From ef95ecad13aeb8dec2db889bfe17c400acd4f220 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Wed, 23 Oct 2024 14:21:44 +0200
Subject: [PATCH 01/16] LIBSTELL: Added QI target variables to STELLOPT

---
 .../Sources/STELLOPT/stellopt_input_mod.f90    | 18 ++++++++++++++++++
 LIBSTELL/Sources/STELLOPT/stellopt_targets.f90 |  4 ++++
 2 files changed, 22 insertions(+)

diff --git a/LIBSTELL/Sources/STELLOPT/stellopt_input_mod.f90 b/LIBSTELL/Sources/STELLOPT/stellopt_input_mod.f90
index 0f1ce4dce..d8a5e95ae 100644
--- a/LIBSTELL/Sources/STELLOPT/stellopt_input_mod.f90
+++ b/LIBSTELL/Sources/STELLOPT/stellopt_input_mod.f90
@@ -355,6 +355,7 @@ MODULE stellopt_input_mod
                          target_Jstar, sigma_Jstar, NumJstar,&
                          target_helicity, sigma_helicity, helicity,&
                          target_helicity_old, sigma_helicity_old, &
+                         target_quasiiso, sigma_quasiiso, &
                          target_resjac, sigma_resjac, xm_resjac, xn_resjac,&
                          target_separatrix, sigma_separatrix, &
                          r_separatrix, z_separatrix, phi_separatrix, &
@@ -917,6 +918,8 @@ SUBROUTINE init_stellopt_input
       helicity           = CMPLX(0.0,0.0)
       target_helicity_old(:) = 0.0
       sigma_helicity_old(:)  = bigno
+      target_quasiiso(:) = 0.0
+      sigma_quasiiso(:)  = bigno
       target_resjac(:)  = 0.0
       sigma_resjac(:)   = bigno
       xn_resjac(:)      = 0
@@ -1095,6 +1098,7 @@ SUBROUTINE read_stellopt_input(filename, istat)
       target_dkes(1)      = 0.0;  sigma_dkes(1)      = bigno
       target_dkes(2)      = 0.0;  sigma_dkes(2)      = bigno
       target_helicity(1)  = 0.0;  sigma_helicity(1)  = bigno
+      target_quasiiso(1)  = 0.0;  sigma_quasiiso(1)  = bigno
       target_Jstar(1)     = 0.0;  sigma_Jstar(1)     = bigno
       target_dkes_Erdiff(1) = 0.0; sigma_dkes_Erdiff(1) = bigno
       target_dkes_alpha(1) = 0.0; sigma_dkes_alpha(1) = bigno
@@ -1689,6 +1693,20 @@ SUBROUTINE write_optimum_namelist(iunit,istat)
                           'SIGMA_HELICITY_OLD(',ik,') = ',sigma_helicity_old(ik)
          END DO
       END IF
+      IF (ANY(sigma_quasiiso < bigno)) THEN
+         WRITE(iunit,'(A)') '!----------------------------------------------------------------------'
+         WRITE(iunit,'(A)') '!          BOOZER QUASI-ISODYNAMIC METRIC'  
+         WRITE(iunit,'(A)') '!----------------------------------------------------------------------'
+         n=0
+         DO ik = 1,UBOUND(sigma_quasiiso,DIM=1)
+            IF(sigma_quasiiso(ik) < bigno) n=ik
+         END DO
+         DO ik = 1, n
+            IF (sigma_quasiiso(ik) < bigno) WRITE(iunit,"(2(2X,A,I3.3,A,ES22.12E3))") &
+                          'TARGET_QUASIISO(',ik,') = ',target_quasiiso(ik), &
+                          'SIGMA_QUASIISO(',ik,') = ',sigma_quasiiso(ik)
+         END DO
+      END IF
       IF (ANY(sigma_resjac < bigno)) THEN
          WRITE(iunit,'(A)') '!----------------------------------------------------------------------'
          WRITE(iunit,'(A)') '!          BOOZER Resonant Modes'  
diff --git a/LIBSTELL/Sources/STELLOPT/stellopt_targets.f90 b/LIBSTELL/Sources/STELLOPT/stellopt_targets.f90
index 547883c0e..2f894ce04 100644
--- a/LIBSTELL/Sources/STELLOPT/stellopt_targets.f90
+++ b/LIBSTELL/Sources/STELLOPT/stellopt_targets.f90
@@ -157,6 +157,7 @@ MODULE stellopt_targets
       REAL(rprec), DIMENSION(nsd)   ::  target_magwell, sigma_magwell
       REAL(rprec), DIMENSION(nsd)   ::  target_helicity, sigma_helicity
       REAL(rprec), DIMENSION(nsd)   ::  target_helicity_old, sigma_helicity_old
+      REAL(rprec), DIMENSION(nsd)   ::  target_quasiiso, sigma_quasiiso
       COMPLEX                       ::  helicity
       REAL(rprec), DIMENSION(nsd)   ::  target_resjac, sigma_resjac, &
                                         xm_resjac, xn_resjac
@@ -273,6 +274,7 @@ MODULE stellopt_targets
       INTEGER, PARAMETER :: jtarget_neo        = 603
       INTEGER, PARAMETER :: jtarget_Jstar      = 604
       INTEGER, PARAMETER :: jtarget_helicity   = 605
+      INTEGER, PARAMETER :: jtarget_quasiiso   = 6051
       INTEGER, PARAMETER :: jtarget_resjac     = 606
       INTEGER, PARAMETER :: jtarget_txport     = 607
       INTEGER, PARAMETER :: jtarget_dkes       = 608
@@ -417,6 +419,8 @@ SUBROUTINE write_targets(iunit,var_num)
             WRITE(iunit, out_format) 'Trapped Particle J*'
          CASE(jtarget_helicity)
             WRITE(iunit, out_format) 'Boozer Spectrum Helicity'
+         CASE(jtarget_quasiiso)
+            WRITE(iunit, out_format) 'Boozer Quasi-isodynamic metric'
          CASE(jtarget_txport)
             WRITE(iunit, out_format) 'Turbulent Transport'
          CASE(jtarget_orbit)

From 51df9535d6e81b1f5a86f24cbe050ef1c27098b6 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Thu, 24 Oct 2024 06:46:08 +0200
Subject: [PATCH 02/16] STELLOPT: Initial commit of QI metric (not yet working)

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90   | 118 ++++++++++++++++++
 .../Sources/General/stellopt_load_targets.f90 |   3 +
 .../Sources/General/stellopt_renorm.f90       |   2 +
 3 files changed, 123 insertions(+)
 create mode 100644 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
new file mode 100644
index 000000000..55f5d5cbd
--- /dev/null
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -0,0 +1,118 @@
+!-----------------------------------------------------------------------
+!     Subroutine:    chisq_quasiiso
+!     Authors:       S. Lazerson (samuel.lazerson@gauss-fusion.com)
+!     Date:          10/08/2024
+!     Description:   This chisquared functional replicates the QI
+!                    functional described in:
+!                    https://doi.org/10.1017/S002237782300065X
+!                    and
+!                    https://doi.org/10.1103/PRXEnergy.3.023010
+!-----------------------------------------------------------------------
+      SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
+!-----------------------------------------------------------------------
+!     Libraries
+!-----------------------------------------------------------------------
+      USE stellopt_runtime
+      USE stellopt_targets
+      
+!-----------------------------------------------------------------------
+!     Input/Output Variables
+!
+!-----------------------------------------------------------------------
+      IMPLICIT NONE
+      REAL(rprec), INTENT(in)    ::  target(nsd)
+      REAL(rprec), INTENT(in)    ::  sigma(nsd)
+      INTEGER,     INTENT(in)    ::  niter
+      INTEGER,     INTENT(inout) ::  iflag
+      
+!-----------------------------------------------------------------------
+!     Local Variables
+!
+!-----------------------------------------------------------------------
+      INTEGER :: ik, mn, ier, l, lmin
+      INTEGER, PARAMETER :: nalpha = 65 ! must be odd
+      INTEGER, PARAMETER :: ntheta0 = 5
+      INTEGER, PARAMETER :: nlambda = 4
+      REAL(rprec) :: s_temp, iota0, phi, theta, deltaphi
+      REAL(rprec), DIMENSION(:), ALLOCATABLE :: modb, modbs
+
+
+!-----------------------------------------------------------------------
+!     BEGIN SUBROUTINE
+!-----------------------------------------------------------------------
+      IF (iflag < 0) RETURN
+      IF (iflag == 1) WRITE(iunit_out,'(A,2(2X,I3.3))') 'QUASIISO ',1,4
+      IF (iflag == 1) WRITE(iunit_out,'(A)') 'TARGET  SIGMA  VAL'
+      IF (niter >= 0) THEN
+         ! Loop over surfaces
+         DO ik = 1, nsd
+            IF (ABS(sigma(ik)) >= bigno) CYCLE
+            ! Get iota for the surface
+            s_temp = DBLE(ik)/DBLE(ns_b)
+            ier = 0
+            CALL get_equil_iota(s_temp,iota0,ier)
+            ! Calculate the distance to follow a field line
+            deltaphi = pi2/iota0
+            ALLOCATE(modb(nalpha),modbs(nalpha))
+            ! Loop over inital values of theta0
+            DO i = 1, ntheta0
+               DO l = 1, nalpha
+                  phi = deltaphi*(l-1)/(nalpha-1)
+                  theta = theta0 + iota0*phi
+                  DO mn = 1, mnmax_b
+                     modb(l) = bmnc_(mn,ik)*COS(ixm_b(mn)*theta+ixn_b(mn)*phi/nfp_b)
+                  END DO
+               END DO
+               ! Find min/max values
+               lmin = MINLOC(modb)
+               ! Sort the arrays
+               lh = FLOOR(nalpha/2)+1
+               modb = CSHIFT(modb,lmin-lh) !BOOSH
+               ! Squash the array
+               modbs = modb
+               DO l = lh,nalpha
+                  IF (modbs(l)<modbs(l-1)) modbs(l) = modbs(l-1)
+               END DO
+               DO l = 1, lh
+                  IF (modbs(l)<modbs(l+1)) modbs(l) = modbs(l+1)
+               END DO
+               ! Stretch the array
+               Bmin = MINVAL(modb)
+               Bmax = MAXVAL(modb)
+               DO l = 1, lh
+                  modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(1)-Bmin)
+               END DO
+               DO l = lh, nalpha
+                  modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(nalpha)-Bmin)
+               END DO
+               ! Now calculate the J's
+               
+            END DO
+
+         mtargets = mtargets + 1
+         targets(mtargets) = 0.0
+         sigmas(mtargets)  = bigno
+         vals(mtargets)    = 0.0
+         IF (iflag == 1) WRITE(iunit_out,'(3ES22.12E3)') target,sigma,0.0,vals(mtargets)
+         END DO
+      ELSE
+         ! Consistency check
+         mboz = MAX(6*mpol, 2, mboz)             
+         nboz = MAX(2*ntor-1, 0, nboz)     
+         ! CALCULATE mnboz_b becasue we don't know it yet (setup_booz.f)
+         mnboz_b = (2*nboz+1)*(mboz-1) + (nboz + 1)
+         DO ik = 1, nsd
+            IF (ABS(sigma(ik)) < bigno) THEN
+               lbooz(ik) = .TRUE.
+               DO mn = 1, mnboz_b
+                  mtargets = mtargets + 1
+                  IF (niter == -2) target_dex(mtargets) = jtarget_qi
+               END DO
+            END IF
+         END DO
+      END IF
+      RETURN
+!-----------------------------------------------------------------------
+!     END SUBROUTINE
+!-----------------------------------------------------------------------
+      END SUBROUTINE chisq_quasiiso
diff --git a/STELLOPTV2/Sources/General/stellopt_load_targets.f90 b/STELLOPTV2/Sources/General/stellopt_load_targets.f90
index 840982820..de9b9c586 100644
--- a/STELLOPTV2/Sources/General/stellopt_load_targets.f90
+++ b/STELLOPTV2/Sources/General/stellopt_load_targets.f90
@@ -272,6 +272,9 @@ SUBROUTINE stellopt_load_targets(m, fvec, iflag, ncnt)
       ! |Bmn| Helicity (OLD)
       IF (ANY(sigma_helicity_old < bigno)) &
          CALL chisq_helicity_ornl(target_helicity_old, sigma_helicity_old, ncnt,iflag)
+      ! |Bmn| Helicity (OLD)
+      IF (ANY(sigma_quasiiso < bigno)) &
+         CALL chisq_quasiiso(target_quasiiso, sigma_quasiiso, ncnt,iflag)
       ! J*
       IF (ANY(sigma_Jstar < bigno)) &
          CALL chisq_jstar(target_Jstar, sigma_Jstar, ncnt,iflag)
diff --git a/STELLOPTV2/Sources/General/stellopt_renorm.f90 b/STELLOPTV2/Sources/General/stellopt_renorm.f90
index 4402fa7e7..22c7306b8 100644
--- a/STELLOPTV2/Sources/General/stellopt_renorm.f90
+++ b/STELLOPTV2/Sources/General/stellopt_renorm.f90
@@ -146,6 +146,8 @@ SUBROUTINE stellopt_renorm(m1,fvec)
                WHERE(sigma_magwell<bigno) sigma_magwell = sigma_magwell/temp
             CASE(jtarget_helicity)
                WHERE(ABS(sigma_helicity)<bigno) sigma_helicity = sigma_helicity/temp
+            CASE(jtarget_quasiiso)
+               WHERE(sigma_quasiiso<bigno) sigma_quasiiso = sigma_quasiiso/temp
             CASE(jtarget_txport)
                WHERE(ABS(sigma_txport)<bigno) sigma_txport = sigma_txport/temp
             CASE DEFAULT

From 52390e974b95972101291c91d615b8bffbe9cdf6 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sun, 27 Oct 2024 14:46:30 +0100
Subject: [PATCH 03/16] STELLOPT: Quasiiso now runs.

---
 STELLOPTV2/ObjectList                       |   1 +
 STELLOPTV2/STELLOPTV2.dep                   |   7 ++
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 111 ++++++++++++++++----
 3 files changed, 99 insertions(+), 20 deletions(-)

diff --git a/STELLOPTV2/ObjectList b/STELLOPTV2/ObjectList
index b2b460980..2f027307f 100644
--- a/STELLOPTV2/ObjectList
+++ b/STELLOPTV2/ObjectList
@@ -1,4 +1,5 @@
 ObjectFiles = \
+chisq_quasiiso.o \
 stellopt_read_cws.o \
 stellopt_write_header.o \
 chisq_dkes_alpha.o \
diff --git a/STELLOPTV2/STELLOPTV2.dep b/STELLOPTV2/STELLOPTV2.dep
index 0cf028067..5b31d8d36 100644
--- a/STELLOPTV2/STELLOPTV2.dep
+++ b/STELLOPTV2/STELLOPTV2.dep
@@ -279,6 +279,13 @@ chisq_helicity_ornl.o : \
       equil_vals.o \
       $(LIB_DIR)/$(LOCTYPE)/read_boozer_mod.o
 
+
+chisq_quasiiso.o : \
+      stellopt_runtime.o \
+      $(LIB_DIR)/$(LOCTYPE)/stellopt_targets.o \
+      equil_vals.o \
+      $(LIB_DIR)/$(LOCTYPE)/read_boozer_mod.o
+
 chisq_resjac.o : \
       stellopt_runtime.o \
       $(LIB_DIR)/$(LOCTYPE)/stellopt_targets.o \
diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index 55f5d5cbd..9e5d6b9d9 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -14,6 +14,9 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
 !-----------------------------------------------------------------------
       USE stellopt_runtime
       USE stellopt_targets
+      USE equil_utils, ONLY: get_equil_iota
+      USE read_boozer_mod
+      USE vmec_input, ONLY: mpol, ntor
       
 !-----------------------------------------------------------------------
 !     Input/Output Variables
@@ -29,12 +32,15 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
 !     Local Variables
 !
 !-----------------------------------------------------------------------
-      INTEGER :: ik, mn, ier, l, lmin
+      INTEGER :: ik, mn, ier, i, l, m, lmin, lmax, i1, i2, lh, lr
       INTEGER, PARAMETER :: nalpha = 65 ! must be odd
       INTEGER, PARAMETER :: ntheta0 = 5
       INTEGER, PARAMETER :: nlambda = 4
-      REAL(rprec) :: s_temp, iota0, phi, theta, deltaphi
-      REAL(rprec), DIMENSION(:), ALLOCATABLE :: modb, modbs
+      REAL(rprec) :: s_temp, iota0, phi, theta, deltaphi, ftemp, norm, &
+         Bmax, Bmin, Bmir, lambda, theta0, phimin,phimax
+      REAL(rprec), DIMENSION(:), ALLOCATABLE :: modb, modbs, dl, &
+         integral_A, integral_B
+      REAL(rprec), DIMENSION(:,:), ALLOCATABLE :: J_I, J_C
 
 
 !-----------------------------------------------------------------------
@@ -42,8 +48,13 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
 !-----------------------------------------------------------------------
       IF (iflag < 0) RETURN
       IF (iflag == 1) WRITE(iunit_out,'(A,2(2X,I3.3))') 'QUASIISO ',1,4
-      IF (iflag == 1) WRITE(iunit_out,'(A)') 'TARGET  SIGMA  VAL'
+      IF (iflag == 1) WRITE(iunit_out,'(A)') 'TARGET  SIGMA  VAL  K'
       IF (niter >= 0) THEN
+         ! Allocate helpers along field line
+         ALLOCATE(modb(nalpha),modbs(nalpha),dl(nalpha),integral_A(nalpha),&
+            integral_B(nalpha))
+         ! Allocate J arrays
+         ALLOCATE(J_C(nlambda,ntheta0),J_I(nlambda,ntheta0))
          ! Loop over surfaces
          DO ik = 1, nsd
             IF (ABS(sigma(ik)) >= bigno) CYCLE
@@ -51,23 +62,46 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
             s_temp = DBLE(ik)/DBLE(ns_b)
             ier = 0
             CALL get_equil_iota(s_temp,iota0,ier)
-            ! Calculate the distance to follow a field line
-            deltaphi = pi2/iota0
-            ALLOCATE(modb(nalpha),modbs(nalpha))
             ! Loop over inital values of theta0
+            J_C = 0.0; J_I = 0.0
             DO i = 1, ntheta0
+               ! Calculate the distance to follow a field line
+               deltaphi = pi2/iota0
+               modb = 0.0
+               modbs = 0.0
+               !theta0 = pi2*i/(ntheta0-1)
+               theta0 = 0.0
                DO l = 1, nalpha
                   phi = deltaphi*(l-1)/(nalpha-1)
                   theta = theta0 + iota0*phi
-                  DO mn = 1, mnmax_b
-                     modb(l) = bmnc_(mn,ik)*COS(ixm_b(mn)*theta+ixn_b(mn)*phi/nfp_b)
+                  DO mn = 1, mnboz_b
+                     !PRINT *,ik,mn,bmnc_b(mn,ik),ixm_b(mn),theta,ixn_b(mn),phi,nfp_b
+                     modb(l) = modb(l)+bmnc_b(mn,ik)*COS(DBLE(ixm_b(mn))*theta+DBLE(ixn_b(mn))*phi/nfp_b)
                   END DO
                END DO
+               !WRITE(290+i,*) modb; CALL FLUSH(290+i)
                ! Find min/max values
-               lmin = MINLOC(modb)
+               lmin = MINLOC(modb,DIM=1)
+               lmax = MAXLOC(modb,DIM=1)
+               phimin = deltaphi*(lmin-1)/(nalpha-1)
+               phimax = deltaphi*(lmax-1)/(nalpha-1)
+               deltaphi = ABS(phimax-phimin)*2.0
+               ! Now recalculate modb centered around lmin
+               modb = 0
+               DO l = 1, nalpha
+                  phi = deltaphi*(l-lmin-1)/(nalpha-1) - deltaphi/2
+                  theta = theta0 + iota0*phi
+                  DO mn = 1, mnboz_b
+                     !PRINT *,ik,mn,bmnc_b(mn,ik),ixm_b(mn),theta,ixn_b(mn),phi,nfp_b
+                     modb(l) = modb(l)+bmnc_b(mn,ik)*COS(DBLE(ixm_b(mn))*theta+DBLE(ixn_b(mn))*phi/nfp_b)
+                  END DO
+               END DO
                ! Sort the arrays
-               lh = FLOOR(nalpha/2)+1
+               lh = FLOOR(nalpha*0.5)+1
+               PRINT *,lh,lmin
+               !WRITE(300+i,*) modb; CALL FLUSH(300+i)
                modb = CSHIFT(modb,lmin-lh) !BOOSH
+               !WRITE(310+i,*) modb; CALL FLUSH(310+i)
                ! Squash the array
                modbs = modb
                DO l = lh,nalpha
@@ -76,25 +110,62 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                DO l = 1, lh
                   IF (modbs(l)<modbs(l+1)) modbs(l) = modbs(l+1)
                END DO
+               !WRITE(320+i,*) modbs; CALL FLUSH(320+i)
                ! Stretch the array
                Bmin = MINVAL(modb)
                Bmax = MAXVAL(modb)
+               !PRINT *,Bmin,Bmax
                DO l = 1, lh
                   modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(1)-Bmin)
                END DO
                DO l = lh, nalpha
                   modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(nalpha)-Bmin)
                END DO
-               ! Now calculate the J's
-               
+               !WRITE(330+i,*) modbs; CALL FLUSH(330+i)
+               ! We need dl (missing B.grad(phi) term)
+               dl = modb*deltaphi/(nalpha-1)
+               !WRITE(340+i,*) dl; CALL FLUSH(340+i)
+               ! Now we evaluate integrals for different values of lambda
+               ! Alpha is enclosing loop
+               DO m = 1, nlambda
+                  Bmir = Bmin+0.9*(Bmax-Bmin)*DBLE(m)/DBLE(nlambda)
+                  lambda = 1.0/Bmir
+                  i1 = COUNT(modbs(1:lh)>Bmir) + 1
+                  i2 = COUNT(modbs(lh:nalpha)<Bmir) + lh - 1
+                  print *, nlambda,i1,i2,Bmin,Bmir,Bmax
+                  i1 = MAX(i1,1); i2 = MIN(i2,nalpha)
+                  integral_A = 1.0 - lambda * modb
+                  !WRITE(400+m,*) integral_A; CALL FLUSH(400+m)
+                  integral_A = SIGN(1.0_rprec,integral_A)*SQRT(ABS(integral_A))*dl
+                  !WRITE(410+m,*) integral_A; CALL FLUSH(410+m)
+                  integral_B = 1.0 - lambda * modbs
+                  !WRITE(420+m,*) integral_B; CALL FLUSH(420+m)
+                  integral_B = SQRT(integral_B)*dl
+                  !WRITE(430+m,*) integral_B; CALL FLUSH(430+m)
+                  PRINT *,'A :',integral_A(i1:i2)
+                  PRINT *,'B :',integral_B(i1:i2)
+                  J_I(m,i) = SUM(integral_A(i1:i2))
+                  J_C(m,i) = SUM(integral_B(i1:i2))
+               END DO
             END DO
-
-         mtargets = mtargets + 1
-         targets(mtargets) = 0.0
-         sigmas(mtargets)  = bigno
-         vals(mtargets)    = 0.0
-         IF (iflag == 1) WRITE(iunit_out,'(3ES22.12E3)') target,sigma,0.0,vals(mtargets)
+            WRITE(500,*) J_I
+            WRITE(501,*) J_C
+            ! Construct fuctional value
+            DO m = 1, nlambda
+               DO i1 = 1, ntheta0
+                  DO i2 = 1, ntheta0
+                     ftemp = ftemp + J_I(m,i1) - J_C(m,i2)
+                  END DO
+               END DO
+            END DO
+            norm = SUM(J_C+J_I)/(nlambda*ntheta0)
+            mtargets = mtargets + 1
+            targets(mtargets) = 0.0
+            sigmas(mtargets)  = sigma(ik)
+            vals(mtargets)    = ftemp/norm
+            IF (iflag == 1) WRITE(iunit_out,'(3ES22.12E3,2X,I3.3)') target(ik),sigma(ik),vals(mtargets),ik
          END DO
+         DEALLOCATE(modb,modbs,dl,integral_A,integral_B,J_C,J_I)
       ELSE
          ! Consistency check
          mboz = MAX(6*mpol, 2, mboz)             
@@ -106,7 +177,7 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                lbooz(ik) = .TRUE.
                DO mn = 1, mnboz_b
                   mtargets = mtargets + 1
-                  IF (niter == -2) target_dex(mtargets) = jtarget_qi
+                  IF (niter == -2) target_dex(mtargets) = jtarget_quasiiso
                END DO
             END IF
          END DO

From c43163d6c40e0621ef58b0067bc16f6512011f4b Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 28 Oct 2024 09:54:29 +0100
Subject: [PATCH 04/16] STELLOPT: QI metric now runs for multiple fieldlines.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index 9e5d6b9d9..88c6c9152 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -69,8 +69,8 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                deltaphi = pi2/iota0
                modb = 0.0
                modbs = 0.0
-               !theta0 = pi2*i/(ntheta0-1)
-               theta0 = 0.0
+               theta0 = pi2*(i-1)/ntheta0
+               !theta0 = 0.0
                DO l = 1, nalpha
                   phi = deltaphi*(l-1)/(nalpha-1)
                   theta = theta0 + iota0*phi

From 5a2dbea06099d3ab4e19660cd5912dcdee6c40af Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 28 Oct 2024 14:36:09 +0100
Subject: [PATCH 05/16] STELLOPT: Fixed missing build dependencies

---
 STELLOPTV2/STELLOPTV2.dep | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/STELLOPTV2/STELLOPTV2.dep b/STELLOPTV2/STELLOPTV2.dep
index 5b31d8d36..a51389ca0 100644
--- a/STELLOPTV2/STELLOPTV2.dep
+++ b/STELLOPTV2/STELLOPTV2.dep
@@ -283,8 +283,9 @@ chisq_helicity_ornl.o : \
 chisq_quasiiso.o : \
       stellopt_runtime.o \
       $(LIB_DIR)/$(LOCTYPE)/stellopt_targets.o \
-      equil_vals.o \
-      $(LIB_DIR)/$(LOCTYPE)/read_boozer_mod.o
+      equil_utils.o \
+      $(LIB_DIR)/$(LOCTYPE)/read_boozer_mod.o \
+      $(LIB_DIR)/$(LOCTYPE)/vmec_input.o
 
 chisq_resjac.o : \
       stellopt_runtime.o \

From 63f6599dd908945bd7c049a94ecf602567e96765 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 28 Oct 2024 16:37:29 +0100
Subject: [PATCH 06/16] STELLOPT: Quasi-isodynamic target now mostly working.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 53 ++++++++++-----------
 1 file changed, 26 insertions(+), 27 deletions(-)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index 88c6c9152..67b21b0c6 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -42,6 +42,8 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
          integral_A, integral_B
       REAL(rprec), DIMENSION(:,:), ALLOCATABLE :: J_I, J_C
 
+      LOGICAL, PARAMETER :: lwrite_out = .False.
+
 
 !-----------------------------------------------------------------------
 !     BEGIN SUBROUTINE
@@ -65,62 +67,60 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
             ! Loop over inital values of theta0
             J_C = 0.0; J_I = 0.0
             DO i = 1, ntheta0
-               ! Calculate the distance to follow a field line
+               ! Calculate the initial distance to follow a field line
                deltaphi = pi2/iota0
                modb = 0.0
                modbs = 0.0
                theta0 = pi2*(i-1)/ntheta0
-               !theta0 = 0.0
                DO l = 1, nalpha
                   phi = deltaphi*(l-1)/(nalpha-1)
                   theta = theta0 + iota0*phi
                   DO mn = 1, mnboz_b
-                     !PRINT *,ik,mn,bmnc_b(mn,ik),ixm_b(mn),theta,ixn_b(mn),phi,nfp_b
                      modb(l) = modb(l)+bmnc_b(mn,ik)*COS(DBLE(ixm_b(mn))*theta+DBLE(ixn_b(mn))*phi/nfp_b)
                   END DO
                END DO
-               !WRITE(290+i,*) modb; CALL FLUSH(290+i)
-               ! Find min/max values
+               IF (lwrite_out) WRITE(320,*) modb
+               ! Find min/max modB values
                lmin = MINLOC(modb,DIM=1)
                lmax = MAXLOC(modb,DIM=1)
+               ! Recalculate length of fieldline
                phimin = deltaphi*(lmin-1)/(nalpha-1)
                phimax = deltaphi*(lmax-1)/(nalpha-1)
-               deltaphi = ABS(phimax-phimin)*2.0
+               deltaphi = ABS(phimax-phimin)
                ! Now recalculate modb centered around lmin
                modb = 0
                DO l = 1, nalpha
-                  phi = deltaphi*(l-lmin-1)/(nalpha-1) - deltaphi/2
+                  phi = phimin-deltaphi + 2*deltaphi*(l-1)/(nalpha-1)
+                  !phi = deltaphi*(l-lmin-1)/(nalpha-1) - deltaphi/2
                   theta = theta0 + iota0*phi
                   DO mn = 1, mnboz_b
-                     !PRINT *,ik,mn,bmnc_b(mn,ik),ixm_b(mn),theta,ixn_b(mn),phi,nfp_b
                      modb(l) = modb(l)+bmnc_b(mn,ik)*COS(DBLE(ixm_b(mn))*theta+DBLE(ixn_b(mn))*phi/nfp_b)
                   END DO
                END DO
+               IF (lwrite_out) WRITE(321,*) modb
                ! Sort the arrays
-               lh = FLOOR(nalpha*0.5)+1
-               PRINT *,lh,lmin
-               !WRITE(300+i,*) modb; CALL FLUSH(300+i)
-               modb = CSHIFT(modb,lmin-lh) !BOOSH
-               !WRITE(310+i,*) modb; CALL FLUSH(310+i)
+               !lh = FLOOR(nalpha*0.5)+1
+               !modb = CSHIFT(modb,lmin-lh) !BOOSH
+               lh = MINLOC(modb,DIM=1)
                ! Squash the array
                modbs = modb
+               DO l = lh, 1, -1
+                  IF (modbs(l)<modbs(l+1)) modbs(l) = modbs(l+1)
+               END DO
                DO l = lh,nalpha
                   IF (modbs(l)<modbs(l-1)) modbs(l) = modbs(l-1)
                END DO
-               DO l = 1, lh
-                  IF (modbs(l)<modbs(l+1)) modbs(l) = modbs(l+1)
-               END DO
-               !WRITE(320+i,*) modbs; CALL FLUSH(320+i)
+               IF (lwrite_out) WRITE(322,*) modbs
                ! Stretch the array
                Bmin = MINVAL(modb)
                Bmax = MAXVAL(modb)
-               !PRINT *,Bmin,Bmax
                DO l = 1, lh
                   modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(1)-Bmin)
                END DO
                DO l = lh, nalpha
                   modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(nalpha)-Bmin)
                END DO
+               IF (lwrite_out) WRITE(323,*) modbs
                !WRITE(330+i,*) modbs; CALL FLUSH(330+i)
                ! We need dl (missing B.grad(phi) term)
                dl = modb*deltaphi/(nalpha-1)
@@ -132,25 +132,24 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                   lambda = 1.0/Bmir
                   i1 = COUNT(modbs(1:lh)>Bmir) + 1
                   i2 = COUNT(modbs(lh:nalpha)<Bmir) + lh - 1
-                  print *, nlambda,i1,i2,Bmin,Bmir,Bmax
+                  IF (lwrite_out) print *, nlambda,i1,i2,Bmin,Bmir,Bmax
                   i1 = MAX(i1,1); i2 = MIN(i2,nalpha)
                   integral_A = 1.0 - lambda * modb
-                  !WRITE(400+m,*) integral_A; CALL FLUSH(400+m)
                   integral_A = SIGN(1.0_rprec,integral_A)*SQRT(ABS(integral_A))*dl
-                  !WRITE(410+m,*) integral_A; CALL FLUSH(410+m)
+                  IF (lwrite_out) WRITE(324,*) integral_A
                   integral_B = 1.0 - lambda * modbs
-                  !WRITE(420+m,*) integral_B; CALL FLUSH(420+m)
                   integral_B = SQRT(integral_B)*dl
-                  !WRITE(430+m,*) integral_B; CALL FLUSH(430+m)
-                  PRINT *,'A :',integral_A(i1:i2)
-                  PRINT *,'B :',integral_B(i1:i2)
+                  IF (lwrite_out) WRITE(325,*) integral_B
+                  IF (lwrite_out) PRINT *,'A :',integral_A(i1:i2)
+                  IF (lwrite_out) PRINT *,'B :',integral_B(i1:i2)
                   J_I(m,i) = SUM(integral_A(i1:i2))
                   J_C(m,i) = SUM(integral_B(i1:i2))
                END DO
             END DO
-            WRITE(500,*) J_I
-            WRITE(501,*) J_C
+            IF (lwrite_out) WRITE(326,*) J_I
+            IF (lwrite_out) WRITE(327,*) J_C
             ! Construct fuctional value
+            ftemp = 0.0_rprec
             DO m = 1, nlambda
                DO i1 = 1, ntheta0
                   DO i2 = 1, ntheta0

From 683ea01fef19b6fe04cc122733001363115eb103 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 28 Oct 2024 16:56:58 +0100
Subject: [PATCH 07/16] VMEC2STEL: Added QUASIISO target to utility.

---
 VMEC2STEL/Sources/vmec2stel_main.f90 | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/VMEC2STEL/Sources/vmec2stel_main.f90 b/VMEC2STEL/Sources/vmec2stel_main.f90
index b19aaf179..a4451ef48 100644
--- a/VMEC2STEL/Sources/vmec2stel_main.f90
+++ b/VMEC2STEL/Sources/vmec2stel_main.f90
@@ -36,7 +36,8 @@ PROGRAM VMEC2STEL
                                 lkink, lvaciota, ljcurv, loutput_harm, lmode, lorbit, &
                                 lac, lam, lai, lphiedge, lpscale, lcurtor, lkappa, &
                                 lwell, lcurvature, lfieldlines, &
-                                ltxport, ltxport_tem, ltxport_ae, ldkes_erdiff
+                                ltxport, ltxport_tem, ltxport_ae, ldkes_erdiff, &
+                                lquasiiso
       INTEGER                :: m,n,ns,j
       REAL(rprec)            :: bound_min, bound_max, var, var_min, var_max, &
                                 temp, rho_exp,r1t,r2t,z1t, delta, filter_harm, pi2
@@ -107,6 +108,7 @@ PROGRAM VMEC2STEL
       lwell  = .FALSE.
       lcurvature = .FALSE.
       loutput_harm = .FALSE.
+      lquasiiso = .FALSE.
       bound_min = -1.0
       bound_max = 2.0
       filter_harm = 0
@@ -260,6 +262,9 @@ PROGRAM VMEC2STEL
                lwell= .TRUE.
             CASE ("-curvature")
                lcurvature= .TRUE.
+            CASE ("-qi")
+               lquasiiso= .TRUE.
+               lneed_booz = .TRUE.
             CASE ("-help","-h")
                WRITE(6,'(a,f5.2)') 'VMEC2STEL Version ',VMEC2STEL_VERSION
                WRITE(6,*) ' STELLOPTV2 Input Generation Utility'
@@ -290,6 +295,7 @@ PROGRAM VMEC2STEL
                WRITE(6,*) '   -qas              QAS Target'
                WRITE(6,*) '   -qps              QPS Target'
                WRITE(6,*) '   -helical          Helical Target'
+               WRITE(6,*) '   -qi               Quasi-Isodynamic Target'
                WRITE(6,*) '   -balloon          Ballooning Target'
                WRITE(6,*) '   -neo              Neoclassical (NEO) Target'
                WRITE(6,*) '   -dkes             Neoclassical (DKES) Target'
@@ -957,6 +963,12 @@ PROGRAM VMEC2STEL
          IF (lhelical) WRITE(6,'(2X,A)') 'HELICITY = (2,1)'
          WRITE(6,'(2X,A,I3.3,A,I3.3,A,I3.3,A,I3.3,A)') 'TARGET_HELICITY(1:',ns,') = ',ns,'*0.0  SIGMA_HELICITY(1:',ns,') = ',ns,'*-1.0'
       END IF
+      IF (lquasiiso) THEN
+         WRITE(6,'(A)')'!------------------------------------------------------------------------'
+         WRITE(6,'(A)')'!       Quasi-Isodnamic Target (10.1103/PRXEnergy.3.023010)'
+         WRITE(6,'(A)')'!------------------------------------------------------------------------'
+         WRITE(6,'(2X,A,I3.3,A,I3.3,A,I3.3,A,I3.3,A)') 'TARGET_QUASIISO(1:',ns,') = ',ns,'*0.0  SIGMA_QUASIISO(1:',ns,') = ',ns,'*1.0'
+      END IF
       IF (lballoon) THEN
          WRITE(6,'(A)')'!------------------------------------------------------------------------'
          WRITE(6,'(A)')'!       Ballooning Stability (as calculated by COBRA_VMEC)'

From 37112989cf0581cbc6a02cd0be626f4d010ff802 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sun, 10 Nov 2024 13:05:15 +0100
Subject: [PATCH 08/16] STELLOPT: Fixed issue where sometimes TXPORT header
 wouldn't be written to screen.

---
 STELLOPTV2/Sources/General/stellopt_txport.f90 | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/STELLOPTV2/Sources/General/stellopt_txport.f90 b/STELLOPTV2/Sources/General/stellopt_txport.f90
index 4bb44c343..4b34cffd6 100644
--- a/STELLOPTV2/Sources/General/stellopt_txport.f90
+++ b/STELLOPTV2/Sources/General/stellopt_txport.f90
@@ -61,7 +61,7 @@ SUBROUTINE stellopt_txport(lscreen,iflag)
 !        ier         Error flag
 !        iunit       File unit number
 !----------------------------------------------------------------------
-      LOGICAL :: file_test_eig,file_test_omega, lscreen_gene
+      LOGICAL :: file_test_eig,file_test_omega, lscreen_gene, lfirst_pass
       INTEGER :: maxPnt, nalpha0_, ialpha, i, iunit, ik, pol_turns_gene, &
                  iunit_curv, irtmx, irt, iunit_eigen, nu, nv, spawn_procs, &
                  spawn_root, spawn_info, spawn_comm, spawn_intercomm, ier
@@ -128,6 +128,7 @@ SUBROUTINE stellopt_txport(lscreen,iflag)
 !----------------------------------------------------------------------
       IF (iflag < 0) RETURN
       abserr = 1.0E-9
+      lfirst_pass = .TRUE.
 !DEC$ IF DEFINED (TXPORT_OPT)
       IF (lscreen) WRITE(6,'(a)') ' --------------------  TURBULENT TRANSPORT CALC  ----------------------'
       CALL FLUSH(6)
@@ -721,7 +722,7 @@ SUBROUTINE stellopt_txport(lscreen,iflag)
                END SELECT
                WHERE (vqqprox /= vqqprox) vqqprox = bigno
                txport_q(ik,:,:) = vqqprox(:,:)
-               IF (lscreen .and. (ik==1)) WRITE(6,'(A)') '     s    alpha0   iota    shear    Bref    Lref  Q_turb'
+               IF (lscreen .and. lfirst_pass) WRITE(6,'(A)') '     s    alpha0   iota    shear    Bref    Lref  Q_turb'
                IF (lscreen) WRITE(6,'(7(F8.4))')  s,alpha_start_txport,ABS(iot),shat,Ba,a,SUM(SUM(vqqprox,DIM=2)/maxPnt,DIM=1)/nalpha0_
                WRITE(iunit,'(1pe14.6)') SUM(SUM(vqqprox,DIM=2)/maxPnt,DIM=1)/nalpha0_
                DO i = 1, maxPnt
@@ -729,6 +730,7 @@ SUBROUTINE stellopt_txport(lscreen,iflag)
                END DO
                CLOSE(iunit)
                CALL FLUSH(6)
+               lfirst_pass = .FALSE.
             END DO
             DEALLOCATE(phi0_gl,g11,g12,g22,Bhat,abs_jac,L2,L1,dBdt,kp1)
             DEALLOCATE(temp_arr,tout_arr)

From ca58cbeef8ab64ef009ab66d5880ac038f217bb0 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sun, 10 Nov 2024 13:05:51 +0100
Subject: [PATCH 09/16] pySTEL: Added QUASIISO to stellopt reading/plotting
 routines.

---
 pySTEL/STELLOPT.py          | 17 +++++++++++++++--
 pySTEL/libstell/stellopt.py |  2 +-
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/pySTEL/STELLOPT.py b/pySTEL/STELLOPT.py
index 53a17016d..77eca521b 100755
--- a/pySTEL/STELLOPT.py
+++ b/pySTEL/STELLOPT.py
@@ -877,7 +877,7 @@ def LoadSTELLOPT(self):
 					'HELICITY','HELICITY_FULL',\
 					'KINK','ORBIT','JDOTB','J_STAR','NEO','TXPORT','ECEREFLECT',\
 					'S11','S12','S21','S22','MAGWELL',\
-					'CURVATURE_KERT','CURVATURE_P2']
+					'CURVATURE_KERT','CURVATURE_P2','QUASIISO']
 		self.ui.ComboBoxOPTplot_type.clear()
 		self.ui.ComboBoxOPTplot_type.addItem('Chi-Squared')
 		# Handle Chisquared plots
@@ -894,7 +894,7 @@ def LoadSTELLOPT(self):
 					'S11','S12','S21','S22','MAGWELL','VACIOTA',\
 					'CURVATURE_KERT','CURVATURE_P2',\
 					'ECEREFLECT','SXR','IOTA','PRESS','PRESSPRIME'\
-					'VISBREMLINE']:
+					'VISBREMLINE','QUASIISO']:
 			for item in vars(self.stel_data).keys():
 				if (name+'_TARGET' == item):
 					self.ui.ComboBoxOPTplot_type.addItem(name+'_evolution')
@@ -1130,6 +1130,19 @@ def UpdateOptplot(self):
 			self.ax2.set_xlabel('Radial Grid')
 			self.ax2.set_ylabel('Magnetic Well')
 			self.ax2.set_title('Magnetic Well Evolution  (>0 Well)')
+		elif (plot_name == 'QUASIISO_evolution'):
+			x = self.stel_data.QUASIISO_k
+			y = self.stel_data.QUASIISO_MAGWELL
+			t = self.stel_data.QUASIISO_TARGET
+			d = self.stel_data.QUASIISO_SIGMA
+			self.ax2.errorbar(x[0,:],t[0,:],yerr=d[0,:],fmt='ok',fillstyle='none',label='Target')
+			self.ax2.plot(x[0,:],y[0,:],'o',fillstyle='none',label='Initial',color='red')
+			for i in range(1,niter-1,1):
+				self.ax2.plot(x[i,:],y[i,:],'.k',fillstyle='none')
+			self.ax2.plot(x[niter-1,:],y[niter-1,:],'o',fillstyle='none',label='Final',color='green')
+			self.ax2.set_xlabel('Radial Grid')
+			self.ax2.set_ylabel('QI Metric')
+			self.ax2.set_title('Quasi-isodynamic Metric')
 		elif (plot_name == 'CURVATURE_P2'):
 			#x = self.stel_data.TXPORT_S
 			#y = self.stel_data.CURVATURE_P2_P2
diff --git a/pySTEL/libstell/stellopt.py b/pySTEL/libstell/stellopt.py
index eb0ef6456..3ce48f650 100644
--- a/pySTEL/libstell/stellopt.py
+++ b/pySTEL/libstell/stellopt.py
@@ -33,7 +33,7 @@ def __init__(self):
 			'NEO', 'DKES', 'DKES_ERDIFF', 'DKES_ALPHA', 'TXPORT',      \
 			'ORBIT', 'HELICITY', 'HELICITY_FULL', 'JSTAR', 'RESJAC',   \
 			'COIL_BNORM', 'REGCOIL_CHI2_B', 'CURVATURE_P2', 'GAMMA_C', \
-			'KINK']
+			'KINK', 'QUASIISO']
 
 	def read_stellopt_map(self,filename='map.dat'):
 		"""Reads a STELLOPT MAP output file

From 7ec9e71e4d738977c5cd1e728555fe51f11f6430 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sun, 10 Nov 2024 14:44:12 +0100
Subject: [PATCH 10/16] STELLOPT: Fixed bug in QUASIISO lh calculation.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 1 +
 1 file changed, 1 insertion(+)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index 67b21b0c6..5323e73c0 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -102,6 +102,7 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                !lh = FLOOR(nalpha*0.5)+1
                !modb = CSHIFT(modb,lmin-lh) !BOOSH
                lh = MINLOC(modb,DIM=1)
+               lh = MIN(MAX(lh,1),nalpha)
                ! Squash the array
                modbs = modb
                DO l = lh, 1, -1

From 7e3e9283d2447dd5e13d8f0b617756cfcc48bce8 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Sun, 10 Nov 2024 17:42:00 +0100
Subject: [PATCH 11/16] STELLOPT: Adjustment of lh min/max value to avoid
 walking off end of array.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index 5323e73c0..c55318b62 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -102,7 +102,7 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                !lh = FLOOR(nalpha*0.5)+1
                !modb = CSHIFT(modb,lmin-lh) !BOOSH
                lh = MINLOC(modb,DIM=1)
-               lh = MIN(MAX(lh,1),nalpha)
+               lh = MIN(MAX(lh,2),nalpha-1)
                ! Squash the array
                modbs = modb
                DO l = lh, 1, -1

From 6cffe880b1835823f26c36cabe977b445f0fa4fb Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 11 Nov 2024 10:14:20 +0100
Subject: [PATCH 12/16] STELLOPT: Added in array shift in quasi-iso to improve
 calculations.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 26 ++++++++++++---------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index c55318b62..df24a1125 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -98,27 +98,31 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                   END DO
                END DO
                IF (lwrite_out) WRITE(321,*) modb
-               ! Sort the arrays
-               !lh = FLOOR(nalpha*0.5)+1
-               !modb = CSHIFT(modb,lmin-lh) !BOOSH
-               lh = MINLOC(modb,DIM=1)
-               lh = MIN(MAX(lh,2),nalpha-1)
+               ! Find the Bmin and half point
+               lh = FLOOR(nalpha*0.5)+1
+               lmin = MINLOC(modb,DIM=1)
+               lmin = MIN(MAX(lmin,2),nalpha-1)
+               ! Now shift lmin to the middle
+               modb = CSHIFT(modb,lmin-lh) !BOOSH
+               ! Now recalc lh as lmin
+               lmin = MINLOC(modb,DIM=1)
+               lmin = MIN(MAX(lmin,2),nalpha-1)
                ! Squash the array
                modbs = modb
-               DO l = lh, 1, -1
+               DO l = lmin, 1, -1
                   IF (modbs(l)<modbs(l+1)) modbs(l) = modbs(l+1)
                END DO
-               DO l = lh,nalpha
+               DO l = lmin,nalpha
                   IF (modbs(l)<modbs(l-1)) modbs(l) = modbs(l-1)
                END DO
                IF (lwrite_out) WRITE(322,*) modbs
                ! Stretch the array
                Bmin = MINVAL(modb)
                Bmax = MAXVAL(modb)
-               DO l = 1, lh
+               DO l = 1, lmin
                   modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(1)-Bmin)
                END DO
-               DO l = lh, nalpha
+               DO l = lmin, nalpha
                   modbs(l) = Bmin + (Bmax-Bmin)*(modbs(l)-Bmin)/(modbs(nalpha)-Bmin)
                END DO
                IF (lwrite_out) WRITE(323,*) modbs
@@ -131,8 +135,8 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
                DO m = 1, nlambda
                   Bmir = Bmin+0.9*(Bmax-Bmin)*DBLE(m)/DBLE(nlambda)
                   lambda = 1.0/Bmir
-                  i1 = COUNT(modbs(1:lh)>Bmir) + 1
-                  i2 = COUNT(modbs(lh:nalpha)<Bmir) + lh - 1
+                  i1 = COUNT(modbs(1:lmin)>Bmir) + 1
+                  i2 = COUNT(modbs(lmin:nalpha)<Bmir) + lmin - 1
                   IF (lwrite_out) print *, nlambda,i1,i2,Bmin,Bmir,Bmax
                   i1 = MAX(i1,1); i2 = MIN(i2,nalpha)
                   integral_A = 1.0 - lambda * modb

From 18b91176978652a90f1a29212eeb220f5be62732 Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Mon, 11 Nov 2024 20:37:43 +0100
Subject: [PATCH 13/16] STELLOPT: Fixed issue with initalization of quasiiso
 target.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index df24a1125..248ce700d 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -15,8 +15,9 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
       USE stellopt_runtime
       USE stellopt_targets
       USE equil_utils, ONLY: get_equil_iota
-      USE read_boozer_mod
+      USE read_boozer_mod, ONLY: bmnc_b, ixn_b, ixm_b, mnboz_b, ns_b, nfp_b
       USE vmec_input, ONLY: mpol, ntor
+!      USE stel_kinds, ONLY: rprec
       
 !-----------------------------------------------------------------------
 !     Input/Output Variables
@@ -179,10 +180,8 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
          DO ik = 1, nsd
             IF (ABS(sigma(ik)) < bigno) THEN
                lbooz(ik) = .TRUE.
-               DO mn = 1, mnboz_b
-                  mtargets = mtargets + 1
-                  IF (niter == -2) target_dex(mtargets) = jtarget_quasiiso
-               END DO
+               mtargets = mtargets + 1
+               IF (niter == -2) target_dex(mtargets) = jtarget_quasiiso
             END IF
          END DO
       END IF

From f59dcb3e9aa9761b6c33b187c9860b0a1a1a12cb Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Tue, 12 Nov 2024 15:29:01 +0100
Subject: [PATCH 14/16] pySTEL: Fixed bug in STELLOPT related to the QI evo
 plot.

---
 pySTEL/STELLOPT.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pySTEL/STELLOPT.py b/pySTEL/STELLOPT.py
index 77eca521b..c8615ca6d 100755
--- a/pySTEL/STELLOPT.py
+++ b/pySTEL/STELLOPT.py
@@ -1131,8 +1131,8 @@ def UpdateOptplot(self):
 			self.ax2.set_ylabel('Magnetic Well')
 			self.ax2.set_title('Magnetic Well Evolution  (>0 Well)')
 		elif (plot_name == 'QUASIISO_evolution'):
-			x = self.stel_data.QUASIISO_k
-			y = self.stel_data.QUASIISO_MAGWELL
+			x = self.stel_data.QUASIISO_K
+			y = self.stel_data.QUASIISO_VAL
 			t = self.stel_data.QUASIISO_TARGET
 			d = self.stel_data.QUASIISO_SIGMA
 			self.ax2.errorbar(x[0,:],t[0,:],yerr=d[0,:],fmt='ok',fillstyle='none',label='Target')

From 0151d90d3f81d4ba8b86c14bea196ebe6552712a Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Tue, 12 Nov 2024 15:29:20 +0100
Subject: [PATCH 15/16] STELLOPT: Fixed header bug in QI metric.

---
 STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90 b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
index 248ce700d..702cda87c 100644
--- a/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
+++ b/STELLOPTV2/Sources/Chisq/chisq_quasiiso.f90
@@ -50,7 +50,8 @@ SUBROUTINE chisq_quasiiso(target,sigma,niter,iflag)
 !     BEGIN SUBROUTINE
 !-----------------------------------------------------------------------
       IF (iflag < 0) RETURN
-      IF (iflag == 1) WRITE(iunit_out,'(A,2(2X,I3.3))') 'QUASIISO ',1,4
+      ik = COUNT(sigma < bigno)
+      IF (iflag == 1) WRITE(iunit_out,'(A,2(2X,I3.3))') 'QUASIISO ',ik,4
       IF (iflag == 1) WRITE(iunit_out,'(A)') 'TARGET  SIGMA  VAL  K'
       IF (niter >= 0) THEN
          ! Allocate helpers along field line

From 2cbda30a70832308b7e253eb67a7695505f1a07a Mon Sep 17 00:00:00 2001
From: lazersos <lazersos@gmail.com>
Date: Fri, 15 Nov 2024 14:04:30 +0100
Subject: [PATCH 16/16] SHARE: Macport file now uses detection for turning
 optional flags on.

---
 SHARE/make_macports.inc | 43 +++++++++++++++++++++++++++++++++--------
 1 file changed, 35 insertions(+), 8 deletions(-)

diff --git a/SHARE/make_macports.inc b/SHARE/make_macports.inc
index d2c226953..db58d3db1 100644
--- a/SHARE/make_macports.inc
+++ b/SHARE/make_macports.inc
@@ -104,7 +104,8 @@ endif
 #######################################################################
 #            GENE Options
 #######################################################################
-  LGENE = F
+ifneq ("$(wildcard $(GENE_PATH))","")
+  LGENE = T
   GENE_INC = -I$(GENE_PATH)
   GENE_DIR = $(GENE_PATH)
   LIB_GENE = libgene.a
@@ -113,30 +114,42 @@ endif
              -L$(FFTWHOME)/lib -lfftw3 \
              -L$(SLEPC_DIR)/$(PETSC_ARCH)/lib -lslepc \
              -L$(PETSC_DIR)/$(PETSC_ARCH)/lib -lpetsc -lX11
+else
+  LGENE = F
+endif
 
 #######################################################################
 #            COILOPT++ Options
 #######################################################################
-  LCOILOPT = F
+ifneq ("$(wildcard $(COILOPT_PATH))","")
+  LCOILOPT = T
   COILOPT_INC = -I$(COILOPT_PATH)
   COILOPTPP_DIR = $(COILOPT_PATH)
   LIB_COILOPTPP = libcoilopt++.a
   COILOPT_LIB = $(COILOPT_PATH)/$(LIB_COILOPTPP) \
                 -L$(GSLHOME)/lib -lgsl -lgslcblas -lstdc++ -lmpi_cxx
+else
+  LCOILOPT = F
+endif
 
 #######################################################################
 #            TERPSICHORE Options
 #######################################################################
-  LTERPSICHORE= F
+ifneq ("$(wildcard $(TERPSICHORE_PATH))","")
+  LTERPSICHORE= T
   TERPSICHORE_INC = -I$(TERPSICHORE_PATH)
   TERPSICHORE_DIR = $(TERPSICHORE_PATH)
   LIB_TERPSICHORE = libterpsichore.a
   TERPSICHORE_LIB = $(TERPSICHORE_DIR)/$(LIB_TERPSICHORE)
+else
+  LTERPSICHORE = F
+endif
 
 #######################################################################
 #            TRAVIS Options
 #######################################################################
-  LTRAVIS= F
+ifneq ("$(wildcard $(TRAVIS_PATH))","")
+  LTRAVIS = T
   TRAVIS_DIR = $(TRAVIS_PATH)
   LIB_TRAVIS = libtravis64_sopt.a
   LIB_MCONF  = libmconf64.a
@@ -144,35 +157,49 @@ endif
   TRAVIS_LIB = $(TRAVIS_DIR)lib/$(LIB_TRAVIS) \
                $(TRAVIS_DIR)faddeeva_package/lib/$(LIB_FADDEEVA) \
                $(TRAVIS_DIR)magconf/lib/$(LIB_MCONF) -lc++
+else
+  LTRAVIS = F
+endif
 
 #######################################################################
 #            REGCOIL Options
 #######################################################################
-  LREGCOIL= F
+ifneq ("$(wildcard $(REGCOIL_PATH))","")
+  LREGCOIL= T
   REGCOIL_DIR = $(REGCOIL_PATH)
   REGCOIL_INC = -I$(REGCOIL_DIR) 
   LIB_REGCOIL = libregcoil.a
   REGCOIL_LIB = $(REGCOIL_DIR)/$(LIB_REGCOIL) -fopenmp
+else
+  LREGCOIL = F
+endif
 
 #######################################################################
 #            SFINCS Options
 #######################################################################
-
-  LSFINCS = F
+ifneq ("$(wildcard $(SFINCS_PATH))","")
+  LSFINCS = T
   SFINCS_DIR = $(SFINCS_PATH)
   SFINCS_INC = -I$(SFINCS_DIR)
   LIB_SFINCS = libsfincs.a
   SFINCS_LIB = $(SFINCS_DIR)/$(LIB_SFINCS) \
              -L$(PETSC_DIR)/$(PETSC_ARCH)/lib -lpetsc -lX11
+else
+  LSFINCS = F
+endif
 
 #######################################################################
 #            Available Energy Options
 #######################################################################
-  LAEOPT= F
+ifneq ("$(wildcard $(AEOPT_PATH))","")
+  LAEOPT = T
   AEOPT_DIR = $(AEOPT_PATH)
   AEOPT_INC = -I$(AEOPT_DIR) 
   LIB_AEOPT = libtrapAE.a
   AEOPT_LIB = $(AEOPT_PATH)/$(LIB_AEOPT)
+else
+  LAEOPT = F
+endif
 
 #######################################################################
 #            LIBSTELL Shared Options