_char,num_ion_species,roa_surf,arad,kord_pprof)
@@ -298,7 +297,7 @@ SUBROUTINE penta_read_input_files
          U2=1.5d0*D11_mat(num_c,1)/cmul(num_c);
       ENDIF
       ! Change Er test range to V/cm if necessary
-      IF ( input_is_Er) THEN
+      IF ( .not. input_is_Er) THEN
          Er_min = Er_min * Te / arad
          Er_max = Er_max * Te / arad
       ENDIF
@@ -322,9 +321,6 @@ SUBROUTINE penta_read_input_files
       vths=(/vth_e,vth_i/)
       dTdrs=(/dTedr,dTidr/)
       dndrs=(/dnedr,dnidr/)
-      ! Define matrix of friction coefficients (lmat)
-      Call define_friction_coeffs(masses,charges,vths,Temps,dens,loglambda, &
-                            num_species,Smax,lmat)
       RETURN
    END SUBROUTINE penta_read_input_files
 
@@ -412,7 +408,7 @@ SUBROUTINE penta_open_output
       ! Set write status
       IF (i_append == 0) THEN
          fstatus = "unknown"
-         fpos = "asis"
+         fpos = "SEQUENTIAL"
       ELSEIF (i_append == 1) THEN
          fstatus = "old"
          fpos = "append"
@@ -490,8 +486,11 @@ END SUBROUTINE penta_open_output
    SUBROUTINE penta_fit_rad_trans
       USE coeff_var_pass
       USE vmec_var_pass
-      USE PENTA_subroutines, ONLY : fit_coeffs
+      USE PENTA_subroutines, ONLY : fit_coeffs, define_friction_coeffs
       IMPLICIT NONE
+      ! Define matrix of friction coefficients (lmat)
+      Call define_friction_coeffs(masses,charges,vths,Temps,dens,loglambda, &
+                            num_species,Smax,lmat)
       ! Fit radial transport coefficients specific to different methods
       SELECT CASE (Method)
          CASE ('T', 'MBT')
@@ -537,6 +536,7 @@ END SUBROUTINE penta_fit_rad_trans
    SUBROUTINE penta_run_1_init
       IMPLICIT NONE
       INTEGER :: istat
+      CALL init_penta_input
       istat = 0
       CALL read_penta_ion_params_namelist('ion_params',istat)
       istat = 0

From d94e7beba45768d33aec26f3094ec8b03f83af96 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 14:23:17 +0200
Subject: [PATCH 21/47] PENTA: Added subroutines for outputting namelists.

---
 PENTA/Sources/penta_interface_mod.f90 | 91 +++++++++++++++++++++++++++
 1 file changed, 91 insertions(+)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index 07b86cb6c..24480b1e1 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -114,6 +114,43 @@ SUBROUTINE read_penta_ion_params_namelist(filename,istat)
       RETURN
    END SUBROUTINE read_penta_ion_params_namelist
 
+   SUBROUTINE write_ion_params_nml(iunit)
+      IMPLICIT NONE
+      INTEGER(iknd), INTENT(inout) :: iunit
+      CHARACTER(LEN=*), PARAMETER :: outint  = "(2X,A,1X,'=',1X,I0)"
+      INTEGER(iknd) :: k
+      WRITE(iunit,'(A)') '&ION_PARAMS'
+      WRITE(iunit,'(A)') '----------------------------------------------------------------'
+      WRITE(iunit,outint) 'NUM_ION_SPECIES',num_ion_species
+      WRITE(iunit,"(2X,A,1X,'=',4(1X,ES22.12E3))") 'Z_ION_INIT',(Z_ion_init(k), k=1,num_ion_species)
+      WRITE(iunit,"(2X,A,1X,'=',4(1X,ES22.12E3))") 'MIOMP_INIT',(miomp_init(k), k=1,num_ion_species)
+      WRITE(iunit,'(A)') '/\n'
+   END SUBROUTINE write_ion_params_nml
+
+   SUBROUTINE write_ion_params_namelist_byfile(filename)
+      USE safe_open_mod
+      IMPLICIT NONE
+      CHARACTER(LEN=*), INTENT(in) :: filename
+      INTEGER(iknd) :: iunit, istat
+      LOGICAL :: lexists
+      
+      iunit = 100
+      istat = 0
+      INQUIRE(FILE=TRIM(filename),exist=lexists)
+      IF (lexists) THEN
+         CALL safe_open(iunit,istat,TRIM(filename),'old','formatted', access_in='append')
+         !OPEN(unit=iunit, file=TRIM(filename),iostat=istat, status="old", position="append")
+      ELSE
+         CALL safe_open(iunit,istat,TRIM(filename),'replace','formatted')
+         !OPEN(unit=iunit, file=TRIM(filename),iostat=istat, status="new")
+      END IF
+      IF (istat .ne. 0) RETURN
+      CALL write_ion_params_nml(iunit)
+      CLOSE(iunit)
+
+      RETURN
+   END SUBROUTINE write_ion_params_namelist_byfile
+
    SUBROUTINE read_penta_run_params_namelist(filename,istat)
       USE safe_open_mod
       IMPLICIT NONE
@@ -144,6 +181,60 @@ SUBROUTINE read_penta_run_params_namelist(filename,istat)
       RETURN
    END SUBROUTINE read_penta_run_params_namelist
 
+   SUBROUTINE write_run_params_nml(iunit)
+      IMPLICIT NONE
+      INTEGER(iknd), INTENT(inout) :: iunit
+      CHARACTER(LEN=*), PARAMETER :: outboo  = "(2X,A,1X,'=',1X,L1)"
+      CHARACTER(LEN=*), PARAMETER :: outint  = "(2X,A,1X,'=',1X,I0)"
+      CHARACTER(LEN=*), PARAMETER :: outdbl  = "(2X,A,1X,'=',1X,ES22.14)"
+      CHARACTER(LEN=*), PARAMETER :: outstr  = "(2X,A,1X,'=',1X,'''',A,'''')"
+      INTEGER(iknd) :: k
+      WRITE(iunit,'(A)') '&RUN_PARAMS'
+      WRITE(iunit,outboo) 'INPUT_IS_ER',input_is_er
+      WRITE(iunit,outboo) 'LOG_INTERP',log_interp
+      WRITE(iunit,outboo) 'USE_QUANC8',use_quanc8
+      WRITE(iunit,outboo) 'READ_U2_FILE',read_U2_file
+      WRITE(iunit,outboo) 'ADD_SPITZER_TO_D33',Add_Spitzer_to_D33
+      WRITE(iunit,outboo) 'FLUX_CAP',flux_cap
+      WRITE(iunit,outboo) 'OUTPUT_QOT_VS_ER',output_QoT_vs_Er
+      WRITE(iunit,outboo) 'USE_BEAM',use_beam
+      WRITE(iunit,outint) 'NUM_ER_TEST',num_Er_test
+      WRITE(iunit,outint) 'NUMKSTEPS',numksteps
+      WRITE(iunit,outint) 'KORD_PPROF',kord_pprof
+      WRITE(iunit,outint) 'KEORD',keord
+      WRITE(iunit,outint) 'KCORD',kcord
+      WRITE(iunit,outdbl) 'KMIN',kmin
+      WRITE(iunit,outdbl) 'KMAX',kmax
+      WRITE(iunit,outdbl) 'EPSABS',epsabs
+      WRITE(iunit,outdbl) 'EPSREL',epsrel
+      WRITE(iunit,outstr) 'METHOD',method
+      WRITE(iunit,'(A)') '/\n'
+   END SUBROUTINE write_run_params_nml
+
+   SUBROUTINE write_run_params_namelist_byfile(filename)
+      USE safe_open_mod
+      IMPLICIT NONE
+      CHARACTER(LEN=*), INTENT(in) :: filename
+      INTEGER(iknd) :: iunit, istat
+      LOGICAL :: lexists
+      
+      iunit = 100
+      istat = 0
+      INQUIRE(FILE=TRIM(filename),exist=lexists)
+      IF (lexists) THEN
+         CALL safe_open(iunit,istat,TRIM(filename),'old','formatted', access_in='append')
+         !OPEN(unit=iunit, file=TRIM(filename),iostat=istat, status="old", position="append")
+      ELSE
+         CALL safe_open(iunit,istat,TRIM(filename),'replace','formatted')
+         !OPEN(unit=iunit, file=TRIM(filename),iostat=istat, status="new")
+      END IF
+      IF (istat .ne. 0) RETURN
+      CALL write_run_params_nml(iunit)
+      CLOSE(iunit)
+
+      RETURN
+   END SUBROUTINE write_run_params_namelist_byfile
+
    SUBROUTINE penta_init_commandline
       IMPLICIT NONE
       CALL GETCARG(1, arg1, numargs)

From 61a523d36ee8b63a936e2e575901b4b5372cf4bb Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 14:35:15 +0200
Subject: [PATCH 22/47] PENTA: Removed extra files.

---
 PENTA/Sources/penta_input_mod.f | 103 ------------------------
 PENTA/Sources/penta_main.f      | 135 --------------------------------
 2 files changed, 238 deletions(-)
 delete mode 100644 PENTA/Sources/penta_input_mod.f
 delete mode 100644 PENTA/Sources/penta_main.f

diff --git a/PENTA/Sources/penta_input_mod.f b/PENTA/Sources/penta_input_mod.f
deleted file mode 100644
index e4640084d..000000000
--- a/PENTA/Sources/penta_input_mod.f
+++ /dev/null
@@ -1,103 +0,0 @@
-      module penta_input_mod
-      use penta_kind_mod
-      implicit none      
-      INTEGER(iknd), parameter ::  num_ion_max = 20_iknd    !Maximum number of ion species to be read from namelist file
-      INTEGER(iknd) :: num_ion_species ! Number of ion species
-      REAL(rknd), DIMENSION(num_ion_max) :: Z_ion_init,miomp_init  
-
-      namelist / ion_params / num_ion_species,Z_ion_init,miomp_init
-      contains
-
-      SUBROUTINE init_ion_params_nml
-      IMPLICIT NONE
-      num_ion_species = 1
-      Z_ion_init = 1.0_rknd
-      miomp_init = 1.0_rknd
-      END SUBROUTINE init_ion_params_nml
-
-      SUBROUTINE read_ion_params_nml(filename,istat)
-      USE safe_open_mod
-      IMPLICIT NONE
-      ! Subroutine parameters
-      CHARACTER(256), INTENT(INOUT) :: filename
-      INTEGER(iknd), INTENT(INOUT) :: istat
-      ! Local Variables
-      LOGICAL :: lexist
-      INTEGER(iknd) :: iunit
-      CHARACTER(256) :: filename_local
-
-      ! Handle filename
-      filename_local = TRIM(filename)
-
-      !Check which file is available
-      INQUIRE(FILE=TRIM(filename_local),EXIST=lexist)
-      IF (.not. lexist) THEN
-         WRITE(6,*) '   -Could not open input file trying ion_params'
-         filename_local = 'ion_params'
-         INQUIRE(FILE=TRIM(filename_local),EXIST=lexist)
-         IF (.not. lexist) THEN
-            WRITE(6,*) '   -Could not open ion_params file'
-            istat = -1
-            RETURN
-         ENDIF
-      ENDIF
-
-      ! Open and read the file
-      CALL safe_open(iunit,istat,TRIM(filename_local),'old',
-     1                  'formatted')
-      IF (istat /= 0) THEN
-         WRITE(6,*) 'ERROR: Could no open: ',TRIM(filename_local)
-         RETURN
-      ENDIF
-      READ(iunit,NML=ion_params,IOSTAT=istat)
-      IF (istat /= 0) THEN
-         WRITE(6,*) 'ERROR: ion_params in ',TRIM(filename_local)
-         !backspace(iu_nl)
-         !read(iu_nl,fmt='(A)') line
-         !write(6,'(A)') 'Invalid line in namelist: '//TRIM(line)
-         RETURN
-      ENDIF
-      CLOSE(iunit)
-      RETURN
-      END SUBROUTINE read_ion_params_nml
-
-      SUBROUTINE write_ion_params_nml(iunit)
-      IMPLICIT NONE
-      INTEGER(iknd), INTENT(inout) :: iunit
-      CHARACTER(LEN=*), PARAMETER :: outint  = "(2X,A,1X,'=',1X,I0)"
-      INTEGER(iknd) :: k
-      WRITE(iunit,'(A)') '&ION_PARAMS'
-      WRITE(iunit,'(A)') 
-     1'----------------------------------------------------------------'
-      WRITE(iunit,outint) 'NUM_ION_SPECIES',num_ion_species
-      WRITE(iunit,"(2X,A,1X,'=',4(1X,ES22.12E3))") 
-     1'Z_ION_INIT',(Z_ion_init(k), k=1,num_ion_species)
-      WRITE(iunit,"(2X,A,1X,'=',4(1X,ES22.12E3))") 
-     1'MIOMP_INIT',(miomp_init(k), k=1,num_ion_species)
-      WRITE(iunit,'(A)') '/\n'
-      END SUBROUTINE write_ion_params_nml
-
-      SUBROUTINE write_ion_params_namelist_byfile(filename)
-      USE safe_open_mod
-      IMPLICIT NONE
-      CHARACTER(LEN=*), INTENT(in) :: filename
-      INTEGER(iknd) :: iunit, istat
-      LOGICAL :: lexists
-      
-      iunit = 100
-      istat = 0
-      INQUIRE(FILE=TRIM(filename),exist=lexists)
-      IF (lexists) THEN
-         OPEN(unit=iunit, file=TRIM(filename), 
-     1        iostat=istat, status="old", position="append")
-      ELSE
-         OPEN(unit=iunit, file=TRIM(filename), 
-     1        iostat=istat, status="new")
-      END IF
-      IF (istat .ne. 0) RETURN
-      CALL write_ion_params_nml(iunit)
-      CLOSE(iunit)
-
-      RETURN
-      END SUBROUTINE write_ion_params_namelist_byfile
-      end module penta_input_mod
\ No newline at end of file
diff --git a/PENTA/Sources/penta_main.f b/PENTA/Sources/penta_main.f
deleted file mode 100644
index e49aa383a..000000000
--- a/PENTA/Sources/penta_main.f
+++ /dev/null
@@ -1,135 +0,0 @@
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c
-c   -PENTA with Impurities-
-c
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c  To run,type: PENTA_imp [command line arguments]
-c
-c  where the command line arguments are:
-c
-c  1  unique identifier text on DKES database files
-c      i.e., for (m,l,n)star_lijs_***, this would be
-c      the text that replaces *** for the specific surface (ex: hsx_s10)
-c  2  Er,min
-c  3  Er,max  - args 2 and 3 specify the interval in Er over which
-c      the search is done for the ambipolar electric field root.
-c      Er,min and Er,max are dimensionless normalized electric
-c      field variables, i.e.: e<a>Er,min/max/kT_e
-c    - Note if the logical variable input_is_Er below is true then 
-c      the search interval is set by args 2 and 3 as Er (V/cm)
-c  4  flux surface number
-c  5  parameter that determines whether output data should be
-c      written into new files (=0) or appended to
-c      existing files (=1). Typically,when a script is run for a
-c      sequence of flux surfaces, this is set to 0 for the first
-c      surface and to 1 for subsequent surfaces
-c  6  extension of the profile_data_*** file (i.e., the *** text)
-c      that comes from extracting the appropriate profiles from
-c      the VMEC run using the profile_extractor.f code
-c  7  unique identifier on plasma profiles file, i.e., the ***
-c      text in the filename plasma_profiles***.dat. This allows
-c      multiple profiles to be run without having to rename files
-c  8  <B*E||> in T*V/m
-c
-c
-c  Required input files:
-c
-c   [l,m,n]star_lijs_***_s# - where *** is arg1 above and # arg 4.
-c       These files contain the values of efield and cmul and the
-c       corresponding normalized monoenergetic coefficients.  Note
-c       that L* should be L*/e**2 where e is the elementary charge.
-c
-c   ion_params - A file containing the namelist "ion_params" which
-c       defines the variables num_ion_species, Z_ion_init and 
-c       miomp_init which are the number of ion species (integer),
-c       the corresponding ion charge numbers (real, array) and 
-c       the ion to proton mass ratio (real, array) for each 
-c       non-electron species.
-c
-c   profile_data_*** - where *** is arg1 above.  Contains geometry
-c       variables, most likely from a VMEC run.
-c
-c   plasma_profilesXXX.dat - A file containing the plasma profile
-c       data, where XXX is arg8 above.  This file has the format:
-c       row 1: number of radial points for which data is specified.
-c       all other rows: r/a, ne, Te, Ti1, ni1, Ti2, ni2 ...
-c       where the densities are in units of 10**12/cc and the 
-c       temperatures in eV and i1, i2... are the ion species.
-c
-c	Utilde2_profile - Contains the quantity <U**2>, where U is the
-c		PS flow function as defined in Sugama and Nishimura.  The
-c		first row is the number of points, then r/a points and the
-c		corresponding <U**2> value.
-c   
-c  Output files:
-c
-c   "fluxes_vs_roa", "fluxes_vs_Er", "flows_vs_roa", "plasma_profiles_check"
-c
-c   
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c   NOTES
-c    - Be sure to check parameters below
-c    - based on Sugama, Nishimura PoP 9 4637 (2002) and 
-c         Sugama, Nishimura PoP 15, 042502 (2008)
-c    - Some code used from orignal PENTA code, written by Don Spong and 
-c        modified by Jeremy Lore
-c
-c  7/2009 JL
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-      
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c   PROGRAMMING NOTES
-c   -speed optimization
-c   -recursive ambipolar solver
-c     -fix numargs
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c   2024 Notes
-c    - Created PENTA_IMP_MAIN program and changed PENTA_IMP to a
-c      callable subroutine.
-c    - Can read wout files instead of profile_data_****
-c    - Routine to set profiles instead of reading plasma_profiles_****
-c    - Routine to set L/M/NIJ coefficients instead of reading them.
-c    - Routine to set Utilde2 value instead of reading from file.
-c
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-    
-      PROGRAM PENTA_MAIN
-      use penta_kind_mod
-      USE read_wout_mod, ONLY: read_wout_deallocate
-      IMPLICIT NONE
-      integer(iknd) :: numargs, js, i_append
-      real(rknd) :: Er_min, Er_max, B_Eprl
-      character(100) :: arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8
-      character(100) :: coeff_ext, run_ident
-      character(10)  :: pprof_char
-      numargs = 8
-      call getarg(1, arg1)
-      call getarg(2, arg2)
-      call getarg(3, arg3)
-      call getarg(4, arg4)
-      call getarg(5, arg5)
-      call getarg(6, arg6)
-      call getarg(7, arg7)
-      if (numargs .eq. 8) call getarg(8, arg8)
-
-      !store command line args
-      coeff_ext = trim(adjustl(arg1))
-      read(arg2,*) Er_min
-      read(arg3,*) Er_max
-      read(arg4,*) js
-      read(arg5,*) i_append
-      run_ident = trim(adjustl(arg6))
-      pprof_char = trim(adjustl(arg7))
-      if (numargs .eq. 8) read(arg8,*) B_Eprl
-
-      ! Call subroutine
-      CALL PENTA_IMP(coeff_ext, Er_min, Er_max, js, i_append, 
-     1               run_ident, pprof_char, B_Eprl)
-
-      ! DEALLOCATE VMEC DATA
-      CALL read_wout_deallocate
-
-      END PROGRAM PENTA_MAIN
-

From 1e750f7548608105e611c24b8d448cd550bff7f7 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 15:02:56 +0200
Subject: [PATCH 23/47] THIFT: Added prototype of call to PENTA.

---
 THRIFT/Sources/thrift_penta.f90 | 77 +++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 THRIFT/Sources/thrift_penta.f90

diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
new file mode 100644
index 000000000..15786be24
--- /dev/null
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -0,0 +1,77 @@
+!-----------------------------------------------------------------------
+!     Subroutine:    thrift_penta
+!     Authors:       S. Lazerson (samuel.lazerson@gauss-fusion.com)
+!     Date:          08/22/2024
+!     Description:   This subroutine calculates the PENTA data.
+!-----------------------------------------------------------------------
+      SUBROUTINE thrift_penta(lscreen,iflag)
+!-----------------------------------------------------------------------
+!     Libraries
+!-----------------------------------------------------------------------
+      USE thrift_runtime
+      USE thrift_input_mod
+      USE thrift_vars, nrho_thrift => nrho
+      USE thrift_profiles_mod
+      USE thrift_equil
+      USE thrift_funcs
+      USE penta_interface_mod
+      USE mpi_params
+      USE mpi_inc
+!-----------------------------------------------------------------------
+!     Subroutine Parameters
+!        lscreen       Screen output
+!        iflag         Error flag
+!-----------------------------------------------------------------------
+      IMPLICIT NONE
+      LOGICAL, INTENT(in)    :: lscreen
+      INTEGER, INTENT(inout) :: iflag
+!-----------------------------------------------------------------------
+!     Local Variables
+!-----------------------------------------------------------------------
+      INTEGER :: ns_dkes, k
+      REAL(rprec) :: s
+!-----------------------------------------------------------------------
+!     BEGIN SUBROUTINE
+!-----------------------------------------------------------------------
+      IMPLICIT NONE
+      IF (iflag < 0) RETURN
+      IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL FLUX USING PENTA  -------------------'
+      IF (lvmec) THEN
+         ierr_mpi = 0
+         ! PENTA is parallelized over radial surfaces in this routine.
+         ns_dkes = 0
+         DO k = 1, DKES_NS_MAX
+            IF ((DKES_K(k) > 0)) ns_dkes = ns_dkes+1
+         END DO
+         ! Break up work
+         CALL MPI_CALC_MYRANGE(MPI_COMM_MYWORLD,1,ns_dkes,mystart,myend)
+         DO k = mystart,myend
+            ! This part mimics penta_run_1 but without reading the namelists
+            Er_min = -250.0
+            Er_max =  250.0
+            js     =  DKES_K(k)
+            i_append = 0
+            B_Eprl = 0.0
+            Smax   = 1
+            coeff_ext = ''
+            run_ident = ''
+            pprof_char = ''
+            CALL PENTA_ALLOCATE_SPECIES
+            CALL PENTA_READ_INPUT_FILES
+            CALL PENTA_SCREEN_INFO
+            CALL PENTA_ALLOCATE_DKESCOEFF
+            CALL PENTA_FIT_DXX_COEF
+            CALL PENTA_OPEN_OUTPUT
+            CALL PENTA_FIT_RAD_TRANS
+            ! Now the basic steps
+            CALL PENTA_RUN_2_EFIELD
+            CALL PENTA_RUN_3_AMBIPOLAR
+            CALL PENTA_RUN_4_CLEANUP
+         END DO
+      ENDIF
+      IF (lscreen) WRITE(6,'(a)') ' -------------------  NEOCLASSICAL FLUX CALCULATION DONE  ---------------------'
+      RETURN
+!-----------------------------------------------------------------------
+!     END SUBROUTINE
+!-----------------------------------------------------------------------
+      END SUBROUTINE thrift_penta
\ No newline at end of file

From 515faedbabc40b24faa3e0ead2db74cb06e820dc Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 15:41:40 +0200
Subject: [PATCH 24/47] PENTA: Added unique output file names possible.

---
 PENTA/Sources/penta_interface_mod.f90 | 28 +++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index 24480b1e1..f9f97a1df 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -490,11 +490,13 @@ SUBROUTINE penta_screen_info
       RETURN
    END SUBROUTINE penta_screen_info
 
-   SUBROUTINE penta_open_output
+   SUBROUTINE penta_open_output(file_ext)
       USE safe_open_mod
       USE io_unit_spec
       IMPLICIT NONE
+      CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: file_ext
       INTEGER :: istat
+      CHARACTER(LEN=256) :: local_ext
       istat = 0
       ! Set write status
       IF (i_append == 0) THEN
@@ -508,35 +510,41 @@ SUBROUTINE penta_open_output
          CALL FLUSH(6)
          STOP 'Error: Exiting, i_append error in penta.f90'
       END IF
+      ! Create local extension
+      IF (PRESENT(file_ext)) THEN
+         local_ext = "."//TRIM(file_ext)
+      ELSE
+         local_ext = ''
+      END IF
       ! Open files
       !Open(unit=iu_flux_out, file="fluxes_vs_roa", position=Trim(Adjustl(fpos)),status=Trim(Adjustl(fstatus)))
-      CALL safe_open(iu_flux_out, istat, "fluxes_vs_roa", &
+      CALL safe_open(iu_flux_out, istat, "fluxes_vs_roa"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
-      CALL safe_open(iu_pprof_out, istat, "plasma_profiles_check", &
+      CALL safe_open(iu_pprof_out, istat, "plasma_profiles_check"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
-      CALL safe_open(iu_fvEr_out, istat, "fluxes_vs_Er", &
+      CALL safe_open(iu_fvEr_out, istat, "fluxes_vs_Er"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
-      CALL safe_open(iu_flows_out, istat, "flows_vs_roa", &
+      CALL safe_open(iu_flows_out, istat, "flows_vs_roa"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
-      CALL safe_open(iu_flowvEr_out, istat, "flows_vs_Er", &
+      CALL safe_open(iu_flowvEr_out, istat, "flows_vs_Er"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
-      CALL safe_open(iu_Jprl_out, istat, "Jprl_vs_roa", &
+      CALL safe_open(iu_Jprl_out, istat, "Jprl_vs_roa"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
-      CALL safe_open(iu_contraflows_out, istat, "ucontra_vs_roa", &
+      CALL safe_open(iu_contraflows_out, istat, "ucontra_vs_roa"//TRIM(local_ext), &
          Trim(Adjustl(fstatus)), 'formatted',&
          access_in=Trim(Adjustl(fpos)))
       IF (method == 'SN') &
-         CALL safe_open(iu_sigmas_out, istat, "sigmas_vs_roa", &
+         CALL safe_open(iu_sigmas_out, istat, "sigmas_vs_roa"//TRIM(local_ext), &
             Trim(Adjustl(fstatus)), 'formatted',&
             access_in=Trim(Adjustl(fpos)))
       IF (output_QoT_vs_Er) THEN
-         CALL safe_open(iu_QoTvEr_out, istat, "QoTs_vs_Er", &
+         CALL safe_open(iu_QoTvEr_out, istat, "QoTs_vs_Er"//TRIM(local_ext), &
             Trim(Adjustl(fstatus)), 'formatted',&
             access_in=Trim(Adjustl(fpos)))
          Write(iu_QoTvEr_out,'("*",/,"r/a   Er[V/cm]   Q_e/T_e [m**-2s**-1] ",&

From 0f10b84e6b5f04ddc812c15fd1d6442427477a78 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 17 Oct 2024 15:42:05 +0200
Subject: [PATCH 25/47] THRIFT: PENTA interface uses unique output file names.

---
 THRIFT/Sources/thrift_penta.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index 15786be24..e63620b83 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -50,7 +50,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
             Er_min = -250.0
             Er_max =  250.0
             js     =  DKES_K(k)
-            i_append = 0
+            i_append = 1
             B_Eprl = 0.0
             Smax   = 1
             coeff_ext = ''
@@ -61,7 +61,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
             CALL PENTA_SCREEN_INFO
             CALL PENTA_ALLOCATE_DKESCOEFF
             CALL PENTA_FIT_DXX_COEF
-            CALL PENTA_OPEN_OUTPUT
+            CALL PENTA_OPEN_OUTPUT(proc_string)
             CALL PENTA_FIT_RAD_TRANS
             ! Now the basic steps
             CALL PENTA_RUN_2_EFIELD

From 94330d2b2c598f14c57e0417fb62fa2a60d28096 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 12:29:31 +0200
Subject: [PATCH 26/47] PENTA: Added wrapper routines for ion namelist, command
 line, and vmec data

---
 PENTA/Sources/penta_interface_mod.f90 | 81 +++++++++++++++++++++++++++
 1 file changed, 81 insertions(+)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index f9f97a1df..b286ed274 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -82,6 +82,17 @@ SUBROUTINE init_penta_input
       RETURN
    END SUBROUTINE init_penta_input
 
+   SUBROUTINE penta_set_ion_params(num_ion_in, Z_ion_in, miomp_in)
+      IMPLICIT NONE
+      INTEGER, INTENT(in) :: num_ion_in
+      REAL(rknd), DIMENSION(NUM_ION_MAX), INTENT(in) ::  Z_ion_in
+      REAL(rknd), DIMENSION(NUM_ION_MAX), INTENT(in) ::  miomp_in
+      num_ion_species = num_ion_in
+      Z_ion_init = Z_ion_in
+      miomp_init = miomp_in
+      RETURN
+   END SUBROUTINE penta_set_ion_params
+
    SUBROUTINE read_penta_ion_params_namelist(filename,istat)
       USE safe_open_mod
       IMPLICIT NONE
@@ -264,6 +275,29 @@ SUBROUTINE penta_init_commandline
       RETURN
    END SUBROUTINE penta_init_commandline
 
+   SUBROUTINE penta_set_commandline(Er_min_in,Er_max_in,js_in,i_append_in,B_Eprl_in,Smax_in,ext_in,run_in,pprof_in)
+      IMPLICIT NONE
+      REAL(rknd), INTENT(IN) :: Er_min_in
+      REAL(rknd), INTENT(IN) :: Er_max_in
+      INTEGER(iknd), INTENT(IN) :: js_in
+      INTEGER(iknd), INTENT(IN) :: i_append_in
+      REAL(rknd), INTENT(IN) :: B_Eprl_in
+      REAL(rknd), INTENT(IN) :: Smax_in
+      CHARACTER(LEN=*), INTENT(IN) :: ext_in
+      CHARACTER(LEN=*), INTENT(IN) :: run_in
+      CHARACTER(LEN=*), INTENT(IN) :: pprof_in
+      Er_min   = Er_min_in
+      Er_max   = Er_max_in
+      js       = js_in
+      i_append = i_append_in
+      B_Eprl   = B_Eprl_in
+      Smax     = Smax_in
+      coeff_ext  = TRIM(ADJUSTL(ext_in))
+      run_ident  = TRIM(ADJUSTL(run_in))
+      pprof_char = TRIM(ADJUSTL(pprof_in))
+      RETURN
+   END SUBROUTINE penta_set_commandline
+
    SUBROUTINE penta_allocate_species
       USE pprof_pass, ONLY: ni, Ti, dnidr, dTidr
       IMPLICIT NONE
@@ -415,6 +449,53 @@ SUBROUTINE penta_read_input_files
       RETURN
    END SUBROUTINE penta_read_input_files
 
+   SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,bz_in,Bsq_in,B0_in)
+      USE vmec_var_pass
+      IMPLICIT NONE
+      REAL(rknd), INTENT(IN) :: rho
+      REAL(rknd), INTENT(IN) :: A_in
+      REAL(rknd), INTENT(IN) :: R_in
+      REAL(rknd), INTENT(IN) :: V_in
+      REAL(rknd), INTENT(IN) :: chip_in
+      REAL(rknd), INTENT(IN) :: phip_in
+      REAL(rknd), INTENT(IN) :: iota_in
+      REAL(rknd), INTENT(IN) :: bth_in
+      REAL(rknd), INTENT(IN) :: bze_in
+      REAL(rknd), INTENT(IN) :: Bsq_in
+      REAL(rknd), INTENT(IN) :: B0_in
+      REAL(rknd) :: TWOPI
+      TWOPI = 8*ATAN(1.0_rknd)
+      roa_surf = rho
+      arad = A_in
+      Rmajor = R_in
+      r_surf = roa_surf*arad
+      chip = chip_in
+      psip = phip_in
+      iota = iota_in
+      btheta = bth_in
+      bzeta = bze_in
+      Bsq = Bsq_in
+      vol_p = V_in
+      B0 = B0_in
+      ! Note that vp from VMEC comes normalized by 4pi^2
+      ! Therefore we need to denormalize it
+      vol_p = TWOPI*TWOPI*vol_p
+      ! vp_vmec is ~dV/ds, but what we want is dVdr=dVds*dsdr
+      ! Since PENTA uses r/a=sqrt(s), then dVdr=dVds*2*r/a^2 
+      vol_p = vol_p * 2.0_rknd*r_surf/arad**2
+      !Same for psip and chip: need to convert d/ds to d/dr
+      psip = psip * 2.0_rknd*r_surf/arad**2
+      chip = chip * 2.0_rknd*r_surf/arad**2
+      !psip and chip are used to compute flows in theta and zeta direction (see penta.f90)
+      !It is assumed that psip and chip are normalized by 2pi
+      !So need to do it here:
+      psip = psip / TWOPI
+      chip = chip / TWOPI
+      ! For the SN formulation this is the think to do, but not for the the other formulations...
+      b0 = dsqrt(bsq)
+      RETURN
+   END SUBROUTINE penta_set_eq_data
+
    SUBROUTINE penta_fit_DXX_coef
       USE coeff_var_pass
       USE PENTA_subroutines, ONLY : fit_coeffs

From 6608bc53b1ef32557aef35f71519e632d674f902 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 14:16:25 +0200
Subject: [PATCH 27/47] PENTA: Added the missing interfaces to avoid using
 files.

---
 PENTA/Sources/penta_interface_mod.f90 | 125 ++++++++++++++++++++++----
 1 file changed, 108 insertions(+), 17 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index b286ed274..702d40be5 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -399,27 +399,36 @@ SUBROUTINE penta_deallocate_dkescoeff
       RETURN
    END SUBROUTINE penta_deallocate_dkescoeff
 
-   SUBROUTINE penta_read_input_files
+   SUBROUTINE penta_read_input_files(lvmec,lpprof,ldkes,lbeam,lU2)
       USE vmec_var_pass, ONLY: roa_surf, arad, Bsq
       USE pprof_pass
       USE coeff_var_pass, ONLY: D11_mat, cmul, num_c
       USE phys_const, ONLY: p_mass, elem_charge, e_mass
       USE read_input_file_mod
       IMPLICIT NONE
-      CALL read_vmec_file_2(js,run_ident)
-      CALL read_pprof_file(pprof_char,num_ion_species,roa_surf,arad,kord_pprof)
-      CALL read_dkes_star_files(coeff_ext,Add_Spitzer_to_D33,Bsq)
-      IF (use_beam) THEN
-         CALL read_beam_file(roa_surf,kord_pprof)
-      ELSE
-         beam_force = 0._rknd
+      LOGICAL, INTENT(IN) :: lvmec
+      LOGICAL, INTENT(IN) :: lpprof
+      LOGICAL, INTENT(IN) :: ldkes
+      LOGICAL, INTENT(IN) :: lbeam
+      LOGICAL, INTENT(IN) :: lU2
+      IF (lvmec) CALL read_vmec_file_2(js,run_ident)
+      IF (lpprof) CALL read_pprof_file(pprof_char,num_ion_species,roa_surf,arad,kord_pprof)
+      IF (ldkes) CALL read_dkes_star_files(coeff_ext,Add_Spitzer_to_D33,Bsq)
+      IF (lbeam) THEN
+         IF (use_beam) THEN
+            CALL read_beam_file(roa_surf,kord_pprof)
+         ELSE
+            beam_force = 0._rknd
+         ENDIF
       ENDIF
       ! Optionally read file containing <U**2> info.  Else this is 
       ! calculated from the D11* coefficient at high nu/v and Er=0.
-      IF ( read_U2_file ) THEN
-         CALL read_Utilde2_file(roa_surf,U2,kord_pprof)
-      ELSE
-         U2=1.5d0*D11_mat(num_c,1)/cmul(num_c);
+      IF (lU2) THEN
+         IF ( read_U2_file) THEN
+            CALL read_Utilde2_file(roa_surf,U2,kord_pprof)
+         ELSE
+            U2=1.5d0*D11_mat(num_c,1)/cmul(num_c);
+         ENDIF
       ENDIF
       ! Change Er test range to V/cm if necessary
       IF ( .not. input_is_Er) THEN
@@ -449,7 +458,7 @@ SUBROUTINE penta_read_input_files
       RETURN
    END SUBROUTINE penta_read_input_files
 
-   SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,bz_in,Bsq_in,B0_in)
+   SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,bze_in,Bsq_in)
       USE vmec_var_pass
       IMPLICIT NONE
       REAL(rknd), INTENT(IN) :: rho
@@ -462,7 +471,6 @@ SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,b
       REAL(rknd), INTENT(IN) :: bth_in
       REAL(rknd), INTENT(IN) :: bze_in
       REAL(rknd), INTENT(IN) :: Bsq_in
-      REAL(rknd), INTENT(IN) :: B0_in
       REAL(rknd) :: TWOPI
       TWOPI = 8*ATAN(1.0_rknd)
       roa_surf = rho
@@ -476,7 +484,6 @@ SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,b
       bzeta = bze_in
       Bsq = Bsq_in
       vol_p = V_in
-      B0 = B0_in
       ! Note that vp from VMEC comes normalized by 4pi^2
       ! Therefore we need to denormalize it
       vol_p = TWOPI*TWOPI*vol_p
@@ -492,10 +499,94 @@ SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,b
       psip = psip / TWOPI
       chip = chip / TWOPI
       ! For the SN formulation this is the think to do, but not for the the other formulations...
-      b0 = dsqrt(bsq)
+      b0 = dsqrt(Bsq)
       RETURN
    END SUBROUTINE penta_set_eq_data
 
+   SUBROUTINE penta_set_pprof(ne_in,dnedr_in,te_in,dtedr_in,ni_in,dnidr_in,ti_in,dtidr_in)
+      USE pprof_pass
+      IMPLICIT NONE
+      REAL(rknd), INTENT(IN) :: ne_in
+      REAL(rknd), INTENT(IN) :: dnedr_in
+      REAL(rknd), INTENT(IN) :: te_in
+      REAL(rknd), INTENT(IN) :: dtedr_in
+      REAL(rknd), DIMENSION(num_ion_species), INTENT(IN) :: ni_in
+      REAL(rknd), DIMENSION(num_ion_species), INTENT(IN) :: dnidr_in
+      REAL(rknd), DIMENSION(num_ion_species), INTENT(IN) :: ti_in
+      REAL(rknd), DIMENSION(num_ion_species), INTENT(IN) :: dtidr_in
+      ne    = ne_in
+      dnedr = dnedr_in
+      te    = te_in
+      dtedr = dtedr_in
+      ni    = ni_in
+      dnidr = dnidr_in
+      ti    = ni_in
+      dtidr = dnidr_in
+      RETURN
+   END SUBROUTINE penta_set_pprof
+
+   SUBROUTINE penta_set_DKES_star(nc,ne,cmul_in,efield_in,D11_in,D13_in,D33_in)
+      USE vmec_var_pass, ONLY: Bsq
+      USE coeff_var_pass
+      IMPLICIT NONE
+      INTEGER(iknd), INTENT(in) :: nc,ne
+      REAL(rknd), DIMENSION(nc), INTENT(IN) :: cmul_in
+      REAL(rknd), DIMENSION(ne), INTENT(IN) :: efield_in
+      REAL(rknd), DIMENSION(nc,ne), INTENT(IN) :: D11_in
+      REAL(rknd), DIMENSION(nc,ne), INTENT(IN) :: D13_in
+      REAL(rknd), DIMENSION(nc,ne), INTENT(IN) :: D33_in
+      INTEGER :: je, ic
+      REAL(rknd) :: D33_Spitzer
+      num_c = nc
+      num_e = ne
+      IF (ALLOCATED(cmul)) DEALLOCATE(cmul)
+      IF (ALLOCATED(efield)) DEALLOCATE(efield)
+      IF (ALLOCATED(D11_mat)) DEALLOCATE(D11_mat)
+      IF (ALLOCATED(D13_mat)) DEALLOCATE(D13_mat)
+      IF (ALLOCATED(D31_mat)) DEALLOCATE(D31_mat)
+      IF (ALLOCATED(D33_mat)) DEALLOCATE(D33_mat)
+      ALLOCATE(cmul(num_c))
+      ALLOCATE(efield(num_e))
+      ALLOCATE(D11_mat(num_c,num_e))
+      ALLOCATE(D13_mat(num_c,num_e))
+      ALLOCATE(D31_mat(num_c,num_e))
+      ALLOCATE(D33_mat(num_c,num_e))
+      cmul = cmul_in
+      efield = efield_in
+      D11_mat = D11_in
+      D13_mat = D13_in
+      D33_mat = D33_in
+      ! Create D31 using Onsager symmetry
+      D31_mat = -D13_mat
+      IF (Add_Spitzer_to_D33) THEN
+         DO je = 1, num_e
+            DO ic = 1, num_c
+               ! Calculate D33* Spitzer = (2/3)*<B**2>/cmul
+               D33_Spitzer = (2._rknd/3._rknd)*Bsq/cmul(ic)
+               ! Calculate D33*(Physical)=D33*(Spitzer)-D33*
+               D33_mat(ic,je) = D33_Spitzer - D33_mat(ic,je)
+            ENDDO
+         ENDDO
+      END IF
+   END SUBROUTINE penta_set_DKES_star
+
+   SUBROUTINE penta_set_beam(beam_force_in)
+      Use pprof_pass, ONLY: beam_force
+      IMPLICIT NONE
+      REAL(rknd), INTENT(IN) :: beam_force_in
+      beam_force = beam_force_in
+      RETURN
+   END SUBROUTINE penta_set_beam
+
+   SUBROUTINE penta_set_U2(U2_in)
+      USE coeff_var_pass, ONLY: D11_mat,cmul,num_c
+      IMPLICIT NONE
+      REAL(rknd), INTENT(IN), OPTIONAL :: U2_in
+      U2=1.5d0*D11_mat(num_c,1)/cmul(num_c)
+      IF (PRESENT(U2_in)) U2 = U2_in
+      RETURN
+   END SUBROUTINE penta_set_U2
+
    SUBROUTINE penta_fit_DXX_coef
       USE coeff_var_pass
       USE PENTA_subroutines, ONLY : fit_coeffs
@@ -723,7 +814,7 @@ SUBROUTINE penta_run_1_init
       CALL read_penta_run_params_namelist('run_params',istat)
       CALL penta_init_commandline
       CALL penta_allocate_species
-      CALL penta_read_input_files
+      CALL penta_read_input_files(.TRUE.,.TRUE.,.TRUE.,.TRUE.,.TRUE.)
       CALL penta_screen_info
       CALL penta_allocate_dkescoeff
       CALL penta_fit_DXX_coef

From 5636ea4f84ceb104156eea8f24e6cfe56c49e7a2 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 15:43:56 +0200
Subject: [PATCH 28/47] PENTA: Fixed a variable name to reflect dVds value not
 Volume.

---
 PENTA/Sources/penta_interface_mod.f90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index 702d40be5..8cee618db 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -458,13 +458,13 @@ SUBROUTINE penta_read_input_files(lvmec,lpprof,ldkes,lbeam,lU2)
       RETURN
    END SUBROUTINE penta_read_input_files
 
-   SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,bze_in,Bsq_in)
+   SUBROUTINE penta_set_eq_data(rho,A_in,R_in,Vp_in,chip_in,phip_in,iota_in,bth_in,bze_in,Bsq_in)
       USE vmec_var_pass
       IMPLICIT NONE
       REAL(rknd), INTENT(IN) :: rho
       REAL(rknd), INTENT(IN) :: A_in
       REAL(rknd), INTENT(IN) :: R_in
-      REAL(rknd), INTENT(IN) :: V_in
+      REAL(rknd), INTENT(IN) :: Vp_in
       REAL(rknd), INTENT(IN) :: chip_in
       REAL(rknd), INTENT(IN) :: phip_in
       REAL(rknd), INTENT(IN) :: iota_in
@@ -483,7 +483,7 @@ SUBROUTINE penta_set_eq_data(rho,A_in,R_in,V_in,chip_in,phip_in,iota_in,bth_in,b
       btheta = bth_in
       bzeta = bze_in
       Bsq = Bsq_in
-      vol_p = V_in
+      vol_p = Vp_in
       ! Note that vp from VMEC comes normalized by 4pi^2
       ! Therefore we need to denormalize it
       vol_p = TWOPI*TWOPI*vol_p

From b42c44d2d3c6aa9edea5176e9e3a8bcd08c71ef1 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 15:44:45 +0200
Subject: [PATCH 29/47] THRIFT: Added buco, bvco, and bsq splines to support
 PENTA integration.

---
 THRIFT/Sources/thrift_equil.f90     |  3 ++-
 THRIFT/Sources/thrift_load_vmec.f90 | 30 +++++++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/THRIFT/Sources/thrift_equil.f90 b/THRIFT/Sources/thrift_equil.f90
index e399c10aa..94bc2a236 100644
--- a/THRIFT/Sources/thrift_equil.f90
+++ b/THRIFT/Sources/thrift_equil.f90
@@ -27,7 +27,8 @@ MODULE thrift_equil
 
     ! Spline helpers
     INTEGER :: bcs1(2)
-    TYPE(EZspline1_r8) :: iota_spl, phip_spl, vp_spl
+    TYPE(EZspline1_r8) :: iota_spl, phip_spl, vp_spl, bu_spl, bv_spl, &
+                            bsq_spl
 
 
 END MODULE thrift_equil
diff --git a/THRIFT/Sources/thrift_load_vmec.f90 b/THRIFT/Sources/thrift_load_vmec.f90
index c6b50bf36..d1ed29d88 100644
--- a/THRIFT/Sources/thrift_load_vmec.f90
+++ b/THRIFT/Sources/thrift_load_vmec.f90
@@ -230,6 +230,36 @@ SUBROUTINE thrift_load_vmec
       CALL EZspline_setup(vp_spl,vp,iflag,EXACT_DIM=.true.)
       IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: vp',iflag)
 
+      ! BU
+      bcs1=(/ 0, 0/)
+      IF (EZspline_allocated(bu_spl)) CALL EZspline_free(bu_spl,iflag)
+      CALL EZspline_init(bu_spl,ns,bcs1,iflag)
+      IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: bu',iflag)
+      bu_spl%isHermite   = 0
+      FORALL (k=1:ns) bu_spl%x1(k) = sqrt(DBLE(k-1)/DBLE(ns-1))
+      CALL EZspline_setup(bu_spl,buco,iflag,EXACT_DIM=.true.)
+      IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: bu',iflag)
+
+      ! BV
+      bcs1=(/ 0, 0/)
+      IF (EZspline_allocated(bv_spl)) CALL EZspline_free(bv_spl,iflag)
+      CALL EZspline_init(bv_spl,ns,bcs1,iflag)
+      IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: bv',iflag)
+      bv_spl%isHermite   = 0
+      FORALL (k=1:ns) bv_spl%x1(k) = sqrt(DBLE(k-1)/DBLE(ns-1))
+      CALL EZspline_setup(bv_spl,bvco,iflag,EXACT_DIM=.true.)
+      IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: bv',iflag)
+
+      ! BSQ
+      bcs1=(/ 0, 0/)
+      IF (EZspline_allocated(bsq_spl)) CALL EZspline_free(bsq_spl,iflag)
+      CALL EZspline_init(bsq_spl,ns,bcs1,iflag)
+      IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: bsq',iflag)
+      bsq_spl%isHermite   = 0
+      FORALL (k=1:ns) bsq_spl%x1(k) = sqrt(DBLE(k-1)/DBLE(ns-1))
+      CALL EZspline_setup(bsq_spl,bdotb,iflag,EXACT_DIM=.true.)
+      IF (iflag /=0) CALL handle_err(EZSPLINE_ERR,'thrift_load_vmec: bsq',iflag)
+
 
       RETURN
 !----------------------------------------------------------------------

From 9ba34b7a36a110d2c6a162b9b15d0cd36ab6028b Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 15:45:07 +0200
Subject: [PATCH 30/47] THRIFT: PENTA interface updated.

---
 THRIFT/Sources/thrift_penta.f90 | 63 ++++++++++++++++++++++++++-------
 1 file changed, 50 insertions(+), 13 deletions(-)

diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index e63620b83..4fa6ab5cd 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -28,8 +28,11 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !-----------------------------------------------------------------------
 !     Local Variables
 !-----------------------------------------------------------------------
-      INTEGER :: ns_dkes, k
-      REAL(rprec) :: s
+      INTEGER :: ns_dkes, k, ier, j, i, ncstar, nestar
+      REAL(rprec) :: s, rho, iota, phip, chip, btheta, bzeta, bsq, vp, &
+                        te, ne, dtedrho, dnedrho
+      REAL(rprec), DIMENSION(num_ion_species) :: ni,ti, dtidrho, dnidrho
+      REAL(rprec), DIMENSION(:,:), ALLOCATABLE :: D11, D13, D33
 !-----------------------------------------------------------------------
 !     BEGIN SUBROUTINE
 !-----------------------------------------------------------------------
@@ -46,18 +49,52 @@ SUBROUTINE thrift_penta(lscreen,iflag)
          ! Break up work
          CALL MPI_CALC_MYRANGE(MPI_COMM_MYWORLD,1,ns_dkes,mystart,myend)
          DO k = mystart,myend
-            ! This part mimics penta_run_1 but without reading the namelists
-            Er_min = -250.0
-            Er_max =  250.0
-            js     =  DKES_K(k)
-            i_append = 1
-            B_Eprl = 0.0
-            Smax   = 1
-            coeff_ext = ''
-            run_ident = ''
-            pprof_char = ''
+            ! Calc some information
+            s = DKES_K(k)/ns_equil ! <- Need to see if we have this number
+            rho = sqrt(s)
+            ier = 0
+            CALL EZSpline_interp(iota_spl, rho, iota, ier)
+            ier = 0
+            CALL EZSpline_interp(phip_spl, rho, phip, ier)
+            ! PENTA wants d/ds note that this won't work if rho=0
+            phip = 0.5*phip/rho
+            chip = iota * phip
+            ier = 0
+            CALL EZSpline_interp(bu_spl, rho, btheta, ier)
+            ier = 0
+            CALL EZSpline_interp(bv_spl, rho, bzeta, ier)
+            ier = 0
+            CALL EZSpline_interp(bsq_spl, rho, bsq, ier)
+            ier = 0
+            CALL EZSpline_interp(vp_spl, rho, vp, ier)
+            ! Vp = dV/dPHI need dVds with VMEC normalization
+            vp = vp * phip /(pi2*pi2)
+            ! Profiles
+            CALL get_prof_te(rho, THRIFT_T(mytimestep), te)
+            CALL get_prof_ne(rho, THRIFT_T(mytimestep), ne)
+            CALL get_prof_teprime(rho, THRIFT_T(mytimestep), dtedrho)
+            CALL get_prof_neprime(rho, THRIFT_T(mytimestep), dnedrho)
+            DO j = 1, num_ion_species
+               CALL get_prof_ti(rho, THRIFT_T(mytimestep), j, ti(j))
+               CALL get_prof_ni(rho, THRIFT_T(mytimestep), j, ni(j))
+               CALL get_prof_tiprime(rho, THRIFT_T(mytimestep), j, dtidrho(j))
+               CALL get_prof_niprime(rho, THRIFT_T(mytimestep), j, dnidrho(j))
+            ! DKES Data
+            ncstar = COUNT(DKES_NUSTAR < 1E10)
+            nestar = COUNT(DKES_ERSTAR < 1E10)
+
+            ! PENTA
+            CALL PENTA_SET_ION_PARAMS(nion_prof, Zatom_prof, mass_prof/AMU)
+            CALL PENTA_SET_COMMANDLINE(-250.0,250.0,DKES_K(k),1,0.0,1,'','','')
             CALL PENTA_ALLOCATE_SPECIES
-            CALL PENTA_READ_INPUT_FILES
+            CALL PENTA_SET_EQ_DATA(rho,eq_Aminor,eq_Rmajor,vp,chip,phip,iota,btheta,bzeta,bsq)
+            CALL PENTA_SET_PPROF(ne,dnedrho,te,dtedrho,ni,dnidrho,ti,dtidrho)
+            !SUBROUTINE penta_set_DKES_star(nc,ne,cmul_in,efield_in,D11_in,D13_in,D33_in)
+            CALL PENTA_SET_DKES_STAR(ncstar,nestar,DKES_NUSTAR(1:ncstar),DKES_ERSTAR(1:nestar), &
+               D11,D13,D33)
+            CALL PENTA_SET_BEAM(0.0) ! Zero becasue we don't read
+            CALL PENTA_SET_U2() ! Leave blank for default value
+            CALL PENTA_READ_INPUT_FILES(.FALSE.,.FALSE.,.FALSE.,.FALSE.,.FALSE.)
             CALL PENTA_SCREEN_INFO
             CALL PENTA_ALLOCATE_DKESCOEFF
             CALL PENTA_FIT_DXX_COEF

From ba14122f043d6de81480969a2d7a42f39b3667b7 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 15:58:27 +0200
Subject: [PATCH 31/47] PENTA: Fixed type of Smax in interface routine.

---
 PENTA/Sources/penta_interface_mod.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index 8cee618db..fd12a703c 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -282,7 +282,7 @@ SUBROUTINE penta_set_commandline(Er_min_in,Er_max_in,js_in,i_append_in,B_Eprl_in
       INTEGER(iknd), INTENT(IN) :: js_in
       INTEGER(iknd), INTENT(IN) :: i_append_in
       REAL(rknd), INTENT(IN) :: B_Eprl_in
-      REAL(rknd), INTENT(IN) :: Smax_in
+      INTEGER(iknd), INTENT(IN) :: Smax_in
       CHARACTER(LEN=*), INTENT(IN) :: ext_in
       CHARACTER(LEN=*), INTENT(IN) :: run_in
       CHARACTER(LEN=*), INTENT(IN) :: pprof_in

From 32d1db3faacea26efd96737399beda979fff23a0 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 15:59:03 +0200
Subject: [PATCH 32/47] THRIFT: Added VMEC ns helper

---
 THRIFT/Sources/thrift_equil.f90     | 2 +-
 THRIFT/Sources/thrift_load_vmec.f90 | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/THRIFT/Sources/thrift_equil.f90 b/THRIFT/Sources/thrift_equil.f90
index 94bc2a236..41147cfc1 100644
--- a/THRIFT/Sources/thrift_equil.f90
+++ b/THRIFT/Sources/thrift_equil.f90
@@ -23,7 +23,7 @@ MODULE thrift_equil
     IMPLICIT NONE
 
     REAL(rprec) :: bt0, el0, iota0, eq_beta, eq_Aminor, eq_Rmajor, &
-                   eq_phiedge, eq_volume
+                   eq_phiedge, eq_volume, ns_eq
 
     ! Spline helpers
     INTEGER :: bcs1(2)
diff --git a/THRIFT/Sources/thrift_load_vmec.f90 b/THRIFT/Sources/thrift_load_vmec.f90
index d1ed29d88..184cf42ca 100644
--- a/THRIFT/Sources/thrift_load_vmec.f90
+++ b/THRIFT/Sources/thrift_load_vmec.f90
@@ -184,6 +184,7 @@ SUBROUTINE thrift_load_vmec
       ! Helpers
       b0 = RBtor0/Rmajor
       iota0 = iotaf(1)
+      ns_eq = ns
 
       ! We want dV/dPhi = dV/ds*ds/dPhi = dV/ds / (dPhi/ds)
       !     Note that Vp is missing a factor of 4*pi*pi

From 15c86acc12d64d67c0f221ccc4bbdda7cef9d703 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 15:59:40 +0200
Subject: [PATCH 33/47] THRIFT: Made AMU available through the profiles module.

---
 THRIFT/Sources/thrift_profiles_mod.f90 | 2 ++
 THRIFT/Sources/thrift_run_nbcd.f90     | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/THRIFT/Sources/thrift_profiles_mod.f90 b/THRIFT/Sources/thrift_profiles_mod.f90
index 3bf2b5132..23f21bea8 100644
--- a/THRIFT/Sources/thrift_profiles_mod.f90
+++ b/THRIFT/Sources/thrift_profiles_mod.f90
@@ -26,6 +26,8 @@ MODULE thrift_profiles_mod
     INTEGER :: win_raxis_prof, win_taxis_prof, win_NE3D, win_TE3D, &
                win_NI4D, win_TI4D, win_hr, win_ht, win_hri, win_hti, &
                win_Matom_prof, win_Zatom_prof, win_P3D
+
+    REAL(rprec), PARAMETER :: AMU = 1.66053906892D-27
 !-----------------------------------------------------------------------
 !     Input Namelists
 !         NONE
diff --git a/THRIFT/Sources/thrift_run_nbcd.f90 b/THRIFT/Sources/thrift_run_nbcd.f90
index e0db38e0c..1595fd749 100644
--- a/THRIFT/Sources/thrift_run_nbcd.f90
+++ b/THRIFT/Sources/thrift_run_nbcd.f90
@@ -17,7 +17,6 @@ SUBROUTINE thrift_run_nbcd
 !         i           Loop index
 !-----------------------------------------------------------------------
       IMPLICIT NONE
-      REAL(rprec), PARAMETER :: amu = 1.66053906660D-27
       INTEGER :: i
       REAL(rprec) :: mass, NBI_A, NBI_E, NBI_Z, NBI_alpha, NBI_theta, NBI_Pdense ! probably should be inputs
       REAL(rprec) :: ne, Te, Ti, Zeff, InvAspect, G, NBI_V, rho, timenow, jopb

From 8ceb5cef1eb3cc2a05b4c222747794db6a7041ae Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 16:00:42 +0200
Subject: [PATCH 34/47] THRIFT: PENTA added, missing DXX coefficient handling.

---
 THRIFT/ObjectList               |  1 +
 THRIFT/Sources/thrift_penta.f90 | 13 ++++++-------
 THRIFT/THRIFT.dep               | 10 ++++++++++
 3 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/THRIFT/ObjectList b/THRIFT/ObjectList
index 1da248bf7..f237bd14b 100644
--- a/THRIFT/ObjectList
+++ b/THRIFT/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+thrift_penta.o \
 thrift_dkes.o \
 thrift_diagno.o \
 thrift_run_diagnostics.o \
diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index 4fa6ab5cd..26d972821 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -9,7 +9,6 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !     Libraries
 !-----------------------------------------------------------------------
       USE thrift_runtime
-      USE thrift_input_mod
       USE thrift_vars, nrho_thrift => nrho
       USE thrift_profiles_mod
       USE thrift_equil
@@ -28,7 +27,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !-----------------------------------------------------------------------
 !     Local Variables
 !-----------------------------------------------------------------------
-      INTEGER :: ns_dkes, k, ier, j, i, ncstar, nestar
+      INTEGER :: ns_dkes, k, ier, j, i, ncstar, nestar, mystart, myend
       REAL(rprec) :: s, rho, iota, phip, chip, btheta, bzeta, bsq, vp, &
                         te, ne, dtedrho, dnedrho
       REAL(rprec), DIMENSION(num_ion_species) :: ni,ti, dtidrho, dnidrho
@@ -36,7 +35,6 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !-----------------------------------------------------------------------
 !     BEGIN SUBROUTINE
 !-----------------------------------------------------------------------
-      IMPLICIT NONE
       IF (iflag < 0) RETURN
       IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL FLUX USING PENTA  -------------------'
       IF (lvmec) THEN
@@ -50,7 +48,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
          CALL MPI_CALC_MYRANGE(MPI_COMM_MYWORLD,1,ns_dkes,mystart,myend)
          DO k = mystart,myend
             ! Calc some information
-            s = DKES_K(k)/ns_equil ! <- Need to see if we have this number
+            s = DKES_K(k)/ns_eq
             rho = sqrt(s)
             ier = 0
             CALL EZSpline_interp(iota_spl, rho, iota, ier)
@@ -79,20 +77,21 @@ SUBROUTINE thrift_penta(lscreen,iflag)
                CALL get_prof_ni(rho, THRIFT_T(mytimestep), j, ni(j))
                CALL get_prof_tiprime(rho, THRIFT_T(mytimestep), j, dtidrho(j))
                CALL get_prof_niprime(rho, THRIFT_T(mytimestep), j, dnidrho(j))
+            END DO
             ! DKES Data
             ncstar = COUNT(DKES_NUSTAR < 1E10)
             nestar = COUNT(DKES_ERSTAR < 1E10)
 
             ! PENTA
-            CALL PENTA_SET_ION_PARAMS(nion_prof, Zatom_prof, mass_prof/AMU)
-            CALL PENTA_SET_COMMANDLINE(-250.0,250.0,DKES_K(k),1,0.0,1,'','','')
+            CALL PENTA_SET_ION_PARAMS(nion_prof, DBLE(Zatom_prof), Matom_prof/AMU)
+            CALL PENTA_SET_COMMANDLINE(-250.0_rprec,250.0_rprec,DKES_K(k),1,0.0_rprec,1,'','','')
             CALL PENTA_ALLOCATE_SPECIES
             CALL PENTA_SET_EQ_DATA(rho,eq_Aminor,eq_Rmajor,vp,chip,phip,iota,btheta,bzeta,bsq)
             CALL PENTA_SET_PPROF(ne,dnedrho,te,dtedrho,ni,dnidrho,ti,dtidrho)
             !SUBROUTINE penta_set_DKES_star(nc,ne,cmul_in,efield_in,D11_in,D13_in,D33_in)
             CALL PENTA_SET_DKES_STAR(ncstar,nestar,DKES_NUSTAR(1:ncstar),DKES_ERSTAR(1:nestar), &
                D11,D13,D33)
-            CALL PENTA_SET_BEAM(0.0) ! Zero becasue we don't read
+            CALL PENTA_SET_BEAM(0.0_rprec) ! Zero becasue we don't read
             CALL PENTA_SET_U2() ! Leave blank for default value
             CALL PENTA_READ_INPUT_FILES(.FALSE.,.FALSE.,.FALSE.,.FALSE.,.FALSE.)
             CALL PENTA_SCREEN_INFO
diff --git a/THRIFT/THRIFT.dep b/THRIFT/THRIFT.dep
index 018053f37..53398edc0 100644
--- a/THRIFT/THRIFT.dep
+++ b/THRIFT/THRIFT.dep
@@ -135,6 +135,16 @@ thrift_paraexe.o : \
       $(VMEC_DIR)/$(LOCTYPE)/parallel_vmec_module.o \
       $(VMEC_DIR)/$(LOCTYPE)/vmec_params.o
 
+thrift_penta.o : \
+      thrift_runtime.o \
+      thrift_vars.o \
+      thrift_profiles_mod.o \
+      thrift_equil.o \
+      thrift_funcs.o \
+      $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
+      $(LIB_DIR)/$(LOCTYPE)/mpi_params.o  \
+      $(PENTA_DIR)/$(LOCTYPE)/penta_interface_mod.o
+
 thrift_profiles_mod.o : \
       thrift_runtime.o \
       $(LIB_DIR)/$(LOCTYPE)/stel_kinds.o \

From abfab33224eca67b003e61e142423be8e9598b8b Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 17:21:32 +0200
Subject: [PATCH 35/47] DKES: Added some helper vars for THRIFT.

---
 DKES/Sources/General/dkes_realspace.f | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DKES/Sources/General/dkes_realspace.f b/DKES/Sources/General/dkes_realspace.f
index 362ccdd2b..0d297d6d2 100644
--- a/DKES/Sources/General/dkes_realspace.f
+++ b/DKES/Sources/General/dkes_realspace.f
@@ -27,6 +27,7 @@ MODULE dkes_realspace
      1   DKES_L11p, DKES_L33p, DKES_L31p,
      2   DKES_L11m, DKES_L33m, DKES_L31m,
      3   DKES_scal11, DKES_scal33, DKES_scal31
+      INTEGER :: DKES_NK, DKES_NC, DKES_NE                              
 
       CONTAINS
 

From 1ea2341d3b23a21e36d167ae31e418cb94cadbb0 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 18 Oct 2024 17:22:41 +0200
Subject: [PATCH 36/47] THRIFT: DKES and PENTA now integrated.

---
 THRIFT/Sources/thrift_boozer.f90        |  10 +-
 THRIFT/Sources/thrift_dkes.f90          |  22 +++++
 THRIFT/Sources/thrift_equil.f90         |   4 +-
 THRIFT/Sources/thrift_init.f90          |  16 +++-
 THRIFT/Sources/thrift_paraexe.f90       |  10 ++
 THRIFT/Sources/thrift_penta.f90         |  10 +-
 THRIFT/Sources/thrift_run_bootstrap.f90 | 121 ++++++++++++++----------
 THRIFT/Sources/thrift_runtime.f90       |   4 +
 THRIFT/THRIFT.dep                       |   5 +-
 9 files changed, 135 insertions(+), 67 deletions(-)

diff --git a/THRIFT/Sources/thrift_boozer.f90 b/THRIFT/Sources/thrift_boozer.f90
index 896f24e00..4921c7e3d 100644
--- a/THRIFT/Sources/thrift_boozer.f90
+++ b/THRIFT/Sources/thrift_boozer.f90
@@ -63,11 +63,11 @@ SUBROUTINE thrift_boozer(lscreen,iflag)
          CALL MPI_BCAST(nboz_xboozer,1,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
          CALL MPI_BCAST(ns_vmec,1,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
 #endif
-         ! We need to setup the lsurf_boz array
-         IF (ALLOCATED(lsurf_boz)) DEALLOCATE(lsurf_boz)
-         ALLOCATE(lsurf_boz(ns_vmec))
-         lsurf_boz = .FALSE.
-         lsurf_boz(2:ns_vmec) = .TRUE. ! We can probaly do less surfaces in the future
+         ! We need to setup the lsurf_boz array (this in now calculated outside this routine)
+         !IF (ALLOCATED(lsurf_boz)) DEALLOCATE(lsurf_boz)
+         !ALLOCATE(lsurf_boz(ns_vmec))
+         !lsurf_boz = .FALSE.
+         !lsurf_boz(2:ns_vmec) = .TRUE. ! We can probaly do less surfaces in the future
          num_booz = -COUNT(lsurf_boz) ! This tricks the code into not reading the wout or input file
          ! Now read the wout file
          ier = 0
diff --git a/THRIFT/Sources/thrift_dkes.f90 b/THRIFT/Sources/thrift_dkes.f90
index f55a45fb4..e3a38ebda 100644
--- a/THRIFT/Sources/thrift_dkes.f90
+++ b/THRIFT/Sources/thrift_dkes.f90
@@ -17,6 +17,7 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
       USE thrift_funcs
       USE mpi_params
       USE mpi_inc
+      USE mpi_sharmem
       USE read_wout_mod, ONLY: read_wout_file, read_wout_deallocate
       USE read_boozer_mod, ONLY: bcast_boozer_vars
       ! DKES LIBRARIES
@@ -84,6 +85,9 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
          DKES_scal11=0.0; DKES_scal33=0.0; DKES_scal31=0.0
          l = 1
          ! Allocate Helper arrays to loop over dkes runs
+         DKES_NK = COUNT(DKES_K>0)
+         DKES_NC = COUNT(DKES_Nustar<1E10)
+         DKES_NE = COUNT(DKES_Erstar<1E10)
          ALLOCATE(ik_dkes(nruns_dkes),Earr_dkes(nruns_dkes),nuarr_dkes(nruns_dkes))
          IF (myworkid == master) THEN
             DO k = 1, DKES_NS_MAX
@@ -288,6 +292,24 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
          IF (lscreen) WRITE(6,'(a)') ' -----------------  DKES CALCULATION (DONE) ----------------'
          IF (myworkid .ne. master) CALL read_wout_deallocate
 
+         ! Sort out the DKES runs for later use
+         IF (ASSOCIATED(DKES_D11)) CALL mpidealloc(DKES_D11,win_dkes_d11)
+         IF (ASSOCIATED(DKES_D31)) CALL mpidealloc(DKES_D31,win_dkes_d31)
+         IF (ASSOCIATED(DKES_D33)) CALL mpidealloc(DKES_D33,win_dkes_d33)
+         CALL mpialloc(DKES_D11, DKES_NK, DKES_NC, DKES_NE, myid_sharmem, 0, MPI_COMM_MYWORLD, win_dkes_d11)
+         CALL mpialloc(DKES_D31, DKES_NK, DKES_NC, DKES_NE, myid_sharmem, 0, MPI_COMM_MYWORLD, win_dkes_d31)
+         CALL mpialloc(DKES_D33, DKES_NK, DKES_NC, DKES_NE, myid_sharmem, 0, MPI_COMM_MYWORLD, win_dkes_d33)
+         IF (myworkid .eq. master) THEN
+            DO l = 1, nruns_dkes
+               i = MOD(l-1,DKES_NK)+1
+               j = MOD(l-1,DKES_NK*DKES_NE)
+               j = FLOOR(REAL(j) / REAL(DKES_NK))+1
+               k = CEILING(REAL(l) / REAL(DKES_NK*DKES_NE))
+               DKES_D11(i,j,k) = (DKES_L11p(l) + DKES_L11m(l))*0.5
+               DKES_D31(i,j,k) = (DKES_L31p(l) + DKES_L31m(l))*0.5
+               DKES_D33(i,j,k) = (DKES_L33p(l) + DKES_L33m(l))*0.5
+            END DO
+         END IF
       END IF
       IF (lscreen) WRITE(6,'(a)') ' -------------------  DKES NEOCLASSICAL CALCULATION DONE  ---------------------'
       RETURN
diff --git a/THRIFT/Sources/thrift_equil.f90 b/THRIFT/Sources/thrift_equil.f90
index 41147cfc1..950474824 100644
--- a/THRIFT/Sources/thrift_equil.f90
+++ b/THRIFT/Sources/thrift_equil.f90
@@ -21,9 +21,9 @@ MODULE thrift_equil
     !       vp_spl     Spline of dV/dphi
     !-------------------------------------------------------------------
     IMPLICIT NONE
-
+    INTEGER :: ns_eq
     REAL(rprec) :: bt0, el0, iota0, eq_beta, eq_Aminor, eq_Rmajor, &
-                   eq_phiedge, eq_volume, ns_eq
+                   eq_phiedge, eq_volume
 
     ! Spline helpers
     INTEGER :: bcs1(2)
diff --git a/THRIFT/Sources/thrift_init.f90 b/THRIFT/Sources/thrift_init.f90
index 99d6dad86..70032608e 100644
--- a/THRIFT/Sources/thrift_init.f90
+++ b/THRIFT/Sources/thrift_init.f90
@@ -13,7 +13,9 @@ SUBROUTINE thrift_init
       USE thrift_input_mod
       USE thrift_vars
       USE thrift_profiles_mod
-      USE diagno_input_mod, ONLY: read_diagno_input
+      USE diagno_input_mod, ONLY:   read_diagno_input
+      USE penta_interface_mod, ONLY:   init_penta_input, &
+                                       read_penta_run_params_namelist
       USE safe_open_mod
       USE mpi_params
       USE mpi_inc
@@ -61,8 +63,6 @@ SUBROUTINE thrift_init
          WRITE(6,'(A11,F8.4)') '   TEND:   ', tend
       END IF
 
-      ! Create the worker pool
-
       ! Grid allocations
       CALL mpialloc(THRIFT_RHO,       nrho,    myid_sharmem, 0, MPI_COMM_SHARMEM, win_thrift_rho)
       CALL mpialloc(THRIFT_RHOFULL, nrho+2,    myid_sharmem, 0, MPI_COMM_SHARMEM, win_thrift_rhofull)
@@ -142,6 +142,16 @@ SUBROUTINE thrift_init
                STOP
             END IF
             CLOSE(iunit)
+         CASE('dkespenta')
+            ier = 0
+            CALL init_penta_input
+            CALL read_penta_run_params_namelist('input.'//TRIM(id_string),ier)
+            IF (ier < 0 .and. myid == master) THEN
+               WRITE(6,*) '!!!!!!!!!!!!ERRROR!!!!!!!!!!!!!!'
+               WRITE(6,*) '  RUN_PARAMS Namelist not found     '
+               WRITE(6,*) '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!'
+               STOP
+            END IF
          CASE('sfincs')
       END SELECT
 
diff --git a/THRIFT/Sources/thrift_paraexe.f90 b/THRIFT/Sources/thrift_paraexe.f90
index 986a2d9f5..0275f7871 100644
--- a/THRIFT/Sources/thrift_paraexe.f90
+++ b/THRIFT/Sources/thrift_paraexe.f90
@@ -185,6 +185,16 @@ SUBROUTINE thrift_paraexe(in_parameter_1,in_parameter_2,lscreen_local)
                ier = 0
                CALL thrift_diagno(lscreen_local,ier)
                ier_paraexe = ier
+            CASE('dkes')
+               proc_string = file_str
+               ier = 0
+               CALL thrift_dkes(lscreen_local,ier)
+               ier_paraexe = ier
+            CASE('penta')
+               proc_string = file_str
+               ier = 0
+               CALL thrift_penta(lscreen_local,ier)
+               ier_paraexe = ier
             CASE('sfincs')
 !               proc_string = file_str
 !               ier = 0
diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index 26d972821..968fff8d2 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -27,7 +27,8 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !-----------------------------------------------------------------------
 !     Local Variables
 !-----------------------------------------------------------------------
-      INTEGER :: ns_dkes, k, ier, j, i, ncstar, nestar, mystart, myend
+      INTEGER :: ns_dkes, k, ier, j, i, ncstar, nestar, mystart, myend, &
+                 mysurf
       REAL(rprec) :: s, rho, iota, phip, chip, btheta, bzeta, bsq, vp, &
                         te, ne, dtedrho, dnedrho
       REAL(rprec), DIMENSION(num_ion_species) :: ni,ti, dtidrho, dnidrho
@@ -48,7 +49,8 @@ SUBROUTINE thrift_penta(lscreen,iflag)
          CALL MPI_CALC_MYRANGE(MPI_COMM_MYWORLD,1,ns_dkes,mystart,myend)
          DO k = mystart,myend
             ! Calc some information
-            s = DKES_K(k)/ns_eq
+            mysurf = DKES_K(k)
+            s = DBLE(mysurf)/DBLE(ns_eq)
             rho = sqrt(s)
             ier = 0
             CALL EZSpline_interp(iota_spl, rho, iota, ier)
@@ -88,9 +90,9 @@ SUBROUTINE thrift_penta(lscreen,iflag)
             CALL PENTA_ALLOCATE_SPECIES
             CALL PENTA_SET_EQ_DATA(rho,eq_Aminor,eq_Rmajor,vp,chip,phip,iota,btheta,bzeta,bsq)
             CALL PENTA_SET_PPROF(ne,dnedrho,te,dtedrho,ni,dnidrho,ti,dtidrho)
-            !SUBROUTINE penta_set_DKES_star(nc,ne,cmul_in,efield_in,D11_in,D13_in,D33_in)
+            ! Check here we have D31 from DKES but need D13 in PENTA
             CALL PENTA_SET_DKES_STAR(ncstar,nestar,DKES_NUSTAR(1:ncstar),DKES_ERSTAR(1:nestar), &
-               D11,D13,D33)
+               DKES_D11(mysurf,:,:),DKES_D31(mysurf,:,:),DKES_D33(mysurf,:,:))
             CALL PENTA_SET_BEAM(0.0_rprec) ! Zero becasue we don't read
             CALL PENTA_SET_U2() ! Leave blank for default value
             CALL PENTA_READ_INPUT_FILES(.FALSE.,.FALSE.,.FALSE.,.FALSE.,.FALSE.)
diff --git a/THRIFT/Sources/thrift_run_bootstrap.f90 b/THRIFT/Sources/thrift_run_bootstrap.f90
index 8468e08b2..2c9e2bd4b 100644
--- a/THRIFT/Sources/thrift_run_bootstrap.f90
+++ b/THRIFT/Sources/thrift_run_bootstrap.f90
@@ -5,58 +5,75 @@
 !     Description:   This subroutine calls the relevant bootstrap
 !                    current code.
 !-----------------------------------------------------------------------
-      SUBROUTINE thrift_run_bootstrap
-!-----------------------------------------------------------------------
-!     Libraries
-!-----------------------------------------------------------------------
-      USE thrift_runtime
-      USE thrift_vars
-      USE thrift_equil
-      USE thrift_profiles_mod
-      USE thrift_funcs
-!-----------------------------------------------------------------------
-!     Local Variables
-!        ier         Error flag
-!-----------------------------------------------------------------------
-      IMPLICIT NONE
-      INTEGER :: i, ier
-      REAL(rprec) :: epsilon, pp1, pm1, ds
-      REAL(rprec), DIMENSION(:), ALLOCATABLE ::  j_temp
-!----------------------------------------------------------------------
-!     BEGIN SUBROUTINE
-!----------------------------------------------------------------------
-
-      ier = 0
-
-      ! Check to make sure we're not zero beta
-      IF (eq_beta == 0) THEN
-         THRIFT_JBOOT(:,mytimestep) = 0
-         RETURN
-      END IF
-
-      SELECT CASE(TRIM(bootstrap_type))
-         CASE ('model','simple','test')
-
-            ! j_BS = sqrt(epsilon) Rmajor *dp/dPhi
-            ! epsilon = a/R (inverse aspect ratio)
-            ! dp/dPhi : Pa/Wb (toroidal flux derivative)
-            ! dp/dPhi = dp/ds * ds/dPhi
-            !         = dp/ds / Phi_edge
-            ! j_BS = s*sqrt(epsilon)*Rmajor/Phi_edge*dp/ds
-            !      = s*sqrt(aminor*Rmajor)/Phi_edge*dp/ds
-            
-            epsilon = eq_Aminor/eq_Rmajor ! Inverse Aspect Ratio
-            THRIFT_JBOOT(:,mytimestep) = SQRT(eq_Aminor*eq_Rmajor)/eq_phiedge*THRIFT_S*THRIFT_PPRIME(:,mytimestep)
-
-         CASE ('bootsj')
-            CALL thrift_paraexe('booz_xform',proc_string,lscreen_subcodes)
-            CALL thrift_paraexe('bootsj',proc_string,lscreen_subcodes)
-         CASE ('sfincs')
-      END SELECT
+SUBROUTINE thrift_run_bootstrap
+   !-----------------------------------------------------------------------
+   !     Libraries
+   !-----------------------------------------------------------------------
+   USE thrift_runtime
+   USE thrift_vars
+   USE thrift_equil
+   USE thrift_profiles_mod
+   USE thrift_funcs
+   USE booz_params, ONLY: lsurf_boz
+   !-----------------------------------------------------------------------
+   !     Local Variables
+   !        ier         Error flag
+   !-----------------------------------------------------------------------
+   IMPLICIT NONE
+   INTEGER :: i, ier
+   REAL(rprec) :: epsilon, pp1, pm1, ds
+   REAL(rprec), DIMENSION(:), ALLOCATABLE ::  j_temp
+   !----------------------------------------------------------------------
+   !     BEGIN SUBROUTINE
+   !----------------------------------------------------------------------
+
+   ier = 0
 
+   ! Just always check it's deallocated      
+   IF (ALLOCATED(lsurf_boz)) DEALLOCATE(lsurf_boz)
+
+   ! Check to make sure we're not zero beta
+   IF (eq_beta == 0) THEN
+      THRIFT_JBOOT(:,mytimestep) = 0
       RETURN
-!----------------------------------------------------------------------
-!     END SUBROUTINE
-!----------------------------------------------------------------------
-      END SUBROUTINE thrift_run_bootstrap
+   END IF
+
+   SELECT CASE(TRIM(bootstrap_type))
+      CASE ('model','simple','test')
+
+         ! j_BS = sqrt(epsilon) Rmajor *dp/dPhi
+         ! epsilon = a/R (inverse aspect ratio)
+         ! dp/dPhi : Pa/Wb (toroidal flux derivative)
+         ! dp/dPhi = dp/ds * ds/dPhi
+         !         = dp/ds / Phi_edge
+         ! j_BS = s*sqrt(epsilon)*Rmajor/Phi_edge*dp/ds
+         !      = s*sqrt(aminor*Rmajor)/Phi_edge*dp/ds
+         
+         epsilon = eq_Aminor/eq_Rmajor ! Inverse Aspect Ratio
+         THRIFT_JBOOT(:,mytimestep) = SQRT(eq_Aminor*eq_Rmajor)/eq_phiedge*THRIFT_S*THRIFT_PPRIME(:,mytimestep)
+
+      CASE ('bootsj')
+         ALLOCATE(lsurf_boz(ns_eq))
+         lsurf_boz = .FALSE.
+         lsurf_boz(2:ns_eq) = .TRUE.
+         CALL thrift_paraexe('booz_xform',proc_string,lscreen_subcodes)
+         CALL thrift_paraexe('bootsj',proc_string,lscreen_subcodes)
+      CASE ('dkespenta')
+         ALLOCATE(lsurf_boz(ns_eq))
+         lsurf_boz = .FALSE.
+         DO i = 1, DKES_NS_MAX
+            IF (DKES_K(i)<1) CYCLE
+            lsurf_boz(DKES_K(i)) = .TRUE.
+         END DO
+         CALL thrift_paraexe('booz_xform',proc_string,lscreen_subcodes)
+         CALL thrift_paraexe('dkes',proc_string,lscreen_subcodes)
+         CALL thrift_paraexe('penta',proc_string,lscreen_subcodes)
+      CASE ('sfincs')
+   END SELECT
+
+   RETURN
+   !----------------------------------------------------------------------
+   !     END SUBROUTINE
+   !----------------------------------------------------------------------
+   END SUBROUTINE thrift_run_bootstrap
 
diff --git a/THRIFT/Sources/thrift_runtime.f90 b/THRIFT/Sources/thrift_runtime.f90
index c6a4eab77..1c42290fe 100644
--- a/THRIFT/Sources/thrift_runtime.f90
+++ b/THRIFT/Sources/thrift_runtime.f90
@@ -78,6 +78,10 @@ MODULE thrift_runtime
     CHARACTER(256) :: id_string, prof_string, &
                       nbcd_type, proc_string, magdiag_coil
 
+    LOGICAL, DIMENSION(MAXPROFLEN) :: lneed_boozer
+    REAL(rprec), DIMENSION(:,:,:), POINTER :: DKES_D11, DKES_D31, DKES_D33
+    INTEGER :: win_dkes_d11, win_dkes_d31, win_dkes_d33
+
     REAL(rprec), PARAMETER :: THRIFT_VERSION = 0.50 
     !-------------------------------------------------------------------
     !     Subroutines
diff --git a/THRIFT/THRIFT.dep b/THRIFT/THRIFT.dep
index 53398edc0..2319d4038 100644
--- a/THRIFT/THRIFT.dep
+++ b/THRIFT/THRIFT.dep
@@ -78,6 +78,8 @@ thrift_init.o : \
       thrift_runtime.o \
       thrift_vars.o \
       thrift_profiles_mod.o \
+      $(LIB_DIR)/$(LOCTYPE)/diagno_input_mod.o \
+      $(PENTA_DIR)/$(LOCTYPE)/penta_interface_mod.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_inc.o \
       $(LIB_DIR)/$(LOCTYPE)/mpi_params.o  \
       $(LIB_DIR)/$(LOCTYPE)/mpi_sharmem.o \
@@ -173,7 +175,8 @@ thrift_run_bootstrap.o : \
       thrift_runtime.o \
       thrift_equil.o \
       thrift_vars.o \
-      thrift_funcs.o
+      thrift_funcs.o \
+      $(BOOZ_DIR)/$(LOCTYPE)/booz_params.o 
 
 thrift_run_diagnostics.o : \
       thrift_runtime.o \

From 1ac11b6c34dc9cd39f87e86112e75ec55b1d2d26 Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 09:13:10 +0100
Subject: [PATCH 37/47] THRIFT: allow possibility of ntimesteps=1 (which
 corresponds to dt=0)

---
 THRIFT/Sources/thrift_init.f90 | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/THRIFT/Sources/thrift_init.f90 b/THRIFT/Sources/thrift_init.f90
index 8ea32d754..8c55662d8 100644
--- a/THRIFT/Sources/thrift_init.f90
+++ b/THRIFT/Sources/thrift_init.f90
@@ -233,7 +233,19 @@ SUBROUTINE thrift_init
       ENDIF
       
       ! Define grids
-      dt = (tend-tstart)/(ntimesteps-1)
+      IF( ntimesteps==1 ) THEN 
+         dt = 0.0_rprec
+      ELSE IF( ntimesteps > 1) THEN 
+         dt = (tend-tstart)/(ntimesteps-1)
+      ELSE
+         IF(lverb) THEN
+            WRITE(6,*) '!!!!!!!!!!!!ERRROR!!!!!!!!!!!!!!'
+            WRITE(6,*) '          ntimesteps < 1        '
+            WRITE(6,*) '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!'
+            STOP
+         END IF
+      END IF
+
 
       IF (myid_sharmem == master) THEN
         FORALL(i = 1:nrho) THRIFT_RHO(i) = DBLE(i-0.5)/DBLE(nrho) ! (half) rho grid

From 61826a5f9175cd9d158dde01f86d7d89650384b9 Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 09:14:08 +0100
Subject: [PATCH 38/47] THRIFT: add comment when running Bootstrap

---
 THRIFT/Sources/thrift_evolve.f90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/THRIFT/Sources/thrift_evolve.f90 b/THRIFT/Sources/thrift_evolve.f90
index 8bd420ec7..763981d52 100644
--- a/THRIFT/Sources/thrift_evolve.f90
+++ b/THRIFT/Sources/thrift_evolve.f90
@@ -99,6 +99,7 @@ SUBROUTINE thrift_evolve
             CALL update_vars
 
             ! Calculate Bootstrap
+            IF (lverbj) WRITE(6,*) "Running Bootstrap code"
             CALL thrift_run_bootstrap
             THRIFT_JBOOT(:,mytimestep) = boot_factor*THRIFT_JBOOT(:,mytimestep)
 

From 26aee6b3f418df0c22dd8219cd5f5c94430d3a7e Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 09:28:17 +0100
Subject: [PATCH 39/47] THRIFT: printing of vprime was not being done
 correctly; not it is

---
 THRIFT/Sources/thrift_funcs.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/THRIFT/Sources/thrift_funcs.f90 b/THRIFT/Sources/thrift_funcs.f90
index a1df42a44..8dc9df92e 100644
--- a/THRIFT/Sources/thrift_funcs.f90
+++ b/THRIFT/Sources/thrift_funcs.f90
@@ -188,7 +188,7 @@ SUBROUTINE print_calc_vars()
     WRITE(6,*)'   S  VPRIME     BAV   BSQAV        S11    ETAPARA     PPRIME'
     WRITE(6,*)''
     DO i = 1, nsj
-        WRITE(6,'(F5.3,3(1X,F7.3),3(1X,ES10.3))') &
+        WRITE(6,'(F5.3,1(1X,ES10.3),2(1X,F7.3),3(1X,ES10.3))') &
             THRIFT_S(i),THRIFT_VP(i,mytimestep),THRIFT_BAV(i,mytimestep),THRIFT_BSQAV(i,mytimestep), &
             THRIFT_S11(i,mytimestep),THRIFT_ETAPARA(i,mytimestep),THRIFT_PPRIME(i,mytimestep)
     END DO

From ea70e71bf185e86cd622ebe19adf0e1bc73de5a6 Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 15:25:19 +0100
Subject: [PATCH 40/47] DKES: remove prints

---
 DKES/Sources/General/printout.f | 2 --
 1 file changed, 2 deletions(-)

diff --git a/DKES/Sources/General/printout.f b/DKES/Sources/General/printout.f
index 9ed929a6f..2160ed7ac 100644
--- a/DKES/Sources/General/printout.f
+++ b/DKES/Sources/General/printout.f
@@ -145,7 +145,6 @@ SUBROUTINE dkes_printout(fz1p, fz1m, fz3p, fz3m, srces)
 c  in the main DKES routine, only the STELLOPT routine changes this
 c  and allocates these arrays
       IF (ALLOCATED(DKES_L11p) .and. (DKES_rad_dex > 0)) THEN
-!         PRINT *,'got here0'
          DKES_L11p(DKES_rad_dex) = L11p
          DKES_L33p(DKES_rad_dex) = L33p
          DKES_L31p(DKES_rad_dex) = L31p
@@ -155,7 +154,6 @@ SUBROUTINE dkes_printout(fz1p, fz1m, fz3p, fz3m, srces)
          DKES_scal11(DKES_rad_dex) = scal11
          DKES_scal33(DKES_rad_dex) = scal33
          DKES_scal31(DKES_rad_dex) = scal13
-!         PRINT *,'got here1'
       END IF
 
 c  output results summary

From 09baaa6524b5c25709b4bd67bc7328240449dd0a Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 15:33:50 +0100
Subject: [PATCH 41/47] THRIFT: fix integration  of DKES+PENTA in THRIFT

---
 PENTA/Sources/penta_interface_mod.f90 |  18 ++-
 THRIFT/Sources/thrift_boozer.f90      |  11 +-
 THRIFT/Sources/thrift_dkes.f90        |  40 +++--
 THRIFT/Sources/thrift_funcs.f90       |   5 +
 THRIFT/Sources/thrift_penta.f90       | 221 ++++++++++++++++++++------
 5 files changed, 223 insertions(+), 72 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index fd12a703c..ce43c7dbb 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -90,9 +90,12 @@ SUBROUTINE penta_set_ion_params(num_ion_in, Z_ion_in, miomp_in)
       num_ion_species = num_ion_in
       Z_ion_init = Z_ion_in
       miomp_init = miomp_in
+      ! Electrons + ions  (added here because the function where this used to be defined [read_ion_params_namelist] is no longer called) AC 11/2024
+      num_species = num_ion_species + 1_iknd
       RETURN
    END SUBROUTINE penta_set_ion_params
 
+   !! This subroutine is not called since in THRIFT we read the ions data from the h5 file
    SUBROUTINE read_penta_ion_params_namelist(filename,istat)
       USE safe_open_mod
       IMPLICIT NONE
@@ -378,6 +381,17 @@ SUBROUTINE penta_deallocate_species
       IF (ALLOCATED(Er_test_vals)) DEALLOCATE(Er_test_vals)
       IF (ALLOCATED(QoT_i_vs_Er)) DEALLOCATE(QoT_i_vs_Er)
       IF (ALLOCATED(QoT_e_vs_Er)) DEALLOCATE(QoT_e_vs_Er)
+      IF (ALLOCATED(Gammas_ambi)) DEALLOCATE(Gammas_ambi)
+      IF (ALLOCATED(QoTs_ambi)) DEALLOCATE(QoTs_ambi)
+      IF (ALLOCATED(Flows_ambi)) DEALLOCATE(Flows_ambi)
+      IF (ALLOCATED(Jprl_ambi)) DEALLOCATE(Jprl_ambi)
+      IF (ALLOCATED(Jprl_parts)) DEALLOCATE(Jprl_parts)
+      IF (ALLOCATED(J_BS_ambi)) DEALLOCATE(J_BS_ambi)
+      IF (ALLOCATED(sigma_par_ambi)) DEALLOCATE(sigma_par_ambi)
+      IF (ALLOCATED(sigma_par_Spitzer_ambi)) DEALLOCATE(sigma_par_Spitzer_ambi)
+      IF (ALLOCATED(utor)) DEALLOCATE(utor)
+      IF (ALLOCATED(upol)) DEALLOCATE(upol)
+
       RETURN
    END SUBROUTINE penta_deallocate_species
 
@@ -520,8 +534,8 @@ SUBROUTINE penta_set_pprof(ne_in,dnedr_in,te_in,dtedr_in,ni_in,dnidr_in,ti_in,dt
       dtedr = dtedr_in
       ni    = ni_in
       dnidr = dnidr_in
-      ti    = ni_in
-      dtidr = dnidr_in
+      ti    = ti_in
+      dtidr = dtidr_in
       RETURN
    END SUBROUTINE penta_set_pprof
 
diff --git a/THRIFT/Sources/thrift_boozer.f90 b/THRIFT/Sources/thrift_boozer.f90
index 4921c7e3d..2688f6564 100644
--- a/THRIFT/Sources/thrift_boozer.f90
+++ b/THRIFT/Sources/thrift_boozer.f90
@@ -62,6 +62,10 @@ SUBROUTINE thrift_boozer(lscreen,iflag)
          CALL MPI_BCAST(mboz_xboozer,1,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
          CALL MPI_BCAST(nboz_xboozer,1,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
          CALL MPI_BCAST(ns_vmec,1,MPI_INTEGER,master,MPI_COMM_MYWORLD,ierr_mpi)
+
+         !New -- introduced in order to have lsurf_boz calculated by master outside this routine (AC)
+         IF (myworkid /= master) ALLOCATE(lsurf_boz(ns_vmec))
+         CALL MPI_BCAST(lsurf_boz,ns_vmec,MPI_LOGICAL,master,MPI_COMM_MYWORLD,ierr_mpi)
 #endif
          ! We need to setup the lsurf_boz array (this in now calculated outside this routine)
          !IF (ALLOCATED(lsurf_boz)) DEALLOCATE(lsurf_boz)
@@ -229,8 +233,11 @@ SUBROUTINE thrift_boozer(lscreen,iflag)
          IF (ALLOCATED(beta_b)) DEALLOCATE(beta_b); ALLOCATE(beta_b(ns_b)); beta_b=0
          IF (ALLOCATED(buco_b)) DEALLOCATE(buco_b); ALLOCATE(buco_b(ns_b)); buco_b=0
          IF (ALLOCATED(bvco_b)) DEALLOCATE(bvco_b); ALLOCATE(bvco_b(ns_b)); bvco_b=0
-         idx_b = 0
-         idx_b(2:ns_b) = 1
+         ! idx_b = 0
+         ! idx_b(2:ns_b) = 1
+         !NEW (comment lines above and introduce MERGE below) AC, 11/2024
+         idx_b = MERGE(1,0,lsurf_boz)
+         !
          iota_b = hiota
          pres_b = pres
          phip_b = phip
diff --git a/THRIFT/Sources/thrift_dkes.f90 b/THRIFT/Sources/thrift_dkes.f90
index e3a38ebda..021820eec 100644
--- a/THRIFT/Sources/thrift_dkes.f90
+++ b/THRIFT/Sources/thrift_dkes.f90
@@ -45,8 +45,8 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
       INTEGER, DIMENSION(:), ALLOCATABLE :: ik_dkes
       REAL(rprec), DIMENSION(:), ALLOCATABLE :: Earr_dkes, nuarr_dkes
       REAL(rprec), DIMENSION(:), POINTER :: f0p1, f0p2, f0m1, f0m2
-      REAL(rprec) :: tcpu0, tcpu1, tcpui, tcput, tcpu, tcpua, dkes_efield,&
-                     phi_temp
+      REAL(rprec) :: tcpu0, tcpu1, tcpui, tcput, tcpu, tcpua, &
+                     phi_temp, stime, etime
       CHARACTER :: tb*1           
       CHARACTER*50 :: arg1(6)       
       INTEGER :: numargs, iodata, iout_opt, idata, iout
@@ -120,21 +120,22 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
          ! Note there are multile file write statements which can
          ! probably be removed so we only write what we need for PENTA
+         CALL second0(stime)
          DO k = mystart,myend
             ! Setup input
             arg1(1) = TRIM(proc_string)
             WRITE(arg1(2),'(i3)') ik_dkes(k)
             WRITE(arg1(3),'(e20.10)') nuarr_dkes(k)
-            WRITE(arg1(4),'(e20.10)') dkes_efield
+            WRITE(arg1(4),'(e20.10)') Earr_dkes(k) !dkes_efield
             arg1(5) = 'F'
             IF (lscreen .and. lfirst_pass) arg1(5) = 'T'
             WRITE(temp_str,'(i3.3)') k
-            arg1(6) = '_s' // TRIM(temp_str)
+            arg1(6) = '_k' // TRIM(temp_str)
             ier_phi = 0 ! We don't read the boozmn or wout file we've done that already
-            CALL dkes_input_prepare(arg1,6,dkes_input_file,ier_phi)
-            output_file= 'dkesout.' // TRIM(proc_string) // '_s' // TRIM(temp_str)
-            opt_file= 'opt_dkes.' // TRIM(proc_string) // '_s' // TRIM(temp_str)       !DAS 2/21/2000  !Probably won't need
-            summary_file = 'results.' // TRIM(proc_string) //'_s' // TRIM(temp_str) !record file addition
+            CALL dkes_input_prepare_old(arg1,6,dkes_input_file,ier_phi)
+            output_file= 'dkesout.' // TRIM(proc_string) // '_k' // TRIM(temp_str)
+            opt_file= 'opt_dkes.' // TRIM(proc_string) // '_k' // TRIM(temp_str)       !DAS 2/21/2000  !Probably won't need
+            summary_file = 'results.' // TRIM(proc_string) //'_k' // TRIM(temp_str) !record file addition
             !  OPEN INPUT AND OUTPUT FILES FOR READING (AND WRITING OUTPUT)
             idata    = 7
             iout     = 30
@@ -244,11 +245,11 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
                        g31m, g13m, crs1m, crs3m)
                ENDIF
                ! This is a trick to get the arrays corretly sorted
-               DKES_rad_dex = i
+               DKES_rad_dex = k !i ---> I think w/ 'i' is completely wrong!!
                IF (.not. lfirst_pass) lscreen_dkes = .FALSE.
                CALL dkes_printout (f0p1, f0m1, f0p2, f0m2, srces0)
-               DKES_rad_dex = ik_dkes(i)
-               ! End trick
+               DKES_rad_dex = ik_dkes(k) !ik_dkes(i)  -- same here !!!
+               ! End trickMPI_O
                CALL second0 (tcpu1); tcpu = tcpu1 - tcpu0; tcpu0 = tcpu1; tcput = tcput + tcpu; tcpua = tcput/i
                WRITE (ioout, 1100) tcpu
                CLOSE(unit=itab_out)
@@ -261,7 +262,9 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
             CLOSE(unit=ioout)
             CLOSE(unit=ioout_opt)
             lfirst_pass = .FALSE.
+            CALL second0(etime)
          END DO
+         PRINT *, 'I took ', etime-stime,'s.'
          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
          !!!!!! Parallel Work block Done
          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -289,7 +292,7 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
             CALL MPI_REDUCE(DKES_scal31,  DKES_scal31, nruns_dkes, MPI_DOUBLE_PRECISION, MPI_SUM, master, MPI_COMM_MYWORLD, ierr_mpi)
          END IF
 #endif
-         IF (lscreen) WRITE(6,'(a)') ' -----------------  DKES CALCULATION (DONE) ----------------'
+         !IF (lscreen) WRITE(6,'(a)') ' -----------------  DKES CALCULATION (DONE) ----------------'
          IF (myworkid .ne. master) CALL read_wout_deallocate
 
          ! Sort out the DKES runs for later use
@@ -299,16 +302,11 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
          CALL mpialloc(DKES_D11, DKES_NK, DKES_NC, DKES_NE, myid_sharmem, 0, MPI_COMM_MYWORLD, win_dkes_d11)
          CALL mpialloc(DKES_D31, DKES_NK, DKES_NC, DKES_NE, myid_sharmem, 0, MPI_COMM_MYWORLD, win_dkes_d31)
          CALL mpialloc(DKES_D33, DKES_NK, DKES_NC, DKES_NE, myid_sharmem, 0, MPI_COMM_MYWORLD, win_dkes_d33)
+
          IF (myworkid .eq. master) THEN
-            DO l = 1, nruns_dkes
-               i = MOD(l-1,DKES_NK)+1
-               j = MOD(l-1,DKES_NK*DKES_NE)
-               j = FLOOR(REAL(j) / REAL(DKES_NK))+1
-               k = CEILING(REAL(l) / REAL(DKES_NK*DKES_NE))
-               DKES_D11(i,j,k) = (DKES_L11p(l) + DKES_L11m(l))*0.5
-               DKES_D31(i,j,k) = (DKES_L31p(l) + DKES_L31m(l))*0.5
-               DKES_D33(i,j,k) = (DKES_L33p(l) + DKES_L33m(l))*0.5
-            END DO
+            DKES_D11 = RESHAPE( (DKES_L11p + DKES_L11m)*0.5, shape=(/DKES_NK, DKES_NC, DKES_NE/), order=(/2,3,1/) )
+            DKES_D31 = RESHAPE( (DKES_L31p + DKES_L31m)*0.5, shape=(/DKES_NK, DKES_NC, DKES_NE/), order=(/2,3,1/) )
+            DKES_D33 = RESHAPE( (DKES_L33p + DKES_L33m)*0.5, shape=(/DKES_NK, DKES_NC, DKES_NE/), order=(/2,3,1/) )
          END IF
       END IF
       IF (lscreen) WRITE(6,'(a)') ' -------------------  DKES NEOCLASSICAL CALCULATION DONE  ---------------------'
diff --git a/THRIFT/Sources/thrift_funcs.f90 b/THRIFT/Sources/thrift_funcs.f90
index 8dc9df92e..c29abbcb6 100644
--- a/THRIFT/Sources/thrift_funcs.f90
+++ b/THRIFT/Sources/thrift_funcs.f90
@@ -64,6 +64,11 @@ SUBROUTINE update_vars()
             CALL get_prof_etapara(MIN(rho,SQRT(THRIFT_S(nsj-1))),mytime,THRIFT_ETAPARA(i,mytimestep))
         ELSEIF(etapar_type == 'read_from_file') THEN
             CALL get_prof_eta(rho,mytime,THRIFT_ETAPARA(i,mytimestep))
+        ELSEIF(etapar_type == 'dkespenta') THEN
+            IF(bootstrap_type /= 'dkespenta') THEN
+                STOP 'NOT POSSIBLE YET TO COMPUTE etapar FROM dkespenta WITHOUT BOOTSTRAP ALSO FROM dkespenta'
+            END IF
+            ! etapar will be computed when bootstrap code is called after update_vars
         ENDIF
         
         CALL get_prof_p(rho, mytime, THRIFT_P(i,mytimestep))
diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index 968fff8d2..bd04b2595 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -13,6 +13,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
       USE thrift_profiles_mod
       USE thrift_equil
       USE thrift_funcs
+      USE phys_const, ONLY: p_mass
       USE penta_interface_mod
       USE mpi_params
       USE mpi_inc
@@ -28,16 +29,19 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !     Local Variables
 !-----------------------------------------------------------------------
       INTEGER :: ns_dkes, k, ier, j, i, ncstar, nestar, mystart, myend, &
-                 mysurf
-      REAL(rprec) :: s, rho, iota, phip, chip, btheta, bzeta, bsq, vp, &
-                        te, ne, dtedrho, dnedrho
-      REAL(rprec), DIMENSION(num_ion_species) :: ni,ti, dtidrho, dnidrho
+                 mysurf, root_max_Er
+      REAL(rprec) :: s, rho
+      REAL(rprec), DIMENSION(:), ALLOCATABLE :: rho_k, iota, phip, chip, btheta, bzeta, bsq, vp, &
+                        te, ne, dtedrho, dnedrho, EparB, JBS_PENTA, etapar_PENTA, rho_temp, J_temp, eta_temp
+      REAL(rprec), DIMENSION(:,:), ALLOCATABLE :: ni,ti, dtidrho, dnidrho
       REAL(rprec), DIMENSION(:,:), ALLOCATABLE :: D11, D13, D33
+      TYPE(EZspline1_r8) :: J_spl, eta_spl
+      INTEGER :: bcs0(2)
 !-----------------------------------------------------------------------
 !     BEGIN SUBROUTINE
 !-----------------------------------------------------------------------
       IF (iflag < 0) RETURN
-      IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL FLUX USING PENTA  -------------------'
+      IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL BOOTSTRAP USING PENTA  -------------------'
       IF (lvmec) THEN
          ierr_mpi = 0
          ! PENTA is parallelized over radial surfaces in this routine.
@@ -47,52 +51,100 @@ SUBROUTINE thrift_penta(lscreen,iflag)
          END DO
          ! Break up work
          CALL MPI_CALC_MYRANGE(MPI_COMM_MYWORLD,1,ns_dkes,mystart,myend)
-         DO k = mystart,myend
-            ! Calc some information
-            mysurf = DKES_K(k)
-            s = DBLE(mysurf)/DBLE(ns_eq)
-            rho = sqrt(s)
-            ier = 0
-            CALL EZSpline_interp(iota_spl, rho, iota, ier)
-            ier = 0
-            CALL EZSpline_interp(phip_spl, rho, phip, ier)
-            ! PENTA wants d/ds note that this won't work if rho=0
-            phip = 0.5*phip/rho
-            chip = iota * phip
-            ier = 0
-            CALL EZSpline_interp(bu_spl, rho, btheta, ier)
-            ier = 0
-            CALL EZSpline_interp(bv_spl, rho, bzeta, ier)
-            ier = 0
-            CALL EZSpline_interp(bsq_spl, rho, bsq, ier)
-            ier = 0
-            CALL EZSpline_interp(vp_spl, rho, vp, ier)
-            ! Vp = dV/dPHI need dVds with VMEC normalization
-            vp = vp * phip /(pi2*pi2)
-            ! Profiles
-            CALL get_prof_te(rho, THRIFT_T(mytimestep), te)
-            CALL get_prof_ne(rho, THRIFT_T(mytimestep), ne)
-            CALL get_prof_teprime(rho, THRIFT_T(mytimestep), dtedrho)
-            CALL get_prof_neprime(rho, THRIFT_T(mytimestep), dnedrho)
-            DO j = 1, num_ion_species
-               CALL get_prof_ti(rho, THRIFT_T(mytimestep), j, ti(j))
-               CALL get_prof_ni(rho, THRIFT_T(mytimestep), j, ni(j))
-               CALL get_prof_tiprime(rho, THRIFT_T(mytimestep), j, dtidrho(j))
-               CALL get_prof_niprime(rho, THRIFT_T(mytimestep), j, dnidrho(j))
+
+         ALLOCATE(rho_k(ns_dkes),iota(ns_dkes),phip(ns_dkes),chip(ns_dkes),btheta(ns_dkes),bzeta(ns_dkes),bsq(ns_dkes),vp(ns_dkes),EparB(ns_dkes))
+         ALLOCATE(te(ns_dkes),ne(ns_dkes),dtedrho(ns_dkes),dnedrho(ns_dkes))
+         ALLOCATE(ni(ns_dkes,nion_prof),ti(ns_dkes,nion_prof),dtidrho(ns_dkes,nion_prof),dnidrho(ns_dkes,nion_prof))
+         ALLOCATE(JBS_PENTA(ns_dkes),etapar_PENTA(ns_dkes))
+
+         JBS_PENTA = 0.0; etapar_PENTA = 0.0
+
+         IF (myworkid == master) THEN
+            DO k = 1, ns_dkes
+                  mysurf = DKES_K(k)
+                  s = DBLE(mysurf-1) / DBLE(ns_eq-1)
+                  rho = SQRT(s)
+                  rho_k(k) = rho
+
+                  ier = 0
+                  CALL EZSpline_interp(iota_spl, rho, iota(k), ier)
+                  ier = 0
+                  CALL EZSpline_interp(phip_spl, rho, phip(k), ier)
+                  ! PENTA wants d/ds note that this won't work if rho=0
+                  phip(k) = 0.5*phip(k)/rho
+                  chip(k) = iota(k) * phip(k)
+
+                  ier = 0
+                  CALL EZSpline_interp(bu_spl, rho, btheta(k), ier)
+                  ier = 0
+                  CALL EZSpline_interp(bv_spl, rho, bzeta(k), ier)
+                  ier = 0
+                  CALL EZSpline_interp(bsq_spl, rho, bsq(k), ier)
+                  ier = 0
+
+                  CALL EZSpline_interp(vp_spl, rho, vp(k), ier)
+                  ! Vp = dV/dPHI need dVds with VMEC normalization
+                  vp(k) = vp(k) * phip(k) /(pi2*pi2)
+
+                  ! Profiles
+                  CALL get_prof_te(rho, THRIFT_T(mytimestep), te(k))
+                  CALL get_prof_ne(rho, THRIFT_T(mytimestep), ne(k))
+                  CALL get_prof_teprime(rho, THRIFT_T(mytimestep), dtedrho(k))
+                  CALL get_prof_neprime(rho, THRIFT_T(mytimestep), dnedrho(k))
+                  DO j = 1, nion_prof
+                        CALL get_prof_ti(rho, THRIFT_T(mytimestep), j, ti(k,j))
+                        CALL get_prof_ni(rho, THRIFT_T(mytimestep), j, ni(k,j))
+                        CALL get_prof_tiprime(rho, THRIFT_T(mytimestep), j, dtidrho(k,j))
+                        CALL get_prof_niprime(rho, THRIFT_T(mytimestep), j, dnidrho(k,j))
+                  END DO
+
+                  !EparB
+                  EparB(k) = 0.0_rprec !! temporary... cannot do THRIFT_EPARB(mysurf,mytimestep) since this is defined in thrift grid, not vmec... interpolation?
             END DO
-            ! DKES Data
-            ncstar = COUNT(DKES_NUSTAR < 1E10)
-            nestar = COUNT(DKES_ERSTAR < 1E10)
 
+
+            ! print *, 'master_thrift_penta: dkes_d11', DKES_D11
+         END IF
+#if defined(MPI_OPT)
+         CALL MPI_BCAST(rho_k,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(iota,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(phip,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(btheta,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(bzeta,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(bsq,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(vp,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(te,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(ne,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(dtedrho,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(dnedrho,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(ti,ns_dkes*nion_prof,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(ni,ns_dkes*nion_prof,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(dtidrho,ns_dkes*nion_prof,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(dnidrho,ns_dkes*nion_prof,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(EparB,ns_dkes,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         ! VMEC quantities
+         CALL MPI_BCAST(eq_Aminor,1,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         CALL MPI_BCAST(eq_Rmajor,1,MPI_DOUBLE_PRECISION,master,MPI_COMM_MYWORLD,ierr_mpi)
+         
+#endif
+      
+         ! DKES Data
+         ncstar = COUNT(DKES_NUSTAR < 1E10)
+         nestar = COUNT(DKES_ERSTAR < 1E10)
+
+         DO k = mystart,myend
             ! PENTA
-            CALL PENTA_SET_ION_PARAMS(nion_prof, DBLE(Zatom_prof), Matom_prof/AMU)
-            CALL PENTA_SET_COMMANDLINE(-250.0_rprec,250.0_rprec,DKES_K(k),1,0.0_rprec,1,'','','')
+            CALL PENTA_SET_ION_PARAMS(nion_prof, DBLE(Zatom_prof), Matom_prof/p_mass)
+
+            !!! WE NEED TO CHANGE THE EPARB --- it needs to interact with THRIFT...!!!
+            !!! ALSO: IS THIS -250:250 OK?? I PROPOSE TO MOVE THIS TO THE INPUT...
+            CALL PENTA_SET_COMMANDLINE(-250.0_rprec,250.0_rprec,DKES_K(k),1,EparB(k),1,'','','')
             CALL PENTA_ALLOCATE_SPECIES
-            CALL PENTA_SET_EQ_DATA(rho,eq_Aminor,eq_Rmajor,vp,chip,phip,iota,btheta,bzeta,bsq)
-            CALL PENTA_SET_PPROF(ne,dnedrho,te,dtedrho,ni,dnidrho,ti,dtidrho)
-            ! Check here we have D31 from DKES but need D13 in PENTA
+            CALL PENTA_SET_EQ_DATA(rho_k(k),eq_Aminor,eq_Rmajor,vp(k),chip(k),phip(k),iota(k),btheta(k),bzeta(k),bsq(k))
+            CALL PENTA_SET_PPROF(ne(k),dnedrho(k)/eq_Aminor,te(k),dtedrho(k)/eq_Aminor,ni(k,:),dnidrho(k,:)/eq_Aminor,ti(k,:),dtidrho(k,:)/eq_Aminor)
+            ! MAKE CORRECTIONS ON D31 AND D33 -- values coming from DKES2 miss Bsq factors (see J. Lore documentation)
             CALL PENTA_SET_DKES_STAR(ncstar,nestar,DKES_NUSTAR(1:ncstar),DKES_ERSTAR(1:nestar), &
-               DKES_D11(mysurf,:,:),DKES_D31(mysurf,:,:),DKES_D33(mysurf,:,:))
+               DKES_D11(k,:,:), DKES_D31(k,:,:)*SQRT(bsq(k)), DKES_D33(k,:,:)*bsq(k))
             CALL PENTA_SET_BEAM(0.0_rprec) ! Zero becasue we don't read
             CALL PENTA_SET_U2() ! Leave blank for default value
             CALL PENTA_READ_INPUT_FILES(.FALSE.,.FALSE.,.FALSE.,.FALSE.,.FALSE.)
@@ -104,10 +156,85 @@ SUBROUTINE thrift_penta(lscreen,iflag)
             ! Now the basic steps
             CALL PENTA_RUN_2_EFIELD
             CALL PENTA_RUN_3_AMBIPOLAR
+
+            ! Save JBS corresponding to the root that has the largest Er
+            ! This because whenever there are 2 stable roots, a rule of thumb is to pick the one with largest Er
+            root_max_Er = MAXLOC(Er_roots(1:num_roots),1)
+            JBS_PENTA(k) = J_BS_ambi(root_max_Er)
+            etapar_PENTA(k) = sigma_par_ambi(root_max_Er)
+
             CALL PENTA_RUN_4_CLEANUP
          END DO
+
+         !! Bootstrap interpolation onto THRIFT grid
+#if defined(MPI_OPT)
+         CALL MPI_BARRIER(MPI_COMM_MYWORLD,ierr_mpi)
+         IF (myworkid == master) THEN
+            CALL MPI_REDUCE(MPI_IN_PLACE,JBS_PENTA,ns_dkes,MPI_DOUBLE_PRECISION,MPI_SUM,master,MPI_COMM_MYWORLD,ierr_mpi)
+            CALL MPI_REDUCE(MPI_IN_PLACE,etapar_PENTA,ns_dkes,MPI_DOUBLE_PRECISION,MPI_SUM,master,MPI_COMM_MYWORLD,ierr_mpi)
+         ELSE 
+            CALL MPI_REDUCE(JBS_PENTA,JBS_PENTA,ns_dkes,MPI_DOUBLE_PRECISION,MPI_SUM,master,MPI_COMM_MYWORLD,ierr_mpi)
+            CALL MPI_REDUCE(etapar_PENTA,etapar_PENTA,ns_dkes,MPI_DOUBLE_PRECISION,MPI_SUM,master,MPI_COMM_MYWORLD,ierr_mpi)
+            DEALLOCATE(rho_k,iota,phip,chip,btheta,bzeta,bsq,vp,EparB)
+            DEALLOCATE(te,ne,dtedrho,dnedrho)
+            DEALLOCATE(ni,ti,dtidrho,dnidrho)
+            DEALLOCATE(JBS_PENTA,etapar_PENTA)
+            RETURN
+         ENDIF
+#endif
+         
+         IF (myworkid == master) THEN
+
+            ! Interpolate JBS_PENTA and etapar_PENTA at rho=0 and rho=1
+            ALLOCATE(J_temp(ns_dkes+2),eta_temp(ns_dkes+2),rho_temp(ns_dkes+2))
+            rho_temp(1)        = 0.0
+            rho_temp(2:ns_dkes+1) = rho_k
+            rho_temp(ns_dkes+2)   = 1.0
+            !
+            J_temp(2:ns_dkes+1)   = JBS_PENTA
+            J_temp(1)             = J_temp(2) - (J_temp(3)-J_temp(2)) * rho_temp(2) / (rho_temp(3)-rho_temp(2))
+            J_temp(ns_dkes+2)     = JBS_PENTA(ns_dkes-1) + (JBS_PENTA(ns_dkes)-JBS_PENTA(ns_dkes-1)) * (1-rho_k(ns_dkes-1)) / (rho_k(ns_dkes)-rho_k(ns_dkes-1))
+            !
+            eta_temp(2:ns_dkes+1)   = etapar_PENTA
+            eta_temp(1)             = eta_temp(2) - (eta_temp(3)-eta_temp(2)) * rho_temp(2) / (rho_temp(3)-rho_temp(2))
+            eta_temp(ns_dkes+2)     = etapar_PENTA(ns_dkes-1) + (etapar_PENTA(ns_dkes)-etapar_PENTA(ns_dkes-1)) * (1-rho_k(ns_dkes-1)) / (rho_k(ns_dkes)-rho_k(ns_dkes-1))
+
+            ! Splines
+            bcs0=(/ 0, 0/)
+            !JBS
+            CALL EZspline_init(J_spl,ns_dkes+2,bcs0,ier)
+            J_spl%x1        = rho_temp
+            J_spl%isHermite = 1
+            CALL EZspline_setup(J_spl,J_temp,ier,EXACT_DIM=.true.)
+            !etapar
+            CALL EZspline_init(eta_spl,ns_dkes+2,bcs0,ier)
+            eta_spl%x1        = rho_temp
+            eta_spl%isHermite = 1
+            CALL EZspline_setup(eta_spl,eta_temp,ier,EXACT_DIM=.true.)
+            !
+            DEALLOCATE(J_temp,eta_temp,rho_temp)
+
+            ! Calculate J_BS and etapara in THRFIT GRID
+            DO i = 1, nsj
+                  rho = SQRT( THRIFT_S(i) )
+                  CALL EZspline_interp(J_spl,rho,THRIFT_JBOOT(i,mytimestep),ier)
+                  IF( etapar_type == 'dkespenta') CALL EZspline_interp(eta_spl,rho,THRIFT_ETAPARA(i,mytimestep),ier)
+            END DO
+            CALL EZspline_free(J_spl,ier)
+            CALL EZspline_free(eta_spl,ier)
+
+            ! PRINT *, 'THRIFT_JBOOT=', THRIFT_JBOOT(:,mytimestep)
+            ! PRINT *, 'THRIFT_ETAPARA=', THRIFT_ETAPARA(:,mytimestep)
+
+            DEALLOCATE(rho_k,iota,phip,chip,btheta,bzeta,bsq,vp,EparB)
+            DEALLOCATE(te,ne,dtedrho,dnedrho)
+            DEALLOCATE(ni,ti,dtidrho,dnidrho)
+            DEALLOCATE(JBS_PENTA,etapar_PENTA)
+            
+         END IF
+
       ENDIF
-      IF (lscreen) WRITE(6,'(a)') ' -------------------  NEOCLASSICAL FLUX CALCULATION DONE  ---------------------'
+      IF (lscreen) WRITE(6,'(a)') ' -------------------  NEOCLASSICAL BOOTSTRAP CALCULATION DONE  ---------------------'
       RETURN
 !-----------------------------------------------------------------------
 !     END SUBROUTINE

From a28e4efef190b3766b286cc62d2a14e8858c4f80 Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 16:45:28 +0100
Subject: [PATCH 42/47] THRIFT: print to screen

---
 PENTA/Sources/penta_interface_mod.f90 | 9 ++++++---
 THRIFT/Sources/thrift_dkes.f90        | 3 ++-
 THRIFT/Sources/thrift_penta.f90       | 2 ++
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index ce43c7dbb..e38c11c3a 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -1149,9 +1149,12 @@ SUBROUTINE penta_run_4_cleanup
       ! QQ write file with number of roots per surface!
 
       ! Write screen output
-      write(str_num,*) num_roots
-      write(*,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.4))') & 
-        roa_surf,er_roots(1:num_roots)/100._rknd
+      IF (lscreen) THEN
+         write(str_num,*) num_roots
+         write(*,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.4))') & 
+         roa_surf,er_roots(1:num_roots)/100._rknd
+      END IF
+
       ! DEALLOCATE
       CALL penta_deallocate_species
       CALL penta_deallocate_dkescoeff
diff --git a/THRIFT/Sources/thrift_dkes.f90 b/THRIFT/Sources/thrift_dkes.f90
index 021820eec..f3fd0edae 100644
--- a/THRIFT/Sources/thrift_dkes.f90
+++ b/THRIFT/Sources/thrift_dkes.f90
@@ -262,8 +262,9 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
             CLOSE(unit=ioout)
             CLOSE(unit=ioout_opt)
             lfirst_pass = .FALSE.
-            CALL second0(etime)
+            IF(lscreen) WRITE(*, '(I0, A, I0, A, I0, A)') k, ' in [', mystart, ',', myend, '] completed'
          END DO
+         CALL second0(etime)
          PRINT *, 'I took ', etime-stime,'s.'
          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
          !!!!!! Parallel Work block Done
diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index bd04b2595..a7d647b38 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -42,6 +42,8 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !-----------------------------------------------------------------------
       IF (iflag < 0) RETURN
       IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL BOOTSTRAP USING PENTA  -------------------'
+      IF (lscreen) WRITE(6,'(A)') " <r>/<a>","   Er root(s) (V/cm)"
+
       IF (lvmec) THEN
          ierr_mpi = 0
          ! PENTA is parallelized over radial surfaces in this routine.

From d7e6f6cb54d365d023acbb444675ac2cf5f6690a Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 16:47:38 +0100
Subject: [PATCH 43/47] pySTEL: fix bug in plasma class

---
 pySTEL/libstell/plasma.py | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/pySTEL/libstell/plasma.py b/pySTEL/libstell/plasma.py
index 1cab71de0..08380df7d 100644
--- a/pySTEL/libstell/plasma.py
+++ b/pySTEL/libstell/plasma.py
@@ -457,15 +457,15 @@ def write_THRIFT_profiles(self,time_array,filename=None):
         Te = np.tile(Te, (nt,1)).T
         
         # ni
-        
         ni = np.array( [self.get_density(ion,rho) for ion in self.ion_species] )
-        ni = np.tile(ni[:,:,np.newaxis], (1,1,nt)).reshape((nrho,nt,self.num_ion_species))
+        ni = np.repeat(ni[:,:,np.newaxis], nt, axis=2)
+        ni = np.transpose(ni, axes=[1,2,0])
         
         # Ti
-        
         Ti = np.array( [self.get_temperature(ion,rho) for ion in self.ion_species] )
-        Ti = np.tile(Ti[:,:,np.newaxis], (1,1,nt)).reshape((nrho,nt,self.num_ion_species))
-        
+        Ti = np.repeat(Ti[:,:,np.newaxis], nt, axis=2)
+        Ti = np.transpose(Ti, axes=[1,2,0])
+
         hf = h5py.File(filename, 'w')
         
         hf.create_dataset('nrho', data=nrho)
@@ -663,10 +663,11 @@ def print_SFINCS_list_namelist(self,roa_list,folder_path):
             file_content = f"""! Input file for SFINCS version 3.
 
 &general
+RHSmode = 1
 ambipolarSolve = .true. !.false.
-Er_min = -10
-Er_max = 10
-NEr_ambipolarSolve = 10
+!Er_min = -10
+!Er_max = 10
+!NEr_ambipolarSolve = 10
 /
 
 &geometryParameters
@@ -677,7 +678,7 @@ def print_SFINCS_list_namelist(self,roa_list,folder_path):
 inputRadialCoordinateForGradients = 3   !the radial coordinate of the gradients given in species parameters is rN=sqrt(PHI/PHIEDGE)
 
 VMECRadialOption = 1  !get the nearest available flux surface from VMEC HALF grid 
-equilibriumFile = "wout_GIGA_v120.nc"
+equilibriumFile = "wout_beta_2.nc"
 min_Bmn_to_load = 1e-4
 /
 
@@ -710,9 +711,9 @@ def print_SFINCS_list_namelist(self,roa_list,folder_path):
 
 &resolutionParameters
 Ntheta = 23 ! needs to be an odd number
-Nzeta = 121 ! needs to be an odd number and at low collisionality might be needeed to be of the order 100 to converge
+Nzeta = 91 ! needs to be an odd number and at low collisionality might be needeed to be of the order 100 to converge
 
-Nxi = 100
+Nxi = 70
 Nx = 6
 solverTolerance = 1d-6
 /

From b6a4702b4bb0832bb74d67abc420e609b51c2b09 Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 17:01:41 +0100
Subject: [PATCH 44/47] THRIFT: Er_min and Er_max now read from input namelist

---
 PENTA/Sources/penta_interface_mod.f90 | 6 ++++--
 THRIFT/Sources/thrift_penta.f90       | 5 +----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index e38c11c3a..9fa249459 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -26,7 +26,7 @@ MODULE PENTA_INTERFACE_MOD
       iocheck, ie, ind_X, ind_A, ispec1, min_ind, iroot, num_roots
    REAL(rknd) ::  Kmin, Kmax, epsabs, epsrel, Er_min, Er_max, B_Eprl, &
       U2, vth_e, loglambda, Er_test, abs_Er, min_Er, eaEr_o_kTe, cmin, &
-      cmax, emin, emax, sigma_par, sigma_par_Spitzer, J_BS
+      cmax, emin, emax, sigma_par, sigma_par_Spitzer, J_BS, Er_min_Vcm, Er_max_Vcm
    REAL(rknd), DIMENSION(NUM_ION_MAX) ::  Z_ion_init, miomp_init
    REAL(rknd), DIMENSION(NUM_ROOTS_MAX) ::  Er_roots
    REAL(rknd), DIMENSION(:), ALLOCATABLE :: ion_mass, Z_ion, vth_i, &
@@ -49,7 +49,7 @@ MODULE PENTA_INTERFACE_MOD
    NAMELIST /run_params/ input_is_Er, log_interp, use_quanc8, &
       read_U2_file, Add_Spitzer_to_D33, num_Er_test, numKsteps, &
       kord_pprof, keord, kcord, Kmin, Kmax, epsabs, epsrel, Method, &
-      flux_cap, output_QoT_vs_Er, use_beam
+      flux_cap, output_QoT_vs_Er, use_beam, Er_min_Vcm, Er_max_Vcm
 
 !-----------------------------------------------------------------------
 !     SUBROUTINES
@@ -79,6 +79,8 @@ SUBROUTINE init_penta_input
       sigma_par_Spitzer    = 0.0E+0_rknd
       J_BS                 = 0.0E+0_rknd
       method               = 'DKES'
+      Er_min_Vcm           = -250.0_rknd
+      Er_max_Vcm           =  250.0_rknd
       RETURN
    END SUBROUTINE init_penta_input
 
diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index a7d647b38..3c1cb4a97 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -137,10 +137,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
          DO k = mystart,myend
             ! PENTA
             CALL PENTA_SET_ION_PARAMS(nion_prof, DBLE(Zatom_prof), Matom_prof/p_mass)
-
-            !!! WE NEED TO CHANGE THE EPARB --- it needs to interact with THRIFT...!!!
-            !!! ALSO: IS THIS -250:250 OK?? I PROPOSE TO MOVE THIS TO THE INPUT...
-            CALL PENTA_SET_COMMANDLINE(-250.0_rprec,250.0_rprec,DKES_K(k),1,EparB(k),1,'','','')
+            CALL PENTA_SET_COMMANDLINE(Er_min_Vcm,Er_max_Vcm,DKES_K(k),1,EparB(k),1,'','','')
             CALL PENTA_ALLOCATE_SPECIES
             CALL PENTA_SET_EQ_DATA(rho_k(k),eq_Aminor,eq_Rmajor,vp(k),chip(k),phip(k),iota(k),btheta(k),bzeta(k),bsq(k))
             CALL PENTA_SET_PPROF(ne(k),dnedrho(k)/eq_Aminor,te(k),dtedrho(k)/eq_Aminor,ni(k,:),dnidrho(k,:)/eq_Aminor,ti(k,:),dtidrho(k,:)/eq_Aminor)

From cef7043d1a37174c612cc5da05a40383c097993b Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 17:02:48 +0100
Subject: [PATCH 45/47] THRIFT: Close PENTA files in interface

---
 PENTA/Sources/penta_interface_mod.f90 | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index 9fa249459..aafbea630 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -1160,6 +1160,17 @@ SUBROUTINE penta_run_4_cleanup
       ! DEALLOCATE
       CALL penta_deallocate_species
       CALL penta_deallocate_dkescoeff
+
+      ! Close files
+      ! Close output files
+      Close(iu_flux_out)
+      Close(iu_pprof_out)
+      Close(iu_fvEr_out)
+      Close(iu_QoTvEr_out)
+      Close(iu_flows_out)
+      Close(iu_flowvEr_out)
+      Close(iu_Jprl_out)
+      Close(iu_contraflows_out)
    END SUBROUTINE penta_run_4_cleanup
 
 

From f65ce101947877ad0590a9c23bde8866d880652a Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Wed, 13 Nov 2024 17:17:08 +0100
Subject: [PATCH 46/47] PENTA: comment lscreen

---
 PENTA/Sources/penta_interface_mod.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index aafbea630..de4d88a0f 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -1151,11 +1151,11 @@ SUBROUTINE penta_run_4_cleanup
       ! QQ write file with number of roots per surface!
 
       ! Write screen output
-      IF (lscreen) THEN
+      !IF (lscreen) THEN
          write(str_num,*) num_roots
          write(*,'(f7.3,' // trim(adjustl(str_num)) // '(" ",e15.4))') & 
          roa_surf,er_roots(1:num_roots)/100._rknd
-      END IF
+      !END IF
 
       ! DEALLOCATE
       CALL penta_deallocate_species

From e81300ae5b388f74b1604170e434de8326819815 Mon Sep 17 00:00:00 2001
From: ajchcoelho <antonio.coelho8@gmail.com>
Date: Thu, 14 Nov 2024 11:10:37 +0100
Subject: [PATCH 47/47] THRIFT: Improve prints to command line

---
 PENTA/Sources/penta_interface_mod.f90 | 4 ++--
 THRIFT/Sources/thrift_dkes.f90        | 6 +++---
 THRIFT/Sources/thrift_penta.f90       | 3 ++-
 3 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/PENTA/Sources/penta_interface_mod.f90 b/PENTA/Sources/penta_interface_mod.f90
index de4d88a0f..27182099d 100644
--- a/PENTA/Sources/penta_interface_mod.f90
+++ b/PENTA/Sources/penta_interface_mod.f90
@@ -861,8 +861,8 @@ SUBROUTINE penta_run_2_efield
          Else
             Er_test_vals(min_ind) = Er_test_vals(min_ind + 1)/2._rknd
          EndIf
-         Write(*,'(a,i4,a,f10.3)') 'Cannot use Er=0 with log_interp, using Er(',  &
-            min_ind, ') = ', Er_test_vals(min_ind)
+         ! Write(*,'(a,i4,a,f10.3)') 'Cannot use Er=0 with log_interp, using Er(',  &
+            ! min_ind, ') = ', Er_test_vals(min_ind)
       EndIf
       ! Loop over Er to get fluxes as a function of Er
       Do ie = 1,num_Er_test
diff --git a/THRIFT/Sources/thrift_dkes.f90 b/THRIFT/Sources/thrift_dkes.f90
index f3fd0edae..a0c91b901 100644
--- a/THRIFT/Sources/thrift_dkes.f90
+++ b/THRIFT/Sources/thrift_dkes.f90
@@ -124,12 +124,12 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
          DO k = mystart,myend
             ! Setup input
             arg1(1) = TRIM(proc_string)
-            WRITE(arg1(2),'(i3)') ik_dkes(k)
+            WRITE(arg1(2),'(i4)') ik_dkes(k)
             WRITE(arg1(3),'(e20.10)') nuarr_dkes(k)
             WRITE(arg1(4),'(e20.10)') Earr_dkes(k) !dkes_efield
             arg1(5) = 'F'
             IF (lscreen .and. lfirst_pass) arg1(5) = 'T'
-            WRITE(temp_str,'(i3.3)') k
+            WRITE(temp_str,'(i4.4)') k
             arg1(6) = '_k' // TRIM(temp_str)
             ier_phi = 0 ! We don't read the boozmn or wout file we've done that already
             CALL dkes_input_prepare_old(arg1,6,dkes_input_file,ier_phi)
@@ -265,7 +265,7 @@ SUBROUTINE thrift_dkes(lscreen,iflag)
             IF(lscreen) WRITE(*, '(I0, A, I0, A, I0, A)') k, ' in [', mystart, ',', myend, '] completed'
          END DO
          CALL second0(etime)
-         PRINT *, 'I took ', etime-stime,'s.'
+         WRITE(*, '(A, I0, A, F8.2, A, I0, A)') 'Processor ', myworkid, ' took ', etime-stime,'s to compute ', myend-mystart+1, ' DKES coefficients.'
          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
          !!!!!! Parallel Work block Done
          !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git a/THRIFT/Sources/thrift_penta.f90 b/THRIFT/Sources/thrift_penta.f90
index 3c1cb4a97..4eeb18662 100644
--- a/THRIFT/Sources/thrift_penta.f90
+++ b/THRIFT/Sources/thrift_penta.f90
@@ -42,7 +42,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
 !-----------------------------------------------------------------------
       IF (iflag < 0) RETURN
       IF (lscreen) WRITE(6,'(a)') ' --------------------  NEOCLASSICAL BOOTSTRAP USING PENTA  -------------------'
-      IF (lscreen) WRITE(6,'(A)') " <r>/<a>","   Er root(s) (V/cm)"
+      IF (lscreen) Write(*,*) " <r>/<a>","   Er root(s) (V/cm)"
 
       IF (lvmec) THEN
          ierr_mpi = 0
@@ -174,6 +174,7 @@ SUBROUTINE thrift_penta(lscreen,iflag)
          ELSE 
             CALL MPI_REDUCE(JBS_PENTA,JBS_PENTA,ns_dkes,MPI_DOUBLE_PRECISION,MPI_SUM,master,MPI_COMM_MYWORLD,ierr_mpi)
             CALL MPI_REDUCE(etapar_PENTA,etapar_PENTA,ns_dkes,MPI_DOUBLE_PRECISION,MPI_SUM,master,MPI_COMM_MYWORLD,ierr_mpi)
+            CALL FLUSH(6)
             DEALLOCATE(rho_k,iota,phip,chip,btheta,bzeta,bsq,vp,EparB)
             DEALLOCATE(te,ne,dtedrho,dnedrho)
             DEALLOCATE(ni,ti,dtidrho,dnidrho)