Growth rate calculation functionality added to gslayer.f

docs/examples/a10_ideal_example/slayer.in

@@ -2,16 +2,16 @@
 
     !!! FOR READING IN ASCII TABLE, SET INPUT_FLAG
     input_flag=f         ! reads profile quantities (n_e, t_e, etc.) from an ascii table
-    infile='/fusion/projects/codes/gpec/GPEC-1.5/docs/examples/a10_ideal_example/a10_prof1.txt'  ! Path to ascii table of profile quantities read when using input_flag
-
+    infile=''  ! Path to ascii table of profile quantities read when using input_flag
+    ncfile=''  ! Path to netCDF file of STRIDE outputs
     !!! FOR MANUALLY ENTERING KINETIC QUANTITIES @ RATIONAL SURFACE, SET PARAMS_FLAG
-    params_flag=t        ! calculates normalized parameters from profile quantities
+    params_flag=f        ! calculates normalized parameters from profile quantities
     mm=2                 ! poloidal mode number
     nn=1                 ! toroidal mode number
     n_e=7.77E+17         ! electron density [m^-3]
     t_e=25.8             ! electron temperature [eV]
     t_i=25.8             ! ion temperature [eV]
-    sval=729.0           ! magnetic shear at the layer
+    sval=2.0             ! magnetic shear at the layer
     bt=1.0               ! toroidal field [T]
     rs=0.17              ! minor radius of resonant surface [m]
     R0=2.0               ! major radius of magnetic axis [m]
@@ -21,7 +21,7 @@
     qval=2.0             ! q of resonant surface
     mu_i=2.0             ! ion mass ratio to proton ??
     zeff=2.0             ! plasma Z_effective
-    inpr=0.0001          ! Prantdl number
+    inpr=0.1             ! Prantdl number
     inpe=0.0             ! Electron viscosity
 
     !!! IF INPUT_FLAG & PARAMS_FLAG ARE FALSE, MANUALLY ENTER DIMENSIONLESS QUANTITIES @ RATIONAL SURFACE
@@ -56,7 +56,8 @@
     bin_flag=t           ! writes results to binary files
     netcdf_flag=f        ! writes results to netcdf files
     stability_flag=f     ! calculate delta dependence on complex Q
-    bal_flag=t           ! calculate the resonant field penetration threshold from torque balance
+    est_gamma_flag=t     ! Calculate estimated growth rates on each rational surface
+    !bal_flag=f           ! calculate the resonant field penetration threshold from torque balance
 /
 &SLAYER_DIAGNOSE
     riccati_out=f        ! writes LSDOE Riccati integration to an ascii file

input/slayer.in

@@ -1,45 +1,60 @@
 &SLAYER_INPUT
-
-    !!! FOR READING IN ASCII TABLE, SET INPUT_FLAG = TRUE
     input_flag=f         ! reads profile quantities (n_e, t_e, etc.) from an ascii table
-    infile=''  ! Path to ascii table of profile quantities read when using input_flag
-    ncfile=''  ! Path to netCDF file of STRIDE outputs
-
-    !!! FOR MANUALLY ENTERING KINETIC QUANTITIES @ RATIONAL SURFACE, SET PARAMS_FLAG = TRUE
+    infile=''            ! Path to ascii table of profile quantities read when using input_flag
+    ncfile=''            ! Path to netCDF file of STRIDE outputs
     params_flag=f        ! calculates normalized parameters from profile quantities
+    ! >>>
+    ! >>> Input rational surface quantities
+    ! >>>
     mm=2                 ! poloidal mode number
     nn=1                 ! toroidal mode number
-    n_e=7.77E+17         ! electron density [m^-3]
-    t_e=25.8             ! electron temperature [eV]
-    t_i=25.8             ! ion temperature [eV]
-    sval=2.0             ! magnetic shear at the layer
-    bt=1.0               ! toroidal field [T]
-    rs=0.17              ! minor radius of resonant surface [m]
-    R0=2.0               ! major radius of magnetic axis [m]
-    omega=5.45E+04       ! ExB frequency [1/s]
+    n_e=5.50E+19         ! electron density [m^-3]
+    t_e=1000.0           ! electron temperature [eV]
+    t_i=1000.0           ! ion temperature [eV]
+    sval=1.5             ! magnetic shear at the layer
+    bt=2.0               ! toroidal field [T]
+    rs=0.5               ! minor radius of resonant surface [m]
+    R0=1.67              ! major radius of magnetic axis [m]
+    omega=5.00E+03       ! ExB frequency [Hz]
     l_t=0.11             ! temperature gradient scale length
     l_n=0.25             ! density gradient scale length
     qval=2.0             ! q of resonant surface
-    mu_i=2.0             ! ion mass ratio to proton ??
+    mu_i=2.0             ! ion mass ratio to proton mass, 2 for deuterium plasma
     zeff=2.0             ! plasma Z_effective
-    inpr=10.0            ! Prantdl number
-    inpr_prof=10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0 ! Prandtl number profile
-    inpe=0.0             ! Electron viscosity (if > 0.0, Pe_flag=t will be overridden and this value used instead)
-
-    !!! IF INPUT_FLAG & PARAMS_FLAG ARE FALSE, MANUALLY ENTER DIMENSIONLESS QUANTITIES @ RATIONAL SURFACE HERE
-    inQ=23.0             ! normalized ExB frequency
-    inQ_e=2.0            ! normalized electron diamagnetic frequency
-    inQ_i=-2.0           ! normalized ion diamagnetic frequency
-    inc_beta=0.7         ! dimensionless measure of the plasma pressure
-    inds=6.0             ! normalized ion sound radius
-    intau=1.0            ! ion temperature divided by electron temperature
-    Q0=4.0               ! unnecessary placeholder variable for inQ?
-    delta_n_p=0          ! delta offset used for jxb calculations. Default is (1e-2,1e-2).
+    dr_val=-0.1          ! GGJ resistive interchange criterion D_R
+    dgeo_val=10.0        ! J.W. Connor geometric prefactor for Delta_crit
+    chi_p_prof=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2 ! Rational surface anomalous perpendicular energy diffusivity profile
+    chi_t_prof=0.2,0.2,0.2,0.2,0.2,0.2,0.2,0.2 ! Rational surface anomalous perpendicular ion momentum diffusivity profile
+    kappa_prof=0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 ! Rational surface thermal conductivity profile (NOTE: set > 0 to override chi_p_prof)
+    ! >>>
+    ! >>> Input normalized layer parameters. If read_eq=f, each will individually override internal calcuation using above inputs
+    ! >>>
+    inpr=0.0             ! Prantdl number. Set /= 0.0 to override internal calculation
+    inpe=0.0             ! electron viscosity
+    inQ=1.0              ! normalized ExB frequency. TO DO: update for mode rotation frequency calculation! 
+    inQ_e=0.0            ! normalized electron diamagnetic frequency. Set /= 0.0 to override internal calculation
+    inQ_i=0.0            ! normalized ion diamagnetic frequency. Set /= 0.0 to override internal calculation
+    inc_beta=0.0         ! dimensionless measure of the plasma pressure. Set /= 0.0 to override internal calculation
+    inds=0.0             ! normalized ion sound radius, or normalized ion skin depth. Set /= 0.0 to override internal calculation
+    intau=1.0            ! ratio of ion to electron temperature
+    Q0=1.0               ! unnecessary placeholder variable for inQ?
+    delta_prime=(0.0,0.0)  ! input Delta' or (Delta' - Delta_crit) for growth rate calculation, set /= 0.0 to override internal calculation
+    delta_n_p=(0.01,0.01)  ! delta offset used for jxb calculations. Default for latter is (1e-2,1e-2).
+    ingamma=(0.0,0.0)     ! input (Re(Q),Im(Q)) to calculate inner layer Delta. Set /= 0.0 to override internal root finding
 /
+
 &SLAYER_CONTROL
     inum=400             ! resolution to find error field thresholds.
     jnum=100             ! resolution for 2d scan along with Q,omega.
-    knum=100             ! resolution for 2d scan alont with the other.
+    knum=100             ! resolution for 2d scan along with the other.
+    Q_num=100            ! resolution for stability scan along Re(Q),Im(Q) axes
+    scan_width=1.5       ! stability scan width for Re(Q),Im(Q) scan
+    AMR_passes=4
+    msing_max=2          ! number of surfaces to include in coupled tearing growth rate calculation
+    dc_type="toroidal"   ! Delta_crit type, options are "toroidal", "lar", and "rfitzp"
+    read_eq=f            ! read in equilibrium quantities from STRIDE and kinetic file. Set all normalized params to 0.0
+    Pperp_Ptor_flag=t    ! Use R. Fitzpatrick formalism (inc. anomalous diffusion) for growth rate calculation
+    coupling_flag=t      ! Solve determinant problem and output 2D scan 
     QPscan_flag=f        ! scan (Q,P) space for delta and torque.
     Qscan_flag=f         ! scan Q space
     QPescan_flag=f       ! scan (Q,Pe) space for delta and torque.
@@ -50,18 +65,27 @@
     nbtscan_flag=f       ! scan (n,bt) space for error fields.
     parflow_flag=f       ! set parallel flow on
     PeOhmOnly_flag=t     ! only include Pe from Ohm's law
-    Pe_flag=f            ! Not operational yet. If true, it will calculate classical inpe value from inpr and include in SLAYER run
+    Pe_flag=f            ! if true, calculate classical inpe value from inpr and include in SLAYER run
     layfac=0.02          ! layfac*EXP(ifac*ATAN2(AIMAG(Q-Q_e),REAL(Q-Q_e)) is added to Q_e if ABS(Q-Q_e)<layfac). Default is 0.02.
 /
+
 &SLAYER_OUTPUT
     verbose=t            ! prints progress to terminal
-    ascii_flag=t         ! writes results to ascii files
+    ascii_flag=f         ! writes results to ascii files
     bin_flag=f           ! writes results to binary files
     netcdf_flag=f        ! writes results to netcdf files
+    est_gamma_flag=t     ! Calculate and output growth rate estimate
+    match_gamma_flag=t ! Find Delta_hat = Delta_prime match to solve for growth rate
     stability_flag=f     ! calculate delta dependence on complex Q
+    stabscan_flag=f      ! Generate Re(Q),Im(Q) scan and output as ASCII
+    coupled_stabscan_flag=f      ! Generate Re(Q),Im(Q) scan and output as ASCII
+    amr_flag=t           ! Generate Re(Q),Im(Q) scan and output as ASCII
+    br_th_flag=f         ! Calculate br_th
     bal_flag=f           ! calculate the resonant field penetration threshold from torque balance
 /
+
 &SLAYER_DIAGNOSE
     riccati_out=f        ! writes LSDOE Riccati integration to an ascii file
-    params_check=t       ! prints the primary parameters to the terminal when they are calculated
+    riccatiscan_flag=f
+    params_check=f       ! prints the primary parameters to the terminal when they are calculated
 /

install/DEPENDENCIES.inc

@@ -194,8 +194,11 @@
 ../slayer/sglobal.o: ../equil/local.o
 ../slayer/params.o : ../slayer/sglobal.o
 ../slayer/delta.o : ../slayer/sglobal.o
-../slayer/gslayer.o : ../slayer/sglobal.o ../slayer/delta.o
-../slayer/slayer.o : ../slayer/sglobal.o ../slayer/params.o ../slayer/delta.o
+../slayer/slayer_netcdf.o : ../slayer/sglobal.o ../slayer/version.inc
+../slayer/layerinputs.o : ../slayer/sglobal.o ../slayer/params.o ../slayer/slayer_netcdf.o ../pentrc/inputs.o ../equil/equil.o ../equil/spline.o ../equil/bicube.o
+../slayer/gslayer.o : ../slayer/sglobal.o ../slayer/params.o ../slayer/delta.o ../slayer/layerinputs.o ../slayer/slayer_netcdf.o
+../slayer/growthrates.o : ../slayer/sglobal.o ../slayer/params.o ../slayer/delta.o ../slayer/layerinputs.o ../slayer/slayer_netcdf.o
+../slayer/slayer.o : ../slayer/sglobal.o ../slayer/params.o ../slayer/delta.o ../slayer/gslayer.o ../slayer/growthrates.o ../slayer/layerinputs.o
 
 # COIL
 ../coil/coil.o: ../equil/local.o ../equil/bicube.o ../coil/version.inc

install/RULES.inc

@@ -121,7 +121,7 @@ FCMULTI = $(FC) $(FFLAGS) -I../equil
 	$(FCMULTI) $(MODFLAG) ../multi -c $< -o $@
 
 # SLAYER
-FCSLAYER = $(FC) $(FFLAGS) $(OMPFLAG) -I$(MATHINC) -I$(NETCDFINC) -I../equil
+FCSLAYER = $(FC) $(FFLAGS) $(OMPFLAG) -I$(MATHINC) -I$(NETCDFINC) -I../equil -I../slayer -I../pentrc
 ../slayer/%.o: ../slayer/%.f
 	$(FCSLAYER) $(MODFLAG) ../slayer -c $< -o $@
 ../slayer/%.o: ../slayer/%.F

install/TARGETS.inc

@@ -307,17 +307,29 @@ rmatch: v neededdeps $(RMATCH_OBJS) equil lsode
 	$(call print_success,rmatch -> $(BINDIR)/rmatch)
 
 # SLAYER
+../slayer/version.inc:
+	@ver="`git describe --tags`"; \
+	if [ ! -f $@ ] || ! grep -F "'$$ver'" $@ >/dev/null 2>&1; then \
+		echo ">>> Updating version file"; \
+		echo "      CHARACTER(len=*), PARAMETER :: version ='$$ver'" | tee $@; \
+	else \
+		echo ">>> Git version unchanged!"; \
+	fi
+	$(call print_success,version file updated: $@)
+
 SLAYER_LIBS = \
+	-lpentrc \
 	-llsode \
 	-lequil \
+	-lharvest \
 	$(MATHLIBS) \
 	$(NETCDFLIBS) \
 	$(NETCDF_EXTRA_LIBS)
 SLAYER_LIBDIRS = \
 	-L$(LIBDIR) \
 	-L$(MATHDIR) \
 	-L$(NETCDFDIR)
-slayer: v neededdeps $(SLAYER_OBJS) lsode equil
+slayer: v neededdeps $(SLAYER_OBJS) lsode equil pentrc harvest
 	mkdir -p $(BINDIR)
 	rm -f ../slayer/slayer
 	$(FCSLAYER) -o ../slayer/slayer $(SLAYER_OBJS) $(SLAYER_LIBDIRS) $(SLAYER_LIBS) $(LDFLAGS)

pentrc/inputs.f90

@@ -217,6 +217,7 @@ subroutine read_kin(file,zi,zimp,mi,mimp,nfac,tfac,wefac,wpfac,write_log)
         do i=1,5
             tmp%fs(0:,i) = table(1:,i+1)
         enddo
+
         call spline_fit(tmp,"extrap")
         if(write_log) print *,"Formed temporary spline"
 

rmatch/match.f

@@ -92,12 +92,16 @@ MODULE match_mod
      $           deltac_flag=.FALSE.,deltaj_flag=.FALSE.,
      $           match_flag=.FALSE.
       LOGICAL :: bin_rpecsol=.FALSE.,out_rpecsol=.FALSE.
+      LOGICAL :: detgrid_flag=.FALSE.
       CHARACTER(10) :: model="deltac"
       INTEGER :: msing,totmsing,nstep=32,qscan_ising=1
       INTEGER :: scan_nstep, scan_estep
       INTEGER :: nroot=1,iroot,totnsol,ising_output=1,itermax=500
+      INTEGER :: detgrid_nre=64, detgrid_nim=64
       REAL(r8) :: eta(20),dlim=1000,massden(20),rotation(20)=0,ntor=1
       REAL(r8) :: scan_x0,scan_x1,relax_fac,scan_e0,scan_e1
+      REAL(r8) :: detgrid_re_min=-1.0, detgrid_re_max=1.0,
+     $            detgrid_im_min=-1.0, detgrid_im_max=1.0
       REAL(r8), DIMENSION(:), ALLOCATABLE :: taur_save
       REAL(r8), DIMENSION(:), ALLOCATABLE :: zo_out,zi_in
       COMPLEX(r8) :: initguess
@@ -137,7 +141,10 @@ SUBROUTINE match_run
      $                         deflate,nroot,match_flag,ising_output,
      $                         match_sol,matrix_diagnose,fulldomain,
      $                         coil,itermax,relax_fac,init_scan_flag,
-     $                         scan_e0,scan_e1,eqscan_flag,scan_estep
+     $                         scan_e0,scan_e1,eqscan_flag,scan_estep,
+     $                         detgrid_flag,detgrid_nre,detgrid_nim,
+     $                         detgrid_re_min,detgrid_re_max,
+     $                         detgrid_im_min,detgrid_im_max
       NAMELIST/rmatch_output/ bin_rpecsol,out_rpecsol
       NAMELIST/nyquist_input/nyquist
 10    FORMAT(1x,"Eigenvalue=",1p,2e11.3)
@@ -246,7 +253,12 @@ SUBROUTINE match_run
 c-----------------------------------------------------------------------
 c     scan eigen value (Q) for different inner models.
 c-----------------------------------------------------------------------
-      IF(qscan_flag) CALL match_qscan        
+      IF(qscan_flag) CALL match_qscan
+c-----------------------------------------------------------------------
+c     2D complex-Q grid scan of the full match_delta determinant
+c     (patch added for Julia↔Fortran apples-to-apples comparison).
+c-----------------------------------------------------------------------
+      IF(detgrid_flag) CALL match_detgrid
 c-----------------------------------------------------------------------
 c     nyquist plot.
 c-----------------------------------------------------------------------
@@ -475,6 +487,17 @@ FUNCTION match_delta(guess,mat) RESULT(det)
             zi_in(ising)=0
             q_in(ising)=q_deltac
             sol=0
+c     -- PATCH (Julia/Fortran benchmark) --
+c     Dump per-surface Δ for each match_delta call so we can compare
+c     Julia's Galerkin output to Fortran's at the same Q. Writes to
+c     delta_per_surface.out (appended each call; nuke before a run).
+            OPEN(UNIT=42, FILE='delta_per_surface.out',
+     $           POSITION='APPEND')
+            WRITE(42,'(2e22.14, i5, 4e22.14)')
+     $           REAL(guess_modify), AIMAG(guess_modify), ising,
+     $           REAL(deltar(ising,1)), AIMAG(deltar(ising,1)),
+     $           REAL(deltar(ising,2)), AIMAG(deltar(ising,2))
+            CLOSE(UNIT=42)
          END SELECT
 c-----------------------------------------------------------------------
 c     construct the matching matrix.
@@ -963,7 +986,52 @@ SUBROUTINE match_qscan
 c-----------------------------------------------------------------------
       CALL program_stop("Normal termination for q scan.")
       END SUBROUTINE match_qscan
-
+
+c-----------------------------------------------------------------------
+c     subprogram 7b. match_detgrid.
+c     scan match_delta on a 2D Q_re × Q_im grid and write an ascii dump
+c     (detgrid.out, format "qre qim re_det im_det") plus a binary
+c     (detgrid.bin). Patch added for Julia↔Fortran apples-to-apples
+c     comparison of the coupled GGJ dispersion relation.
+c-----------------------------------------------------------------------
+      SUBROUTINE match_detgrid
+      INTEGER :: ire, iim
+      REAL(r8) :: qre, qim, dre, dim
+      COMPLEX(r8) :: guess, det
+      COMPLEX(r8), DIMENSION(4*msing,4*msing) :: mat
+ 10   FORMAT(1p,4e20.11)
+      WRITE(*,*) "DETGRID: 2D scan of match_delta(Q, mat)"
+      WRITE(*,'(2x,a,i4,a,i4)') "nre=",detgrid_nre," nim=",detgrid_nim
+      WRITE(*,'(2x,a,2e12.3)') "Re(Q) range:",
+     $     detgrid_re_min, detgrid_re_max
+      WRITE(*,'(2x,a,2e12.3)') "Im(Q) range:",
+     $     detgrid_im_min, detgrid_im_max
+      OPEN(UNIT=bin_unit,FILE="detgrid.bin",STATUS="REPLACE",
+     $     FORM="UNFORMATTED")
+      CALL ascii_open(out_unit,"detgrid.out","REPLACE")
+      WRITE(out_unit,'(a)') "# Q_re   Q_im   Re(det)   Im(det)"
+      WRITE(bin_unit) detgrid_nre, detgrid_nim, msing
+      dre = (detgrid_re_max - detgrid_re_min) / MAX(1, detgrid_nre - 1)
+      dim = (detgrid_im_max - detgrid_im_min) / MAX(1, detgrid_nim - 1)
+      DO iim = 1, detgrid_nim
+         qim = detgrid_im_min + (iim-1) * dim
+         DO ire = 1, detgrid_nre
+            qre = detgrid_re_min + (ire-1) * dre
+            guess = CMPLX(qre, qim, r8)
+            det = match_delta(guess, mat)
+            WRITE(out_unit,10) qre, qim, REAL(det,r8), AIMAG(det)
+            WRITE(bin_unit) REAL(qre,4), REAL(qim,4),
+     $                       REAL(REAL(det,r8),4), REAL(AIMAG(det),4)
+         ENDDO
+         IF (MOD(iim, MAX(1,detgrid_nim/10)) == 0)
+     $      WRITE(*,'(4x,a,i4,a,i4)') "row ",iim," /",detgrid_nim
+      ENDDO
+      CALL ascii_close(out_unit)
+      WRITE(bin_unit)
+      CLOSE(UNIT=bin_unit)
+      WRITE(*,*) "DETGRID: wrote detgrid.out and detgrid.bin"
+      CALL program_stop("Normal termination for detgrid scan.")
+      END SUBROUTINE match_detgrid
 c-----------------------------------------------------------------------
 c     subprogram 8. match_delta_jardin.
 c     finite differential method of GGJ.