From 44995a79168cf9ddfbd08fd8e4a7518e4b6f6816 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Mon, 2 Aug 2021 10:06:52 +0200
Subject: [PATCH] Origin contains now HeLaZ 3D version (2D is saved in a
branch)
---
src/advance_field.F90 | 48 +--
src/advance_field_adapt.F90 | 36 +-
src/array_mod.F90 | 49 +--
src/auxval.F90 | 55 +--
src/basic_mod.F90 | 28 +-
src/closure_mod.F90 | 119 +++----
src/collision_mod.F90 | 318 +++++++++--------
src/compute_Sapj.F90 | 141 ++++----
src/diagnose.F90 | 204 +++++++----
src/diagnostics_par_mod.F90 | 4 +-
src/fields_mod.F90 | 10 +-
src/fourier_mod.F90 | 42 +--
src/ghosts_mod.F90 | 36 +-
src/grid_mod.F90 | 229 +++++++------
src/inital.F90 | 398 +++++++---------------
src/initial_par_mod.F90 | 6 +
src/lin_coeff_and_geometry.F90 | 12 +-
src/memory.F90 | 71 ++--
src/model_mod.F90 | 22 +-
src/moments_eq_rhs.F90 | 403 ++++++++--------------
src/numerics.F90 | 150 ++++++++
src/poisson.F90 | 64 ++--
src/ppinit.F90 | 10 +-
src/processing_mod.F90 | 117 ++++---
src/restarts_mod.F90 | 58 ++--
src/stepon.F90 | 50 +--
src/utility_mod.F90 | 65 +++-
wk/HD_study.m | 88 -----
wk/ZF_fourier_analysis.m | 17 +-
wk/analysis_1D.m | 90 ++---
wk/analysis_2D.m | 275 +++++++--------
wk/analysis_3D.m | 510 ++++++++++++++++++++++++++++
wk/compile_cosolver_mat.m | 12 +-
wk/compute_collision_mat.m | 12 +-
wk/continue_multiple_runs_marconi.m | 39 +--
wk/daint_run.m | 18 +-
wk/fig_post_processing.m | 4 +-
wk/flux_results.m | 20 +-
wk/izar_run.m | 18 +-
wk/linear_study.m | 66 ++--
wk/load_multiple_outputs_marconi.m | 8 +-
wk/local_run.m | 31 +-
wk/marconi_scaling.m | 18 +-
wk/open_figure_script.m | 9 +-
wk/photomaton.m | 127 +++----
wk/plot_cosol_mat.m | 63 ++++
wk/ppb110_run.m | 8 +-
wk/spectral_analysis.m | 18 +-
48 files changed, 2388 insertions(+), 1808 deletions(-)
create mode 100644 src/numerics.F90
delete mode 100644 wk/HD_study.m
create mode 100644 wk/analysis_3D.m
create mode 100644 wk/plot_cosol_mat.m
diff --git a/src/advance_field.F90 b/src/advance_field.F90
index b5429068..77c8b760 100644
--- a/src/advance_field.F90
+++ b/src/advance_field.F90
@@ -30,27 +30,27 @@ CONTAINS
SELECT CASE (updatetlevel)
CASE(1)
DO istage=1,ntimelevel
- moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,1) = moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,1) &
- + dt*b_E(istage)*moments_rhs_e(ips_e:ipe_e,ijs_e:ije_e,:,:,istage)
+ moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,1) = moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,1) &
+ + dt*b_E(istage)*moments_rhs_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,istage)
END DO
! Advance ions
DO istage=1,ntimelevel
- moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,1) = moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,1) &
- + dt*b_E(istage)*moments_rhs_i(ips_i:ipe_i,ijs_i:ije_i,:,:,istage)
+ moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,1) = moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,1) &
+ + dt*b_E(istage)*moments_rhs_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,istage)
END DO
CASE DEFAULT
! Advance electrons
- moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel) = moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,1);
+ moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,updatetlevel) = moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,1);
DO istage=1,updatetlevel-1
- moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel) = moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel) &
- + dt*A_E(updatetlevel,istage)*moments_rhs_e(ips_e:ipe_e,ijs_e:ije_e,:,:,istage)
+ moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,updatetlevel) = moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,updatetlevel) &
+ + dt*A_E(updatetlevel,istage)*moments_rhs_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,istage)
END DO
! Advance ions
- moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel) = moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,1);
+ moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,updatetlevel) = moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,1);
DO istage=1,updatetlevel-1
- moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel) = moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel) &
- + dt*A_E(updatetlevel,istage)*moments_rhs_i(ips_i:ipe_i,ijs_i:ije_i,:,:,istage)
+ moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,updatetlevel) = moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,updatetlevel) &
+ + dt*A_E(updatetlevel,istage)*moments_rhs_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,istage)
END DO
END SELECT
! Execution time end
@@ -68,26 +68,30 @@ CONTAINS
use prec_const
IMPLICIT NONE
- COMPLEX(dp), DIMENSION ( ikrs:ikre, ikzs:ikze, ntimelevel ) :: f
- COMPLEX(dp), DIMENSION ( ikrs:ikre, ikzs:ikze, ntimelevel ) :: f_rhs
+ COMPLEX(dp), DIMENSION ( ikxs:ikxe, ikys:ikye, izs:ize, ntimelevel ) :: f
+ COMPLEX(dp), DIMENSION ( ikxs:ikxe, ikys:ikye, izs:ize, ntimelevel ) :: f_rhs
INTEGER :: istage
SELECT CASE (updatetlevel)
CASE(1)
- DO ikz=ikzs,ikze
- DO ikr=ikrs,ikre
- DO istage=1,ntimelevel
- f(ikr,ikz,1) = f(ikr,ikz,1) + dt*b_E(istage)*f_rhs(ikr,ikz,istage)
+ DO iky=ikys,ikye
+ DO ikx=ikxs,ikxe
+ DO iz=izs,ize
+ DO istage=1,ntimelevel
+ f(ikx,iky,iz,1) = f(ikx,iky,iz,1) + dt*b_E(istage)*f_rhs(ikx,iky,iz,istage)
+ END DO
END DO
END DO
END DO
CASE DEFAULT
- DO ikz=ikzs,ikze
- DO ikr=ikrs,ikre
- f(ikr,ikz,updatetlevel) = f(ikr,ikz,1);
- DO istage=1,updatetlevel-1
- f(ikr,ikz,updatetlevel) = f(ikr,ikz,updatetlevel) + &
- dt*A_E(updatetlevel,istage)*f_rhs(ikr,ikz,istage)
+ DO iky=ikys,ikye
+ DO ikx=ikxs,ikxe
+ DO iz=izs,ize
+ f(ikx,iky,iz,updatetlevel) = f(ikx,iky,iz,1);
+ DO istage=1,updatetlevel-1
+ f(ikx,iky,iz,updatetlevel) = f(ikx,iky,iz,updatetlevel) + &
+ dt*A_E(updatetlevel,istage)*f_rhs(ikx,iky,iz,istage)
+ END DO
END DO
END DO
END DO
diff --git a/src/advance_field_adapt.F90 b/src/advance_field_adapt.F90
index 23809044..aed2a7e3 100644
--- a/src/advance_field_adapt.F90
+++ b/src/advance_field_adapt.F90
@@ -27,8 +27,8 @@ CONTAINS
use prec_const
IMPLICIT NONE
- COMPLEX(dp), DIMENSION ( ikrs:ikre, ikzs:ikze, ntimelevel ) :: f
- COMPLEX(dp), DIMENSION ( ikrs:ikre, ikzs:ikze, ntimelevel ) :: f_rhs
+ COMPLEX(dp), DIMENSION ( ikxs:ikxe, ikys:ikye, ntimelevel ) :: f
+ COMPLEX(dp), DIMENSION ( ikxs:ikxe, ikys:ikye, ntimelevel ) :: f_rhs
REAL(dp) :: error
INTEGER :: istage
@@ -39,37 +39,37 @@ CONTAINS
CASE ('DOPRI5_ADAPT')
error = 0._dp
- DO ikz=ikzs,ikze
- DO ikr=ikrs,ikre
- fs = f(ikr,ikz,1)
+ DO iky=ikys,ikye
+ DO ikx=ikxs,ikxe
+ fs = f(ikx,iky,1)
DO istage=1,ntimelevel
- f(ikr,ikz,1) = f(ikr,ikz,1) + dt*b_E(istage)*f_rhs(ikr,ikz,istage)
- fs = fs + dt*b_Es(istage)*f_rhs(ikr,ikz,istage)
+ f(ikx,iky,1) = f(ikx,iky,1) + dt*b_E(istage)*f_rhs(ikx,iky,istage)
+ fs = fs + dt*b_Es(istage)*f_rhs(ikx,iky,istage)
END DO
- IF ( ABS(f(ikr,ikz,1) - fs) .GT. error ) THEN
- error = ABS(f(ikr,ikz,1) - fs)
+ IF ( ABS(f(ikx,iky,1) - fs) .GT. error ) THEN
+ error = ABS(f(ikx,iky,1) - fs)
ENDIF
END DO
END DO
IF (error > TOL)
CASE DEFAULT
- DO ikz=ikzs,ikze
- DO ikr=ikrs,ikre
- fs = f(ikr,ikz,1)
+ DO iky=ikys,ikye
+ DO ikx=ikxs,ikxe
+ fs = f(ikx,iky,1)
DO istage=1,ntimelevel
- f(ikr,ikz,1) = f(ikr,ikz,1) + dt*b_E(istage)*f_rhs(ikr,ikz,istage)
+ f(ikx,iky,1) = f(ikx,iky,1) + dt*b_E(istage)*f_rhs(ikx,iky,istage)
END DO
END DO
END DO
END SELECT
CASE DEFAULT
- DO ikz=ikzs,ikze
- DO ikr=ikrs,ikre
- f(ikr,ikz,updatetlevel) = f(ikr,ikz,1);
+ DO iky=ikys,ikye
+ DO ikx=ikxs,ikxe
+ f(ikx,iky,updatetlevel) = f(ikx,iky,1);
DO istage=1,updatetlevel-1
- f(ikr,ikz,updatetlevel) = f(ikr,ikz,updatetlevel) + &
- dt*A_E(updatetlevel,istage)*f_rhs(ikr,ikz,istage)
+ f(ikx,iky,updatetlevel) = f(ikx,iky,updatetlevel) + &
+ dt*A_E(updatetlevel,istage)*f_rhs(ikx,iky,istage)
END DO
END DO
END DO
diff --git a/src/array_mod.F90 b/src/array_mod.F90
index 85560f4a..1cb6d141 100644
--- a/src/array_mod.F90
+++ b/src/array_mod.F90
@@ -3,41 +3,50 @@ MODULE array
use prec_const
implicit none
- ! Arrays to store the rhs, for time integration
- COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_rhs_e ! (ip,ij,ikr,ikz,updatetlevel)
- COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_rhs_i ! (ip,ij,ikr,ikz,updatetlevel)
+ ! Arrays to store the rhs, for time integration (ip,ij,ikx,iky,iz,updatetlevel)
+ COMPLEX(dp), DIMENSION(:,:,:,:,:,:), ALLOCATABLE :: moments_rhs_e
+ COMPLEX(dp), DIMENSION(:,:,:,:,:,:), ALLOCATABLE :: moments_rhs_i
- ! To load collision matrix
+ ! To load collision matrix (ip1,ij1,ip2,ij2)
REAL(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: Ceepj, CeipjT
REAL(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: CeipjF
REAL(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: Ciipj, CiepjT
REAL(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: CiepjF
- ! Collision term
- COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: TColl_e, TColl_i
- COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: TColl_e_local, TColl_i_local
+ ! Collision term (ip,ij,ikx,iky,iz)
+ COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: TColl_e, TColl_i
+ COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: TColl_e_local, TColl_i_local
! dnjs coefficient storage (in, ij, is)
COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: dnjs
- ! Kernel function evaluation
+ ! lin rhs p,j coefficient storage (ip,ij)
+ REAL(dp), DIMENSION(:,:), ALLOCATABLE :: xnepj,xnipj
+ REAL(dp), DIMENSION(:), ALLOCATABLE :: xnepp1j, xnepm1j, xnepp2j, xnepm2j, xnepjp1, xnepjm1
+ REAL(dp), DIMENSION(:), ALLOCATABLE :: xnipp1j, xnipm1j, xnipp2j, xnipm2j, xnipjp1, xnipjm1
+ REAL(dp), DIMENSION(:,:), ALLOCATABLE :: xphij, xphijp1, xphijm1
+
+ ! Curvature array
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: Ckxky
+
+ ! Kernel function evaluation (ij,ikx,iky)
REAL(dp), DIMENSION(:,:,:), ALLOCATABLE :: kernel_e
REAL(dp), DIMENSION(:,:,:), ALLOCATABLE :: kernel_i
- ! Non linear term array (ip,ij,ikr,ikz)
- COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: Sepj ! electron
- COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: Sipj ! ion
+ ! Non linear term array (ip,ij,ikx,iky,iz)
+ COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: Sepj ! electron
+ COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: Sipj ! ion
- ! Gyrocenter density for electron and ions (meant for 2D output)
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: Ne00
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: Ni00
+ ! Gyrocenter density for electron and ions (ikx,iky,iz)
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: Ne00
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: Ni00
- ! particle density for electron and ions (meant for 2D output)
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: dens_e
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: dens_i
+ ! particle density for electron and ions (ikx,iky,iz)
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: dens_e
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: dens_i
- ! particle temperature for electron and ions (meant for 2D output)
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: temp_e
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: temp_i
+ ! particle temperature for electron and ions (ikx,iky,iz)
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: temp_e
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: temp_i
END MODULE array
diff --git a/src/auxval.F90 b/src/auxval.F90
index ff50aba0..f1c3fd69 100644
--- a/src/auxval.F90
+++ b/src/auxval.F90
@@ -7,49 +7,60 @@ subroutine auxval
USE model
USE fourier, ONLY: init_grid_distr_and_plans, alloc_local_1, alloc_local_2
use prec_const
+ USE numerics
IMPLICIT NONE
INTEGER :: irows,irowe, irow, icol, i_
IF (my_id .EQ. 0) WRITE(*,*) '=== Set auxiliary values ==='
IF (NON_LIN) THEN
- CALL init_grid_distr_and_plans(Nr,Nz)
+ CALL init_grid_distr_and_plans(Nx,Ny)
ELSE
CALL init_1Dgrid_distr
ENDIF
+ ! Init the grids
+ CALL set_pgrid ! parallel kin (MPI distributed)
+ CALL set_jgrid ! perp kin
- CALL set_pgrid
- CALL set_jgrid
-
- CALL set_krgrid ! MPI Distributed dimension
- CALL set_kzgrid
- CALL set_kpgrid
+ CALL set_kxgrid ! radial modes (MPI distributed by FFTW)
+ CALL set_kygrid ! azymuthal modes
+ CALL set_kpgrid ! perpendicular modes
+ CALL set_zgrid ! field aligned angle
CALL memory ! Allocate memory for global arrays
+ CALL lin_coeff_and_geometry ! precompute coeff for lin equation and geometry
+
+ CALL evaluate_kernels ! precompute the kernels
+
+ IF ( NON_LIN ) THEN;
+ CALL build_dnjs_table ! precompute the Laguerre nonlin product coeffs
+ ENDIF
+
!! Display parallel settings
DO i_ = 0,num_procs-1
CALL mpi_barrier(MPI_COMM_WORLD, ierr)
IF (my_id .EQ. i_) THEN
IF (my_id .EQ. 0) WRITE(*,*) ''
IF (my_id .EQ. 0) WRITE(*,*) '--------- Parallel environement ----------'
- IF (my_id .EQ. 0) WRITE(*,'(A9,I3,A10,I3,A10,I3)') 'n_procs= ', num_procs, ', num_procs_p = ', num_procs_p, ', num_procs_kr = ', num_procs_kr
+ IF (my_id .EQ. 0) WRITE(*,'(A9,I3,A10,I3,A10,I3)') 'n_procs= ', num_procs, ', num_procs_p = ', num_procs_p, ', num_procs_kx = ', num_procs_kx
IF (my_id .EQ. 0) WRITE(*,*) ''
WRITE(*,'(A9,I3,A10,I3,A10,I3)')&
- 'my_id = ', my_id, ', rank_p = ', rank_p, ', rank_kr = ', rank_kr
- WRITE(*,'(A22,I3,A10,I3)')&
- ' ips_e = ', ips_e, ', ikrs = ', ikrs
- WRITE(*,'(A22,I3,A10,I3)')&
- ' ipe_e = ', ipe_e, ', ikre = ', ikre
- WRITE(*,'(A22,I3,A10,I3)')&
- ' ips_i = ', ips_i, ', ikzs = ', ikzs
- WRITE(*,'(A22,I3,A10,I3)')&
- ' ipe_i = ', ipe_i, ', ikze = ', ikze
-
- ! WRITE(*,'(A9,I3,A10,I3,A10,I3,A10,I3)')&
- ! ' ips_e = ',ips_e,', ipe_e = ',ipe_e,', ips_i = ',ips_i,', ipe_i = ',ipe_i
- ! WRITE (*,'(A9,I3,A10,I3,A10,I3,A10,I3,A10,I3)') &
- ! ' ikrs = ', ikrs, ', ikre = ', ikre, ', ikzs = ', ikzs, ', ikze = ', ikze
+ 'my_id = ', my_id, ', rank_p = ', rank_p, ', rank_kx = ', rank_kx
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' ips_e = ', ips_e, ', ipe_e = ', ipe_e
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' ijs_e = ', ijs_e, ', ije_e = ', ije_e
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' ips_i = ', ips_i, ', ipe_i = ', ipe_i
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' ijs_i = ', ijs_i, ', ije_i = ', ije_i
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' ikxs = ', ikxs , ', ikxe = ', ikxe
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' ikys = ', ikys , ', ikye = ', ikye
+ WRITE(*,'(A22,I3,A11,I3)')&
+ ' izs = ', izs , ', ize = ', ize
IF (my_id .NE. num_procs-1) WRITE (*,*) ''
IF (my_id .EQ. num_procs-1) WRITE(*,*) '------------------------------------------'
ENDIF
diff --git a/src/basic_mod.F90 b/src/basic_mod.F90
index 4516673b..29f0d4f0 100644
--- a/src/basic_mod.F90
+++ b/src/basic_mod.F90
@@ -12,8 +12,8 @@ MODULE basic
real(dp) :: time = 0 ! Current simulation time (Init from restart file)
INTEGER :: comm0 ! Default communicator with a topology
- INTEGER :: comm_p, comm_kr ! Communicators for 1-dim cartesian subgrids of comm0
- INTEGER :: commr_p0 ! Communicators along kr for only rank 0 on p
+ INTEGER :: comm_p, comm_kx ! Communicators for 1-dim cartesian subgrids of comm0
+ INTEGER :: commr_p0 ! Communicators along kx for only rank 0 on p
INTEGER :: jobnum = 0 ! Job number
INTEGER :: step = 0 ! Calculation step of this run
@@ -26,10 +26,10 @@ MODULE basic
INTEGER :: my_id ! Rank in COMM_WORLD
INTEGER :: num_procs ! number of MPI processes
INTEGER :: num_procs_p ! Number of processes in p
- INTEGER :: num_procs_kr ! Number of processes in r
- INTEGER :: rank_0, rank_p, rank_kr! Ranks in comm0, comm_p, comm_kr
+ INTEGER :: num_procs_kx ! Number of processes in r
+ INTEGER :: rank_0, rank_p, rank_kx! Ranks in comm0, comm_p, comm_kx
INTEGER :: nbr_L, nbr_R ! Left and right neighbours (along p)
- INTEGER :: nbr_T, nbr_B ! Top and bottom neighbours (along kr)
+ INTEGER :: nbr_T, nbr_B ! Top and bottom neighbours (along kx)
INTEGER :: iframe0d ! counting the number of times 0d datasets are outputed (for diagnose)
INTEGER :: iframe1d ! counting the number of times 1d datasets are outputed (for diagnose)
@@ -52,8 +52,8 @@ MODULE basic
real(dp) :: maxruntime = 1e9 ! Maximum simulation CPU time
INTERFACE allocate_array
- MODULE PROCEDURE allocate_array_dp1,allocate_array_dp2,allocate_array_dp3,allocate_array_dp4
- MODULE PROCEDURE allocate_array_dc1,allocate_array_dc2,allocate_array_dc3,allocate_array_dc4, allocate_array_dc5
+ MODULE PROCEDURE allocate_array_dp1,allocate_array_dp2,allocate_array_dp3,allocate_array_dp4, allocate_array_dp5, allocate_array_dp6
+ MODULE PROCEDURE allocate_array_dc1,allocate_array_dc2,allocate_array_dc3,allocate_array_dc4, allocate_array_dc5, allocate_array_dc6
MODULE PROCEDURE allocate_array_i1,allocate_array_i2,allocate_array_i3,allocate_array_i4
MODULE PROCEDURE allocate_array_l1,allocate_array_l2,allocate_array_l3,allocate_array_l4
END INTERFACE allocate_array
@@ -168,6 +168,13 @@ CONTAINS
a=0.0_dp
END SUBROUTINE allocate_array_dp5
+ SUBROUTINE allocate_array_dp6(a,is1,ie1,is2,ie2,is3,ie3,is4,ie4,is5,ie5,is6,ie6)
+ IMPLICIT NONE
+ real(dp), DIMENSION(:,:,:,:,:,:), ALLOCATABLE, INTENT(INOUT) :: a
+ INTEGER, INTENT(IN) :: is1,ie1,is2,ie2,is3,ie3,is4,ie4,is5,ie5,is6,ie6
+ ALLOCATE(a(is1:ie1,is2:ie2,is3:ie3,is4:ie4,is5:ie5,is6:ie6))
+ a=0.0_dp
+ END SUBROUTINE allocate_array_dp6
!========================================
SUBROUTINE allocate_array_dc1(a,is1,ie1)
@@ -210,6 +217,13 @@ CONTAINS
a=CMPLX(0.0_dp,0.0_dp)
END SUBROUTINE allocate_array_dc5
+ SUBROUTINE allocate_array_dc6(a,is1,ie1,is2,ie2,is3,ie3,is4,ie4,is5,ie5,is6,ie6)
+ IMPLICIT NONE
+ DOUBLE COMPLEX, DIMENSION(:,:,:,:,:,:), ALLOCATABLE, INTENT(INOUT) :: a
+ INTEGER, INTENT(IN) :: is1,ie1,is2,ie2,is3,ie3,is4,ie4,is5,ie5,is6,ie6
+ ALLOCATE(a(is1:ie1,is2:ie2,is3:ie3,is4:ie4,is5:ie5,is6:ie6))
+ a=CMPLX(0.0_dp,0.0_dp)
+ END SUBROUTINE allocate_array_dc6
!========================================
SUBROUTINE allocate_array_i1(a,is1,ie1)
diff --git a/src/closure_mod.F90 b/src/closure_mod.F90
index f8846d4a..4185a1a1 100644
--- a/src/closure_mod.F90
+++ b/src/closure_mod.F90
@@ -15,84 +15,73 @@ CONTAINS
! Positive Oob indices are approximated with a model
SUBROUTINE apply_closure_model
IMPLICIT NONE
- complex(dp) :: i_kz
- real(dp) :: taue_qe_etaB_nu, taui_qi_etaB_nu
- real(dp) :: sqpp2pp1_e, sqpp2pp1_i, sqpp1p_e, sqpp1p_i
- real(dp) :: p_dp, j_dp
- ! Spare some computations
- taue_qe_etaB_nu = tau_e*eta_B/q_e/nu
- taui_qi_etaB_nu = tau_i*eta_B/q_i/nu
- sqpp2pp1_e = SQRT((pmaxe_dp+2)*(pmaxe_dp+1))
- sqpp2pp1_i = SQRT((pmaxi_dp+2)*(pmaxi_dp+1))
- sqpp1p_e = SQRT((pmaxe_dp+1)*(pmaxe_dp))
- sqpp1p_i = SQRT((pmaxi_dp+1)*(pmaxi_dp))
CALL cpu_time(t0_clos)
! zero truncation, An+1=0 for n+1>nmax
IF (CLOS .EQ. 0) THEN
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ DO iz = izs,ize
+ DO ip = ipsg_e,ipeg_e
+ moments_e(ip,ijsg_e,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ip,ijeg_e,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ DO ij = ijsg_e,ijeg_e
+ moments_e(ipsg_e+1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ipsg_e ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ipeg_e-1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ipeg_e ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ kernel_e(ijsg_e,ikx,iky) = 0._dp
+ kernel_e(ijeg_e,ikx,iky) = 0._dp
- DO ip = ipsg_e,ipeg_e
- moments_e(ip,ijsg_e,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ip,ijeg_e,ikr,ikz,updatetlevel) = 0._dp
+ DO ip = ipsg_i,ipeg_i
+ moments_i(ip,ijsg_i,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ip,ijeg_i,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ DO ij = ijsg_i,ijeg_i
+ moments_i(ipsg_i+1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ipsg_i ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ipeg_i-1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ipeg_i ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ kernel_i(ijsg_i,ikx,iky) = 0._dp
+ kernel_i(ijeg_i,ikx,iky) = 0._dp
ENDDO
- DO ij = ijsg_e,ijeg_e
- moments_e(ipsg_e+1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ipsg_e ,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ipeg_e-1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ipeg_e ,ij,ikr,ikz,updatetlevel) = 0._dp
- ENDDO
- kernel_e(ijsg_e,ikr,ikz) = 0._dp
- kernel_e(ijeg_e,ikr,ikz) = 0._dp
-
- DO ip = ipsg_i,ipeg_i
- moments_i(ip,ijsg_i,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ip,ijeg_i,ikr,ikz,updatetlevel) = 0._dp
- ENDDO
- DO ij = ijsg_i,ijeg_i
- moments_i(ipsg_i+1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ipsg_i ,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ipeg_i-1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ipeg_i ,ij,ikr,ikz,updatetlevel) = 0._dp
- ENDDO
- kernel_i(ijsg_i,ikr,ikz) = 0._dp
- kernel_i(ijeg_i,ikr,ikz) = 0._dp
-
ENDDO
ENDDO
! zero truncation, An+1=0 for n+1>nmax
ELSEIF (CLOS .EQ. 1) THEN
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ DO iz = izs,ize
+ DO ip = ipsg_e,ipeg_e
+ moments_e(ip,ijsg_e,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ip,ijeg_e,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ DO ij = ijsg_e,ijeg_e
+ moments_e(ipsg_e+1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ipsg_e ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ipeg_e-1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_e(ipeg_e ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ kernel_e(ijsg_e,ikx,iky) = 0._dp
+ kernel_e(ijeg_e,ikx,iky) = 0._dp
- DO ip = ipsg_e,ipeg_e
- moments_e(ip,ijsg_e,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ip,ijeg_e,ikr,ikz,updatetlevel) = 0._dp
+ DO ip = ipsg_i,ipeg_i
+ moments_i(ip,ijsg_i,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ip,ijeg_i,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ DO ij = ijsg_i,ijeg_i
+ moments_i(ipsg_i+1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ipsg_i ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ipeg_i-1,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ moments_i(ipeg_i ,ij,ikx,iky,iz,updatetlevel) = 0._dp
+ ENDDO
+ kernel_i(ijsg_i,ikx,iky) = 0._dp
+ kernel_i(ijeg_i,ikx,iky) = 0._dp
ENDDO
- DO ij = ijsg_e,ijeg_e
- moments_e(ipsg_e+1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ipsg_e ,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ipeg_e-1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_e(ipeg_e ,ij,ikr,ikz,updatetlevel) = 0._dp
- ENDDO
- kernel_e(ijsg_e,ikr,ikz) = 0._dp
- kernel_e(ijeg_e,ikr,ikz) = 0._dp
-
- DO ip = ipsg_i,ipeg_i
- moments_i(ip,ijsg_i,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ip,ijeg_i,ikr,ikz,updatetlevel) = 0._dp
- ENDDO
- DO ij = ijsg_i,ijeg_i
- moments_i(ipsg_i+1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ipsg_i ,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ipeg_i-1,ij,ikr,ikz,updatetlevel) = 0._dp
- moments_i(ipeg_i ,ij,ikr,ikz,updatetlevel) = 0._dp
- ENDDO
- kernel_i(ijsg_i,ikr,ikz) = 0._dp
- kernel_i(ijeg_i,ikr,ikz) = 0._dp
-
ENDDO
ENDDO
ELSE
diff --git a/src/collision_mod.F90 b/src/collision_mod.F90
index 668e32c7..b6dca646 100644
--- a/src/collision_mod.F90
+++ b/src/collision_mod.F90
@@ -1,13 +1,5 @@
module collision
! contains the Hermite-Laguerre collision operators. Solved using COSOlver.
-USE fields
-USE array
-USE basic
-USE grid
-USE prec_const
-USE time_integration
-USE model
-USE utility
IMPLICIT NONE
PUBLIC :: compute_TColl
@@ -20,34 +12,38 @@ CONTAINS
!******************************************************************************!
!! Doughtery gyrokinetic collision operator for electrons
!******************************************************************************!
- SUBROUTINE DoughertyGK_e(ip_,ij_,ikr_,ikz_,TColl_)
+ SUBROUTINE DoughertyGK_e(ip_,ij_,ikx_,iky_,iz_,TColl_)
+ USE fields, ONLY: moments_e, phi
+ USE grid, ONLY: parray_e, jarray_e, kxarray, kyarray, Jmaxe
+ USE array, ONLY: kernel_e
+ USE basic
+ USE model, ONLY: sigmae2_taue_o2, qe_taue, nu_ee
+ USE time_integration, ONLY : updatetlevel
IMPLICIT NONE
- INTEGER, INTENT(IN) :: ip_,ij_,ikr_,ikz_
- COMPLEX(dp), INTENT(OUT) :: TColl_
+ INTEGER, INTENT(IN) :: ip_,ij_,ikx_,iky_,iz_
+ COMPLEX(dp), INTENT(OUT) :: TColl_
COMPLEX(dp) :: n_,upar_,uperp_,Tpar_, Tperp_, T_
COMPLEX(dp) :: nadiab_moment_0j
REAL(dp) :: Knp0, Knp1, Knm1
INTEGER :: in_
- REAL(dp) :: n_dp, j_dp, p_dp, be_, be_2, q_e_tau_e
+ REAL(dp) :: n_dp, j_dp, p_dp, be_, be_2
!** Auxiliary variables **
p_dp = REAL(parray_e(ip_),dp)
j_dp = REAL(jarray_e(ij_),dp)
- be_2 = (krarray(ikr_)**2 + kzarray(ikz_)**2) * sigmae2_taue_o2 ! this is (be/2)^2
- ! ibe_ = imagu*2._dp*SQRT(be_2)
+ be_2 = (kxarray(ikx_)**2 + kyarray(iky_)**2) * sigmae2_taue_o2 ! this is (be/2)^2
be_ = 2_dp*SQRT(be_2) ! this is be
- q_e_tau_e = q_e/tau_e
!** Assembling collison operator **
! Velocity-space diffusion (similar to Lenhard Bernstein)
! -nuee (p + 2j + b^2/2) Nepj
- TColl_ = -(p_dp + 2._dp*j_dp + 2._dp*be_2)*moments_e(ip_,ij_,ikr_,ikz_,updatetlevel)
+ TColl_ = -(p_dp + 2._dp*j_dp + 2._dp*be_2)*moments_e(ip_,ij_,ikx_,iky_,iz_,updatetlevel)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Non zero term for p = 0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
IF( p_dp .EQ. 0 ) THEN ! Kronecker p0
! Get adiabatic moment
- TColl_ = TColl_ - (p_dp + 2._dp*j_dp + 2._dp*be_2) * q_e_tau_e * Kernel_e(ij_,ikr_,ikz_)*phi(ikr_,ikz_)
+ TColl_ = TColl_ - (p_dp + 2._dp*j_dp + 2._dp*be_2) * qe_taue * Kernel_e(ij_,ikx_,iky_)*phi(ikx_,iky_,iz_)
!** build required fluid moments **
n_ = 0._dp
upar_ = 0._dp; uperp_ = 0._dp
@@ -55,26 +51,26 @@ CONTAINS
DO in_ = 1,jmaxe+1
n_dp = REAL(in_-1,dp)
! Store the kernels for sparing readings
- Knp0 = Kernel_e(in_,ikr_,ikz_)
- Knp1 = Kernel_e(in_+1,ikr_,ikz_)
- Knm1 = Kernel_e(in_-1,ikr_,ikz_)
+ Knp0 = Kernel_e(in_,ikx_,iky_)
+ Knp1 = Kernel_e(in_+1,ikx_,iky_)
+ Knm1 = Kernel_e(in_-1,ikx_,iky_)
! Nonadiabatic moments (only different from moments when p=0)
- nadiab_moment_0j = moments_e(1,in_ ,ikr_,ikz_,updatetlevel) + q_e_tau_e * Knp0 *phi(ikr_,ikz_)
+ nadiab_moment_0j = moments_e(1,in_ ,ikx_,iky_,iz_,updatetlevel) + qe_taue*Knp0*phi(ikx_,iky_,iz_)
! Density
n_ = n_ + Knp0 * nadiab_moment_0j
! Perpendicular velocity
uperp_ = uperp_ + be_*0.5_dp*(Knp0 - Knm1) * nadiab_moment_0j
! Parallel temperature
- Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_e(3,in_,ikr_,ikz_,updatetlevel) + nadiab_moment_0j)
+ Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_e(3,in_,ikx_,iky_,iz_,updatetlevel) + nadiab_moment_0j)
! Perpendicular temperature
Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1._dp)*Knp1 - n_dp*Knm1)*nadiab_moment_0j
ENDDO
T_ = (Tpar_ + 2._dp*Tperp_)/3._dp - n_
! Add energy restoring term
- TColl_ = TColl_ + T_* 4._dp * j_dp * Kernel_e(ij_,ikr_,ikz_)
- TColl_ = TColl_ - T_* 2._dp * (j_dp + 1._dp) * Kernel_e(ij_+1,ikr_,ikz_)
- TColl_ = TColl_ - T_* 2._dp * j_dp * Kernel_e(ij_-1,ikr_,ikz_)
- TColl_ = TColl_ + uperp_*be_* (Kernel_e(ij_,ikr_,ikz_) - Kernel_e(ij_-1,ikr_,ikz_))
+ TColl_ = TColl_ + T_* 4._dp * j_dp * Kernel_e(ij_ ,ikx_,iky_)
+ TColl_ = TColl_ - T_* 2._dp * (j_dp + 1._dp) * Kernel_e(ij_+1,ikx_,iky_)
+ TColl_ = TColl_ - T_* 2._dp * j_dp * Kernel_e(ij_-1,ikx_,iky_)
+ TColl_ = TColl_ + uperp_*be_* (Kernel_e(ij_,ikx_,iky_) - Kernel_e(ij_-1,ikx_,iky_))
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Non zero term for p = 1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -83,9 +79,9 @@ CONTAINS
upar_ = 0._dp
DO in_ = 1,jmaxe+1
! Parallel velocity
- upar_ = upar_ + Kernel_e(in_,ikr_,ikz_) * moments_e(2,in_,ikr_,ikz_,updatetlevel)
+ upar_ = upar_ + Kernel_e(in_,ikx_,iky_) * moments_e(2,in_,ikx_,iky_,iz_,updatetlevel)
ENDDO
- TColl_ = TColl_ + upar_*Kernel_e(ij_,ikr_,ikz_)
+ TColl_ = TColl_ + upar_*Kernel_e(ij_,ikx_,iky_)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Non zero term for p = 2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -97,20 +93,20 @@ CONTAINS
DO in_ = 1,jmaxe+1
n_dp = REAL(in_-1,dp)
! Store the kernels for sparing readings
- Knp0 = Kernel_e(in_,ikr_,ikz_)
- Knp1 = Kernel_e(in_+1,ikr_,ikz_)
- Knm1 = Kernel_e(in_-1,ikr_,ikz_)
+ Knp0 = Kernel_e(in_ ,ikx_,iky_)
+ Knp1 = Kernel_e(in_+1,ikx_,iky_)
+ Knm1 = Kernel_e(in_-1,ikx_,iky_)
! Nonadiabatic moments (only different from moments when p=0)
- nadiab_moment_0j = moments_e(1,in_ ,ikr_,ikz_,updatetlevel) + q_e_tau_e*Knp0*phi(ikr_,ikz_)
+ nadiab_moment_0j = moments_e(1,in_,ikx_,iky_,iz_,updatetlevel) + qe_taue*Knp0*phi(ikx_,iky_,iz_)
! Density
n_ = n_ + Knp0 * nadiab_moment_0j
! Parallel temperature
- Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_e(3,in_,ikr_,ikz_,updatetlevel) + nadiab_moment_0j)
+ Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_e(3,in_,ikx_,iky_,iz_,updatetlevel) + nadiab_moment_0j)
! Perpendicular temperature
- Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1) * Knp1 - n_dp * Knm1)*nadiab_moment_0j
+ Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1._dp)*Knp1 - n_dp*Knm1)*nadiab_moment_0j
ENDDO
T_ = (Tpar_ + 2._dp*Tperp_)/3._dp - n_
- TColl_ = TColl_ + T_*SQRT2*Kernel_e(ij_,ikr_,ikz_)
+ TColl_ = TColl_ + T_*SQRT2*Kernel_e(ij_,ikx_,iky_)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ENDIF
@@ -121,33 +117,39 @@ CONTAINS
!******************************************************************************!
!! Doughtery gyrokinetic collision operator for ions
!******************************************************************************!
- SUBROUTINE DoughertyGK_i(ip_,ij_,ikr_,ikz_,TColl_)
+ SUBROUTINE DoughertyGK_i(ip_,ij_,ikx_,iky_,iz_,TColl_)
+ USE fields, ONLY: moments_i, phi
+ USE grid, ONLY: parray_i, jarray_i, kxarray, kyarray, Jmaxi
+ USE array, ONLY: kernel_i
+ USE basic
+ USE model, ONLY: sigmai2_taui_o2, qi_taui, nu_i
+ USE time_integration, ONLY : updatetlevel
IMPLICIT NONE
- INTEGER, INTENT(IN) :: ip_,ij_,ikr_,ikz_
- COMPLEX(dp), INTENT(OUT) :: TColl_
+ INTEGER, INTENT(IN) :: ip_,ij_,ikx_,iky_,iz_
+ COMPLEX(dp), INTENT(OUT) :: TColl_
COMPLEX(dp) :: n_,upar_,uperp_,Tpar_, Tperp_, T_
+ COMPLEX(dp) :: bi_, bi_2
COMPLEX(dp) :: nadiab_moment_0j
REAL(dp) :: Knp0, Knp1, Knm1
INTEGER :: in_
- REAL(dp) :: n_dp, j_dp, p_dp, bi_, bi_2, q_i_tau_i
+ REAL(dp) :: n_dp, j_dp, p_dp
!** Auxiliary variables **
p_dp = REAL(parray_i(ip_),dp)
j_dp = REAL(jarray_i(ij_),dp)
- bi_2 = (krarray(ikr_)**2 + kzarray(ikz_)**2) * sigmai2_taui_o2 ! this is (bi/2)^2
+ bi_2 = (kxarray(ikx_)**2 + kyarray(iky_)**2) * sigmai2_taui_o2 ! this is (bi/2)^2
bi_ = 2_dp*SQRT(bi_2) ! this is be
- q_i_tau_i = q_i/tau_i
!** Assembling collison operator **
! Velocity-space diffusion (similar to Lenhard Bernstein)
! -nui (p + 2j + b^2/2) Nipj
- TColl_ = -(p_dp + 2._dp*j_dp + 2._dp*bi_2)*moments_i(ip_,ij_,ikr_,ikz_,updatetlevel)
+ TColl_ = -(p_dp + 2._dp*j_dp + 2._dp*bi_2)*moments_i(ip_,ij_,ikx_,iky_,iz_,updatetlevel)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Non zero term for p = 0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
IF( p_dp .EQ. 0 ) THEN ! Kronecker p0
! Get adiabatic moment
- TColl_ = TColl_ - (p_dp + 2._dp*j_dp + 2._dp*bi_2) * q_i_tau_i * Kernel_i(ij_,ikr_,ikz_)*phi(ikr_,ikz_)
+ TColl_ = TColl_ - (p_dp + 2._dp*j_dp + 2._dp*bi_2) * qi_taui * Kernel_i(ij_,ikx_,iky_)*phi(ikx_,iky_,iz_)
!** build required fluid moments **
n_ = 0._dp
upar_ = 0._dp; uperp_ = 0._dp
@@ -155,46 +157,41 @@ CONTAINS
DO in_ = 1,jmaxi+1
n_dp = REAL(in_-1,dp)
! Store the kernels for sparing readings
- Knp0 = Kernel_i(in_,ikr_,ikz_)
- Knp1 = Kernel_i(in_+1,ikr_,ikz_)
- Knm1 = Kernel_i(in_-1,ikr_,ikz_)
+ Knp0 = Kernel_i(in_,ikx_,iky_)
+ Knp1 = Kernel_i(in_+1,ikx_,iky_)
+ Knm1 = Kernel_i(in_-1,ikx_,iky_)
! Nonadiabatic moments (only different from moments when p=0)
- nadiab_moment_0j = moments_i(1,in_ ,ikr_,ikz_,updatetlevel) + q_i_tau_i * Knp0 *phi(ikr_,ikz_)
+ nadiab_moment_0j = moments_i(1,in_ ,ikx_,iky_,iz_,updatetlevel) + qi_taui*Knp0*phi(ikx_,iky_,iz_)
! Density
n_ = n_ + Knp0 * nadiab_moment_0j
! Perpendicular velocity
- ! uperp_ = uperp_ + ibi_*0.5_dp*Kernel_i(in_,ikr_,ikz_) * (nadiab_moment_0j - nadiab_moment_0jp1)
- ! uperp_ = uperp_ + b_i*0.5_dp*Kernel_i(in_,ikr_,ikz_) * (nadiab_moment_0j - nadiab_moment_0jp1)
uperp_ = uperp_ + bi_*0.5_dp*(Knp0 - Knm1) * nadiab_moment_0j
! Parallel temperature
- Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_i(3,in_,ikr_,ikz_,updatetlevel) + nadiab_moment_0j)
+ Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_i(3,in_,ikx_,iky_,iz_,updatetlevel) + nadiab_moment_0j)
! Perpendicular temperature
- ! Tperp_ = Tperp_ + Kernel_i(in_,ikr_,ikz_) * ((2._dp*n_dp+1._dp)* nadiab_moment_0j &
- ! - n_dp * nadiab_moment_0jm1 &
- ! - (n_dp+1)* nadiab_moment_0jp1)
- Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1) * Knp1 - n_dp * Knm1)*nadiab_moment_0j
+ Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1._dp)*Knp1 - n_dp*Knm1)*nadiab_moment_0j
ENDDO
T_ = (Tpar_ + 2._dp*Tperp_)/3._dp - n_
! Add energy restoring term
- TColl_ = TColl_ + T_* 4._dp * j_dp * Kernel_i(ij_,ikr_,ikz_)
- TColl_ = TColl_ - T_* 2._dp * (j_dp + 1._dp) * Kernel_i(ij_+1,ikr_,ikz_)
- TColl_ = TColl_ - T_* 2._dp * j_dp * Kernel_i(ij_-1,ikr_,ikz_)
- TColl_ = TColl_ + uperp_*bi_* (Kernel_i(ij_,ikr_,ikz_) - Kernel_i(ij_-1,ikr_,ikz_))
+ TColl_ = TColl_ + T_* 4._dp * j_dp * Kernel_i(ij_ ,ikx_,iky_)
+ TColl_ = TColl_ - T_* 2._dp * (j_dp + 1._dp) * Kernel_i(ij_+1,ikx_,iky_)
+ TColl_ = TColl_ - T_* 2._dp * j_dp * Kernel_i(ij_-1,ikx_,iky_)
+ TColl_ = TColl_ + uperp_*bi_* (Kernel_i(ij_,ikx_,iky_) - Kernel_i(ij_-1,ikx_,iky_))
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Non zero term for p = 1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
- ELSEIF( p_dp .eq. 1 ) THEN ! kronecker p1
+ ELSEIF( p_dp .eq. 1 ) THEN ! kxonecker p1
!** build required fluid moments **
upar_ = 0._dp
DO in_ = 1,jmaxi+1
! Parallel velocity
- upar_ = upar_ + Kernel_i(in_,ikr_,ikz_) * moments_i(2,in_,ikr_,ikz_,updatetlevel)
+ upar_ = upar_ + Kernel_i(in_,ikx_,iky_) * moments_i(2,in_,ikx_,iky_,iz_,updatetlevel)
ENDDO
- TColl_ = TColl_ + upar_*Kernel_i(ij_,ikr_,ikz_)
+ TColl_ = TColl_ + upar_*Kernel_i(ij_,ikx_,iky_)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Non zero term for p = 2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
- ELSEIF( p_dp .eq. 2 ) THEN ! kronecker p2
+ ELSEIF( p_dp .eq. 2 ) THEN ! kxonecker p2
!** build required fluid moments **
n_ = 0._dp
upar_ = 0._dp; uperp_ = 0._dp
@@ -202,20 +199,20 @@ CONTAINS
DO in_ = 1,jmaxi+1
n_dp = REAL(in_-1,dp)
! Store the kernels for sparing readings
- Knp0 = Kernel_i(in_,ikr_,ikz_)
- Knp1 = Kernel_i(in_+1,ikr_,ikz_)
- Knm1 = Kernel_i(in_-1,ikr_,ikz_)
+ Knp0 = Kernel_i(in_ ,ikx_,iky_)
+ Knp1 = Kernel_i(in_+1,ikx_,iky_)
+ Knm1 = Kernel_i(in_-1,ikx_,iky_)
! Nonadiabatic moments (only different from moments when p=0)
- nadiab_moment_0j = moments_i(1,in_ ,ikr_,ikz_,updatetlevel) + q_i_tau_i * Knp0*phi(ikr_,ikz_)
+ nadiab_moment_0j = moments_i(1,in_,ikx_,iky_,iz_,updatetlevel) + qi_taui*Knp0*phi(ikx_,iky_,iz_)
! Density
n_ = n_ + Knp0 * nadiab_moment_0j
! Parallel temperature
- Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_i(3,in_,ikr_,ikz_,updatetlevel) + nadiab_moment_0j)
+ Tpar_ = Tpar_ + Knp0 * (SQRT2*moments_i(3,in_,ikx_,iky_,iz_,updatetlevel) + nadiab_moment_0j)
! Perpendicular temperature
- Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1) * Knp1 - n_dp * Knm1)*nadiab_moment_0j
+ Tperp_ = Tperp_ + ((2._dp*n_dp+1._dp)*Knp0 - (n_dp+1._dp)*Knp1 - n_dp*Knm1)*nadiab_moment_0j
ENDDO
T_ = (Tpar_ + 2._dp*Tperp_)/3._dp - n_
- TColl_ = TColl_ + T_*SQRT2*Kernel_i(ij_,ikr_,ikz_)
+ TColl_ = TColl_ + T_*SQRT2*Kernel_i(ij_,ikx_,iky_)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ENDIF
@@ -225,66 +222,76 @@ CONTAINS
END SUBROUTINE DoughertyGK_i
!******************************************************************************!
- !! compute the collision terms in a (Np x Nj x Nkr x Nkz) matrix all at once
+ !! compute the collision terms in a (Np x Nj x Nkx x Nky) matrix all at once
!******************************************************************************!
SUBROUTINE compute_TColl
+ USE fields
+ USE grid
+ USE array
+ USE basic
+ USE prec_const
+ USE time_integration
+ USE model
+ USE utility
IMPLICIT NONE
COMPLEX(dp), DIMENSION(1:pmaxe+1) :: local_sum_e, buffer_e, total_sum_e
COMPLEX(dp), DIMENSION(ips_e:ipe_e) :: TColl_distr_e
COMPLEX(dp), DIMENSION(1:pmaxi+1) :: local_sum_i, buffer_i, total_sum_i
COMPLEX(dp), DIMENSION(ips_i:ipe_i) :: TColl_distr_i
COMPLEX(dp) :: TColl
- INTEGER :: ikrs_C, ikre_C, ikzs_C, ikze_C
+ INTEGER :: ikxs_C, ikxe_C, ikys_C, ikye_C
! Execution time start
CALL cpu_time(t0_coll)
IF (ABS(CO) .GE. 2) THEN !compute only if COSOlver matrices are used
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- ! Electrons
- DO ij = 1,Jmaxe+1
- ! Loop over all p to compute sub collision term
- DO ip = 1,Pmaxe+1
- CALL apply_COSOlver_mat_e(ip,ij,ikr,ikz,TColl)
- local_sum_e(ip) = TColl
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ DO iz = izs,ize
+ ! Electrons
+ DO ij = 1,Jmaxe+1
+ ! Loop over all p to compute sub collision term
+ DO ip = 1,Pmaxe+1
+ CALL apply_COSOlver_mat_e(ip,ij,ikx,iky,iz,TColl)
+ local_sum_e(ip) = TColl
+ ENDDO
+ IF (num_procs_p .GT. 1) THEN
+ ! Sum up all the sub collision terms on root 0
+ CALL MPI_REDUCE(local_sum_e, buffer_e, pmaxe+1, MPI_DOUBLE_COMPLEX, MPI_SUM, 0, comm_p, ierr)
+ ! distribute the sum over the process among p
+ CALL MPI_SCATTERV(buffer_e, counts_np_e, displs_np_e, MPI_DOUBLE_COMPLEX,&
+ TColl_distr_e, local_np_e, MPI_DOUBLE_COMPLEX,&
+ 0, comm_p, ierr)
+ ELSE
+ TColl_distr_e = local_sum_e
+ ENDIF
+ ! Write in output variable
+ DO ip = ips_e,ipe_e
+ TColl_e(ip,ij,ikx,iky,iz) = TColl_distr_e(ip)
+ ENDDO
ENDDO
- IF (num_procs_p .GT. 1) THEN
- ! Sum up all the sub collision terms on root 0
- CALL MPI_REDUCE(local_sum_e, buffer_e, pmaxe+1, MPI_DOUBLE_COMPLEX, MPI_SUM, 0, comm_p, ierr)
- ! distribute the sum over the process among p
- CALL MPI_SCATTERV(buffer_e, counts_np_e, displs_np_e, MPI_DOUBLE_COMPLEX,&
- TColl_distr_e, local_np_e, MPI_DOUBLE_COMPLEX,&
- 0, comm_p, ierr)
- ELSE
- TColl_distr_e = local_sum_e
- ENDIF
- ! Write in output variable
- DO ip = ips_e,ipe_e
- TColl_e(ip,ij,ikr,ikz) = TColl_distr_e(ip)
- ENDDO
- ENDDO
- ! Ions
- DO ij = 1,Jmaxi+1
- DO ip = 1,Pmaxi+1
- CALL apply_COSOlver_mat_i(ip,ij,ikr,ikz,TColl)
- local_sum_i(ip) = TColl
- ENDDO
- IF (num_procs_p .GT. 1) THEN
- ! Reduce the local_sums to root = 0
- CALL MPI_REDUCE(local_sum_i, buffer_i, pmaxi+1, MPI_DOUBLE_COMPLEX, MPI_SUM, 0, comm_p, ierr)
- ! buffer contains the entire collision term along p, we scatter it between
- ! the other processes (use of scatterv since Pmax/Np is not an integer)
- CALL MPI_SCATTERV(buffer_i, counts_np_i, displs_np_i, MPI_DOUBLE_COMPLEX,&
- TColl_distr_i, local_np_i, MPI_DOUBLE_COMPLEX, &
- 0, comm_p, ierr)
- ELSE
- TColl_distr_i = local_sum_i
- ENDIF
- ! Write in output variable
- DO ip = ips_i,ipe_i
- TColl_i(ip,ij,ikr,ikz) = TColl_distr_i(ip)
+ ! Ions
+ DO ij = 1,Jmaxi+1
+ DO ip = 1,Pmaxi+1
+ CALL apply_COSOlver_mat_i(ip,ij,ikx,iky,iz,TColl)
+ local_sum_i(ip) = TColl
+ ENDDO
+ IF (num_procs_p .GT. 1) THEN
+ ! Reduce the local_sums to root = 0
+ CALL MPI_REDUCE(local_sum_i, buffer_i, pmaxi+1, MPI_DOUBLE_COMPLEX, MPI_SUM, 0, comm_p, ierr)
+ ! buffer contains the entire collision term along p, we scatter it between
+ ! the other processes (use of scatterv since Pmax/Np is not an integer)
+ CALL MPI_SCATTERV(buffer_i, counts_np_i, displs_np_i, MPI_DOUBLE_COMPLEX,&
+ TColl_distr_i, local_np_i, MPI_DOUBLE_COMPLEX, &
+ 0, comm_p, ierr)
+ ELSE
+ TColl_distr_i = local_sum_i
+ ENDIF
+ ! Write in output variable
+ DO ip = ips_i,ipe_i
+ TColl_i(ip,ij,ikx,iky,iz) = TColl_distr_i(ip)
+ ENDDO
ENDDO
ENDDO
ENDDO
@@ -299,19 +306,26 @@ CONTAINS
!******************************************************************************!
!!!!!!! Compute ion collision term
!******************************************************************************!
- SUBROUTINE apply_COSOlver_mat_e(ip_,ij_,ikr_,ikz_,TColl_)
+ SUBROUTINE apply_COSOlver_mat_e(ip_,ij_,ikx_,iky_,iz_,TColl_)
+ USE fields, ONLY: moments_e, moments_i
+ USE grid
+ USE array
+ USE basic
+ USE time_integration, ONLY: updatetlevel
+ USE utility
+ USE model, ONLY: CO, nu_e, nu_ee
IMPLICIT NONE
- INTEGER, INTENT(IN) :: ip_, ij_ ,ikr_, ikz_
+ INTEGER, INTENT(IN) :: ip_, ij_ ,ikx_, iky_, iz_
COMPLEX(dp), INTENT(OUT) :: TColl_
- INTEGER :: ip2,ij2, p_int,j_int, p2_int,j2_int, ikr_C, ikz_C
+ INTEGER :: ip2,ij2, p_int,j_int, p2_int,j2_int, ikx_C, iky_C
p_int = ip_-1; j_int = ij_-1
IF (CO .GT. 0) THEN ! GK operator (k-dependant)
- ikr_C = ikr_; ikz_C = ikz_
+ ikx_C = ikx_; iky_C = iky_
ELSEIF (CO .LT. 0) THEN ! DK operator (only one mat for every k)
- ikr_C = 1; ikz_C = 1
+ ikx_C = 1; iky_C = 1
ENDIF
TColl_ = 0._dp ! Initialization of the local sum
@@ -321,9 +335,9 @@ CONTAINS
p2_int = parray_e(ip2)
jloopee: DO ij2 = ijs_e,ije_e
j2_int = jarray_e(ij2)
- TColl_ = TColl_ + moments_e(ip2,ij2,ikr_,ikz_,updatetlevel) &
- *( nu_e * CeipjT(bare(p_int,j_int), bare(p2_int,j2_int),ikr_C, ikz_C) &
- +nu_ee * Ceepj (bare(p_int,j_int), bare(p2_int,j2_int),ikr_C, ikz_C))
+ TColl_ = TColl_ + moments_e(ip2,ij2,ikx_,iky_,iz_,updatetlevel) &
+ *( nu_e * CeipjT(bare(p_int,j_int), bare(p2_int,j2_int),ikx_C, iky_C) &
+ +nu_ee * Ceepj (bare(p_int,j_int), bare(p2_int,j2_int),ikx_C, iky_C))
ENDDO jloopee
ENDDO ploopee
@@ -332,8 +346,8 @@ CONTAINS
p2_int = parray_i(ip2)
jloopei: DO ij2 = ijs_i,ije_i
j2_int = jarray_i(ij2)
- TColl_ = TColl_ + moments_i(ip2,ij2,ikr_,ikz_,updatetlevel) &
- *(nu_e * CeipjF(bare(p_int,j_int), bari(p2_int,j2_int),ikr_C, ikz_C))
+ TColl_ = TColl_ + moments_i(ip2,ij2,ikx_,iky_,iz_,updatetlevel) &
+ *(nu_e * CeipjF(bare(p_int,j_int), bari(p2_int,j2_int),ikx_C, iky_C))
END DO jloopei
ENDDO ploopei
@@ -342,19 +356,25 @@ CONTAINS
!******************************************************************************!
!!!!!!! Compute ion collision term
!******************************************************************************!
- SUBROUTINE apply_COSOlver_mat_i(ip_,ij_,ikr_,ikz_,TColl_)
+ SUBROUTINE apply_COSOlver_mat_i(ip_,ij_,ikx_,iky_,iz_,TColl_)
+ USE fields, ONLY : moments_e, moments_i
+ USE grid
+ USE array
+ USE basic
+ USE time_integration, ONLY : updatetlevel
+ USE utility
+ USE model, ONLY: CO, nu_i, nu_ie
IMPLICIT NONE
-
- INTEGER, INTENT(IN) :: ip_, ij_ ,ikr_, ikz_
+ INTEGER, INTENT(IN) :: ip_, ij_ ,ikx_, iky_, iz_
COMPLEX(dp), INTENT(OUT) :: TColl_
- INTEGER :: ip2,ij2, p_int,j_int, p2_int,j2_int, ikr_C, ikz_C
+ INTEGER :: ip2,ij2, p_int,j_int, p2_int,j2_int, ikx_C, iky_C
p_int = ip_-1; j_int = ij_-1
IF (CO .GT. 0) THEN ! GK operator (k-dependant)
- ikr_C = ikr_; ikz_C = ikz_
+ ikx_C = ikx_; iky_C = iky_
ELSEIF (CO .LT. 0) THEN ! DK operator (only one mat for every k)
- ikr_C = 1; ikz_C = 1
+ ikx_C = 1; iky_C = 1
ENDIF
TColl_ = 0._dp ! Initialization
@@ -363,9 +383,9 @@ CONTAINS
p2_int = parray_i(ip2)
jloopii: DO ij2 = ijs_i,ije_i
j2_int = jarray_i(ij2)
- TColl_ = TColl_ + moments_i(ip2,ij2,ikr_,ikz_,updatetlevel) &
- *( nu_ie * CiepjT(bari(p_int,j_int), bari(p2_int,j2_int), ikr_C, ikz_C) &
- +nu_i * Ciipj (bari(p_int,j_int), bari(p2_int,j2_int), ikr_C, ikz_C))
+ TColl_ = TColl_ + moments_i(ip2,ij2,ikx_,iky_,iz_,updatetlevel) &
+ *( nu_ie * CiepjT(bari(p_int,j_int), bari(p2_int,j2_int), ikx_C, iky_C) &
+ +nu_i * Ciipj (bari(p_int,j_int), bari(p2_int,j2_int), ikx_C, iky_C))
ENDDO jloopii
ENDDO ploopii
@@ -373,8 +393,8 @@ CONTAINS
p2_int = parray_e(ip2)
jloopie: DO ij2 = ijs_e,ije_e
j2_int = jarray_e(ij2)
- TColl_ = TColl_ + moments_e(ip2,ij2,ikr_,ikz_,updatetlevel) &
- *(nu_ie * CiepjF(bari(p_int,j_int), bare(p2_int,j2_int), ikr_C, ikz_C))
+ TColl_ = TColl_ + moments_e(ip2,ij2,ikx_,iky_,iz_,updatetlevel) &
+ *(nu_ie * CiepjF(bari(p_int,j_int), bare(p2_int,j2_int), ikx_C, iky_C))
ENDDO jloopie
ENDDO ploopie
@@ -386,6 +406,12 @@ CONTAINS
SUBROUTINE load_COSOlver_mat ! Load a sub matrix from iCa files (works for pmaxa,jmaxa<=P_full,J_full)
use futils
use initial_par
+ USE grid
+ USE array, ONLY: Ceepj, Ciipj, CeipjF, CeipjT, CiepjF, CiepjT
+ USE basic
+ USE time_integration, ONLY : updatetlevel
+ USE utility
+ USE model, ONLY: CO, NON_LIN
IMPLICIT NONE
! Indices for row and columns of the COSOlver matrix (4D compressed 2D matrices)
INTEGER :: irow_sub, irow_full, icol_sub, icol_full
@@ -591,11 +617,11 @@ CONTAINS
ENDDO
CALL closef(fid)
- IF (CO .GT. 0) THEN ! Interpolation of the kperp matrix values on kr kz grid
- IF (my_id .EQ. 0 ) WRITE(*,*) '...Interpolation from matrices kperp to simulation kr,kz...'
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- kperp_sim = SQRT(krarray(ikr)**2+kzarray(ikz)**2) ! current simulation kperp
+ IF (CO .GT. 0) THEN ! Interpolation of the kperp matrix values on kx ky grid
+ IF (my_id .EQ. 0 ) WRITE(*,*) '...Interpolation from matrices kperp to simulation kx,ky...'
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ kperp_sim = SQRT(kxarray(ikx)**2+kyarray(iky)**2) ! current simulation kperp
! Find the interval in kp grid mat where kperp_sim is contained
! Loop over the whole kp mat grid to find the smallest kperp that is
@@ -614,12 +640,12 @@ CONTAINS
zerotoone = (kperp_sim - kp_grid_mat(ikp_prev))/(kp_grid_mat(ikp_next) - kp_grid_mat(ikp_prev))
! Linear interpolation between previous and next kperp matrix values
- Ceepj (:,:,ikr,ikz) = (Ceepj__kp(:,:,ikp_next) - Ceepj__kp(:,:,ikp_prev))*zerotoone + Ceepj__kp(:,:,ikp_prev)
- CeipjT(:,:,ikr,ikz) = (CeipjT_kp(:,:,ikp_next) - CeipjT_kp(:,:,ikp_prev))*zerotoone + CeipjT_kp(:,:,ikp_prev)
- CeipjF(:,:,ikr,ikz) = (CeipjF_kp(:,:,ikp_next) - CeipjF_kp(:,:,ikp_prev))*zerotoone + CeipjF_kp(:,:,ikp_prev)
- Ciipj (:,:,ikr,ikz) = (Ciipj__kp(:,:,ikp_next) - Ciipj__kp(:,:,ikp_prev))*zerotoone + Ciipj__kp(:,:,ikp_prev)
- CiepjT(:,:,ikr,ikz) = (CiepjT_kp(:,:,ikp_next) - CiepjT_kp(:,:,ikp_prev))*zerotoone + CiepjT_kp(:,:,ikp_prev)
- CiepjF(:,:,ikr,ikz) = (CiepjF_kp(:,:,ikp_next) - CiepjF_kp(:,:,ikp_prev))*zerotoone + CiepjF_kp(:,:,ikp_prev)
+ Ceepj (:,:,ikx,iky) = (Ceepj__kp(:,:,ikp_next) - Ceepj__kp(:,:,ikp_prev))*zerotoone + Ceepj__kp(:,:,ikp_prev)
+ CeipjT(:,:,ikx,iky) = (CeipjT_kp(:,:,ikp_next) - CeipjT_kp(:,:,ikp_prev))*zerotoone + CeipjT_kp(:,:,ikp_prev)
+ CeipjF(:,:,ikx,iky) = (CeipjF_kp(:,:,ikp_next) - CeipjF_kp(:,:,ikp_prev))*zerotoone + CeipjF_kp(:,:,ikp_prev)
+ Ciipj (:,:,ikx,iky) = (Ciipj__kp(:,:,ikp_next) - Ciipj__kp(:,:,ikp_prev))*zerotoone + Ciipj__kp(:,:,ikp_prev)
+ CiepjT(:,:,ikx,iky) = (CiepjT_kp(:,:,ikp_next) - CiepjT_kp(:,:,ikp_prev))*zerotoone + CiepjT_kp(:,:,ikp_prev)
+ CiepjF(:,:,ikx,iky) = (CiepjF_kp(:,:,ikp_next) - CiepjF_kp(:,:,ikp_prev))*zerotoone + CiepjF_kp(:,:,ikp_prev)
ENDDO
ENDDO
ELSE ! DK -> No kperp dep, copy simply to final collision matrices
diff --git a/src/compute_Sapj.F90 b/src/compute_Sapj.F90
index 4ef4f87d..e66080a7 100644
--- a/src/compute_Sapj.F90
+++ b/src/compute_Sapj.F90
@@ -1,7 +1,7 @@
SUBROUTINE compute_Sapj
! This routine is meant to compute the non linear term for each specie and degree
!! In real space Sapj ~ b*(grad(phi) x grad(g)) which in moments in fourier becomes
- !! Sapj = Sum_n (ikr Kn phi)#(ikz Sum_s d_njs Naps) - (ikz Kn phi)#(ikr Sum_s d_njs Naps)
+ !! Sapj = Sum_n (ikx Kn phi)#(iky Sum_s d_njs Naps) - (iky Kn phi)#(ikx Sum_s d_njs Naps)
!! where # denotes the convolution.
USE array, ONLY : dnjs, Sepj, Sipj, kernel_i, kernel_e
USE basic
@@ -14,18 +14,22 @@ SUBROUTINE compute_Sapj
IMPLICIT NONE
INCLUDE 'fftw3-mpi.f03'
- COMPLEX(dp), DIMENSION(ikrs:ikre,ikzs:ikze) :: Fr_cmpx, Gz_cmpx
- COMPLEX(dp), DIMENSION(ikrs:ikre,ikzs:ikze) :: Fz_cmpx, Gr_cmpx, F_conv_G
- REAL(dp), DIMENSION(irs:ire,izs:ize) :: fr_real, gz_real
- REAL(dp), DIMENSION(irs:ire,izs:ize) :: fz_real, gr_real, f_times_g
+ COMPLEX(dp), DIMENSION(ikxs:ikxe,ikys:ikye) :: Fx_cmpx, Gy_cmpx
+ COMPLEX(dp), DIMENSION(ikxs:ikxe,ikys:ikye) :: Fy_cmpx, Gx_cmpx, F_conv_G
+ REAL(dp), DIMENSION(ixs:ixe,iys:iye) :: fr_real, gz_real
+ REAL(dp), DIMENSION(ixs:ixe,iys:iye) :: fz_real, gr_real, f_times_g
INTEGER :: in, is
INTEGER :: nmax, smax ! Upper bound of the sums
- REAL(dp):: kr, kz, kerneln
+ REAL(dp):: kx, ky, kerneln
LOGICAL :: COMPUTE_ONLY_EVEN_P = .true.
! Execution time start
CALL cpu_time(t0_Sapj)
+! If we have a parallel dynamic, odd p are coupled with even ones
+IF(Nz .GT. 1) COMPUTE_ONLY_EVEN_P = .false.
+
+zloop: DO iz = izs,ize
!!!!!!!!!!!!!!!!!!!! ELECTRON non linear term computation (Sepj)!!!!!!!!!!
ploope: DO ip = ips_e,ipe_e ! Loop over Hermite moments
@@ -46,56 +50,56 @@ SUBROUTINE compute_Sapj
nloope: DO in = 1,nmax+1 ! Loop over laguerre for the sum
- krloope: DO ikr = ikrs,ikre ! Loop over kr
- kzloope: DO ikz = ikzs,ikze ! Loop over kz
- kr = krarray(ikr)
- kz = kzarray(ikz)
- kerneln = kernel_e(in, ikr, ikz)
+ kxloope: DO ikx = ikxs,ikxe ! Loop over kx
+ kyloope: DO iky = ikys,ikye ! Loop over ky
+ kx = kxarray(ikx)
+ ky = kyarray(iky)
+ kerneln = kernel_e(in, ikx, iky)
! First convolution terms
- Fr_cmpx(ikr,ikz) = imagu*kr* phi(ikr,ikz) * kerneln
- Fz_cmpx(ikr,ikz) = imagu*kz* phi(ikr,ikz) * kerneln
+ Fx_cmpx(ikx,iky) = imagu*kx* phi(ikx,iky,iz) * kerneln
+ Fy_cmpx(ikx,iky) = imagu*ky* phi(ikx,iky,iz) * kerneln
! Second convolution terms
- Gz_cmpx(ikr,ikz) = 0._dp ! initialization of the sum
- Gr_cmpx(ikr,ikz) = 0._dp ! initialization of the sum
+ Gy_cmpx(ikx,iky) = 0._dp ! initialization of the sum
+ Gx_cmpx(ikx,iky) = 0._dp ! initialization of the sum
smax = MIN( (in-1)+(ij-1), jmaxe );
DO is = 1, smax+1 ! sum truncation on number of moments
- Gz_cmpx(ikr,ikz) = Gz_cmpx(ikr,ikz) + &
- dnjs(in,ij,is) * moments_e(ip,is,ikr,ikz,updatetlevel)
- Gr_cmpx(ikr,ikz) = Gr_cmpx(ikr,ikz) + &
- dnjs(in,ij,is) * moments_e(ip,is,ikr,ikz,updatetlevel)
+ Gy_cmpx(ikx,iky) = Gy_cmpx(ikx,iky) + &
+ dnjs(in,ij,is) * moments_e(ip,is,ikx,iky,iz,updatetlevel)
+ Gx_cmpx(ikx,iky) = Gx_cmpx(ikx,iky) + &
+ dnjs(in,ij,is) * moments_e(ip,is,ikx,iky,iz,updatetlevel)
ENDDO
- Gz_cmpx(ikr,ikz) = imagu*kz*Gz_cmpx(ikr,ikz)
- Gr_cmpx(ikr,ikz) = imagu*kr*Gr_cmpx(ikr,ikz)
- ENDDO kzloope
- ENDDO krloope
+ Gy_cmpx(ikx,iky) = imagu*ky*Gy_cmpx(ikx,iky)
+ Gx_cmpx(ikx,iky) = imagu*kx*Gx_cmpx(ikx,iky)
+ ENDDO kyloope
+ ENDDO kxloope
! First term drphi x dzf
- DO ikr = ikrs, ikre
- DO ikz = ikzs, ikze
- cmpx_data_f(ikz,ikr-local_nkr_offset) = Fr_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz) !Anti aliasing filter
- cmpx_data_g(ikz,ikr-local_nkr_offset) = Gz_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz) !Anti aliasing filter
+ DO ikx = ikxs, ikxe
+ DO iky = ikys, ikye
+ cmpx_data_f(iky,ikx-local_nkx_offset) = Fx_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky) !Anti aliasing filter
+ cmpx_data_g(iky,ikx-local_nkx_offset) = Gy_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky) !Anti aliasing filter
ENDDO
ENDDO
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_f, real_data_f)
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_g, real_data_g)
- real_data_c = real_data_c + real_data_f/Nz/Nr * real_data_g/Nz/Nr
+ real_data_c = real_data_c + real_data_f/Ny/Nx * real_data_g/Ny/Nx
! Second term -dzphi x drf
- DO ikr = ikrs, ikre
- DO ikz = ikzs, ikze
- cmpx_data_f(ikz,ikr-local_nkr_offset) = Fz_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz) !Anti aliasing filter
- cmpx_data_g(ikz,ikr-local_nkr_offset) = Gr_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz) !Anti aliasing filter
+ DO ikx = ikxs, ikxe
+ DO iky = ikys, ikye
+ cmpx_data_f(iky,ikx-local_nkx_offset) = Fy_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky) !Anti aliasing filter
+ cmpx_data_g(iky,ikx-local_nkx_offset) = Gx_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky) !Anti aliasing filter
ENDDO
ENDDO
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_f, real_data_f)
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_g, real_data_g)
- real_data_c = real_data_c - real_data_f/Nz/Nr * real_data_g/Nz/Nr
+ real_data_c = real_data_c - real_data_f/Ny/Nx * real_data_g/Ny/Nx
ENDDO nloope
@@ -103,16 +107,16 @@ SUBROUTINE compute_Sapj
call fftw_mpi_execute_dft_r2c(planf, real_data_c, cmpx_data_c)
! Retrieve convolution in input format
- DO ikr = ikrs, ikre
- DO ikz = ikzs, ikze
- Sepj(ip,ij,ikr,ikz) = cmpx_data_c(ikz,ikr-local_nkr_offset)*AA_r(ikr)*AA_z(ikz) !Anti aliasing filter
+ DO ikx = ikxs, ikxe
+ DO iky = ikys, ikye
+ Sepj(ip,ij,ikx,iky,iz) = cmpx_data_c(iky,ikx-local_nkx_offset)*AA_x(ikx)*AA_y(iky) !Anti aliasing filter
ENDDO
ENDDO
ENDDO jloope
ELSE
! Cancel the non lin term if we are dealing with odd Hermite degree
- Sepj(ip,:,:,:) = 0._dp
+ Sepj(ip,:,:,:,iz) = 0._dp
ENDIF
ENDDO ploope
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -137,56 +141,56 @@ SUBROUTINE compute_Sapj
nloopi: DO in = 1,nmax+1 ! Loop over laguerre for the sum
- krloopi: DO ikr = ikrs,ikre ! Loop over kr
- kzloopi: DO ikz = ikzs,ikze ! Loop over kz
- kr = krarray(ikr)
- kz = kzarray(ikz)
- kerneln = kernel_i(in, ikr, ikz)
+ kxloopi: DO ikx = ikxs,ikxe ! Loop over kx
+ kyloopi: DO iky = ikys,ikye ! Loop over ky
+ kx = kxarray(ikx)
+ ky = kyarray(iky)
+ kerneln = kernel_i(in, ikx, iky)
! First convolution terms
- Fr_cmpx(ikr,ikz) = imagu*kr* phi(ikr,ikz) * kerneln
- Fz_cmpx(ikr,ikz) = imagu*kz* phi(ikr,ikz) * kerneln
+ Fx_cmpx(ikx,iky) = imagu*kx* phi(ikx,iky,iz) * kerneln
+ Fy_cmpx(ikx,iky) = imagu*ky* phi(ikx,iky,iz) * kerneln
! Second convolution terms
- Gz_cmpx(ikr,ikz) = 0._dp ! initialization of the sum
- Gr_cmpx(ikr,ikz) = 0._dp ! initialization of the sum
+ Gy_cmpx(ikx,iky) = 0._dp ! initialization of the sum
+ Gx_cmpx(ikx,iky) = 0._dp ! initialization of the sum
smax = MIN( (in-1)+(ij-1), jmaxi );
DO is = 1, smax+1 ! sum truncation on number of moments
- Gz_cmpx(ikr,ikz) = Gz_cmpx(ikr,ikz) + &
- dnjs(in,ij,is) * moments_i(ip,is,ikr,ikz,updatetlevel)
- Gr_cmpx(ikr,ikz) = Gr_cmpx(ikr,ikz) + &
- dnjs(in,ij,is) * moments_i(ip,is,ikr,ikz,updatetlevel)
+ Gy_cmpx(ikx,iky) = Gy_cmpx(ikx,iky) + &
+ dnjs(in,ij,is) * moments_i(ip,is,ikx,iky,iz,updatetlevel)
+ Gx_cmpx(ikx,iky) = Gx_cmpx(ikx,iky) + &
+ dnjs(in,ij,is) * moments_i(ip,is,ikx,iky,iz,updatetlevel)
ENDDO
- Gz_cmpx(ikr,ikz) = imagu*kz*Gz_cmpx(ikr,ikz)
- Gr_cmpx(ikr,ikz) = imagu*kr*Gr_cmpx(ikr,ikz)
- ENDDO kzloopi
- ENDDO krloopi
+ Gy_cmpx(ikx,iky) = imagu*ky*Gy_cmpx(ikx,iky)
+ Gx_cmpx(ikx,iky) = imagu*kx*Gx_cmpx(ikx,iky)
+ ENDDO kyloopi
+ ENDDO kxloopi
! First term drphi x dzf
- DO ikr = ikrs, ikre
- DO ikz = ikzs, ikze
- cmpx_data_f(ikz,ikr-local_nkr_offset) = Fr_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz)
- cmpx_data_g(ikz,ikr-local_nkr_offset) = Gz_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz)
+ DO ikx = ikxs, ikxe
+ DO iky = ikys, ikye
+ cmpx_data_f(iky,ikx-local_nkx_offset) = Fx_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky)
+ cmpx_data_g(iky,ikx-local_nkx_offset) = Gy_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky)
ENDDO
ENDDO
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_f, real_data_f)
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_g, real_data_g)
- real_data_c = real_data_c + real_data_f/Nz/Nr * real_data_g/Nz/Nr
+ real_data_c = real_data_c + real_data_f/Ny/Nx * real_data_g/Ny/Nx
! Second term -dzphi x drf
- DO ikr = ikrs, ikre
- DO ikz = ikzs, ikze
- cmpx_data_f(ikz,ikr-local_nkr_offset) = Fz_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz)
- cmpx_data_g(ikz,ikr-local_nkr_offset) = Gr_cmpx(ikr,ikz)*AA_r(ikr)*AA_z(ikz)
+ DO ikx = ikxs, ikxe
+ DO iky = ikys, ikye
+ cmpx_data_f(iky,ikx-local_nkx_offset) = Fy_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky)
+ cmpx_data_g(iky,ikx-local_nkx_offset) = Gx_cmpx(ikx,iky)*AA_x(ikx)*AA_y(iky)
ENDDO
ENDDO
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_f, real_data_f)
call fftw_mpi_execute_dft_c2r(planb, cmpx_data_g, real_data_g)
- real_data_c = real_data_c - real_data_f/Nz/Nr * real_data_g/Nz/Nr
+ real_data_c = real_data_c - real_data_f/Ny/Nx * real_data_g/Ny/Nx
ENDDO nloopi
@@ -194,16 +198,16 @@ SUBROUTINE compute_Sapj
call fftw_mpi_execute_dft_r2c(planf, real_data_c, cmpx_data_c)
! Retrieve convolution in input format
- DO ikr = ikrs, ikre
- DO ikz = ikzs, ikze
- Sipj(ip,ij,ikr,ikz) = cmpx_data_c(ikz,ikr-local_nkr_offset)*AA_r(ikr)*AA_z(ikz)
+ DO ikx = ikxs, ikxe
+ DO iky = ikys, ikye
+ Sipj(ip,ij,ikx,iky,iz) = cmpx_data_c(iky,ikx-local_nkx_offset)*AA_x(ikx)*AA_y(iky)
ENDDO
ENDDO
ENDDO jloopi
ELSE
! Cancel the non lin term if we are dealing with odd Hermite degree
- Sipj(ip,:,:,:) = 0._dp
+ Sipj(ip,:,:,:,iz) = 0._dp
ENDIF
ENDDO ploopi
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -212,4 +216,5 @@ SUBROUTINE compute_Sapj
CALL cpu_time(t1_Sapj)
tc_Sapj = tc_Sapj + (t1_Sapj - t0_Sapj)
+ENDDO zloop
END SUBROUTINE compute_Sapj
diff --git a/src/diagnose.F90 b/src/diagnose.F90
index d4ecfcce..e66ea02e 100644
--- a/src/diagnose.F90
+++ b/src/diagnose.F90
@@ -25,7 +25,7 @@ SUBROUTINE diagnose(kstep)
! so we need to gather non 5D data on one proc to output it
INTEGER :: parray_e_full(1:pmaxe+1), parray_i_full(1:pmaxi+1)
INTEGER :: jarray_e_full(1:jmaxe+1), jarray_i_full(1:jmaxi+1)
- REAL(dp) :: krarray_full(1:nkr), kzarray_full(1:nkz)
+ REAL(dp) :: kxarray_full(1:Nkx), kyarray_full(1:Nky), zarray_full(1:Nz)
CALL cpu_time(t0_diag) ! Measuring time
!_____________________________________________________________________________
@@ -72,25 +72,34 @@ SUBROUTINE diagnose(kstep)
! J
DO ij = 1,jmaxe+1; jarray_e_full(ij) = (ij-1); END DO
DO ij = 1,jmaxi+1; jarray_i_full(ij) = (ij-1); END DO
- ! Kr
- DO ikr = 1,Nkr
- krarray_full(ikr) = REAL(ikr-1,dp) * deltakr
+ ! kx
+ DO ikx = 1,Nkx
+ kxarray_full(ikx) = REAL(ikx-1,dp) * deltakx
END DO
- ! Kz
- IF (Nkz .GT. 1) THEN
- DO ikz = 1,Nkz
- kzarray_full(ikz) = deltakz*(MODULO(ikz-1,Nkz/2)-Nkz/2*FLOOR(2.*real(ikz-1)/real(Nkz)))
- if (ikz .EQ. Nz/2+1) kzarray(ikz) = -kzarray(ikz)
+ ! ky
+ IF (Nky .GT. 1) THEN
+ DO iky = 1,Nky
+ kyarray_full(iky) = deltaky*(MODULO(iky-1,Nky/2)-Nky/2*FLOOR(2.*real(iky-1)/real(Nky)))
+ if (iky .EQ. Ny/2+1) kyarray(iky) = -kyarray(iky)
END DO
+ ELSE
+ kyarray_full(1) = 0
+ endif
+ ! z
+ IF (Nz .GT. 1) THEN
+ DO iz = 1,Nz
+ zarray_full(iz) = deltaz*(iz-1)
+ END DO
ELSE
- kzarray_full(1) = 0
+ zarray_full(1) = 0
endif
ENDIF
! Grid info
CALL creatg(fidres, "/data/grid", "Grid data")
- CALL putarr(fidres, "/data/grid/coordkr", krarray_full(1:nkr),"kr*rho_s0", ionode=0)
- CALL putarr(fidres, "/data/grid/coordkz", kzarray_full(1:nkz),"kz*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordkx", kxarray_full(1:Nkx),"kx*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordky", kyarray_full(1:Nky),"ky*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordz", zarray_full(1:Nz) ,"z/R", ionode=0)
CALL putarr(fidres, "/data/grid/coordp_e" , parray_e_full(1:pmaxe+1), "p_e", ionode=0)
CALL putarr(fidres, "/data/grid/coordj_e" , jarray_e_full(1:jmaxe+1), "j_e", ionode=0)
CALL putarr(fidres, "/data/grid/coordp_i" , parray_i_full(1:pmaxi+1), "p_i", ionode=0)
@@ -113,33 +122,44 @@ SUBROUTINE diagnose(kstep)
END IF
- ! var2d group (electro. pot., Ni00 moment)
+ ! var2d group (??)
IF (nsave_2d .GT. 0) THEN
CALL creatg(fidres, "/data/var2d", "2d profiles")
CALL creatd(fidres, rank, dims, "/data/var2d/time", "Time t*c_s/R")
CALL creatd(fidres, rank, dims, "/data/var2d/cstep", "iteration number")
+ IF (cstep==0) THEN
+ iframe2d=0
+ ENDIF
+ CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
+ END IF
- IF (write_phi) CALL creatg(fidres, "/data/var2d/phi", "phi")
+ ! var3d group (electro. pot., Ni00 moment)
+ IF (nsave_3d .GT. 0) THEN
+ CALL creatg(fidres, "/data/var3d", "3d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var3d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var3d/cstep", "iteration number")
+
+ IF (write_phi) CALL creatg(fidres, "/data/var3d/phi", "phi")
IF (write_Na00) THEN
- CALL creatg(fidres, "/data/var2d/Ne00", "Ne00")
- CALL creatg(fidres, "/data/var2d/Ni00", "Ni00")
+ CALL creatg(fidres, "/data/var3d/Ne00", "Ne00")
+ CALL creatg(fidres, "/data/var3d/Ni00", "Ni00")
ENDIF
IF (write_dens) THEN
- CALL creatg(fidres, "/data/var2d/dens_e", "dens_e")
- CALL creatg(fidres, "/data/var2d/dens_i", "dens_i")
+ CALL creatg(fidres, "/data/var3d/dens_e", "dens_e")
+ CALL creatg(fidres, "/data/var3d/dens_i", "dens_i")
ENDIF
IF (write_temp) THEN
- CALL creatg(fidres, "/data/var2d/temp_e", "temp_e")
- CALL creatg(fidres, "/data/var2d/temp_i", "temp_i")
+ CALL creatg(fidres, "/data/var3d/temp_e", "temp_e")
+ CALL creatg(fidres, "/data/var3d/temp_i", "temp_i")
ENDIF
IF (cstep==0) THEN
- iframe2d=0
+ iframe3d=0
ENDIF
- CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
+ CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
END IF
! var5d group (moments)
@@ -181,6 +201,7 @@ SUBROUTINE diagnose(kstep)
CALL attach(fidres, TRIM(str), "start_cstep", cstep-1)
CALL attach(fidres, TRIM(str), "start_iframe0d", iframe0d)
CALL attach(fidres, TRIM(str), "start_iframe2d", iframe2d)
+ CALL attach(fidres, TRIM(str), "start_iframe3d", iframe3d)
CALL attach(fidres, TRIM(str), "start_iframe5d", iframe5d)
CALL attach(fidres, TRIM(str), "dt", dt)
CALL attach(fidres, TRIM(str), "tmax", tmax)
@@ -188,7 +209,7 @@ SUBROUTINE diagnose(kstep)
CALL attach(fidres, TRIM(str), "cpu_time", -1)
CALL attach(fidres, TRIM(str), "Nproc", num_procs)
CALL attach(fidres, TRIM(str), "Np_p" , num_procs_p)
- CALL attach(fidres, TRIM(str), "Np_kr",num_procs_kr)
+ CALL attach(fidres, TRIM(str), "Np_kx",num_procs_kx)
CALL attach(fidres, TRIM(str), "write_gamma",write_gamma)
CALL attach(fidres, TRIM(str), "write_phi",write_phi)
CALL attach(fidres, TRIM(str), "write_Na00",write_Na00)
@@ -253,9 +274,13 @@ SUBROUTINE diagnose(kstep)
! empty in our case
! 2.3 2d profiles
- IF (nsave_2d .GT. 0) THEN
- IF (MOD(cstep, nsave_2d) == 0) THEN
- CALL diagnose_2d
+ ! empty in our case
+
+
+ ! 2.3 2d profiles
+ IF (nsave_3d .GT. 0) THEN
+ IF (MOD(cstep, nsave_3d) == 0) THEN
+ CALL diagnose_3d
END IF
END IF
@@ -334,7 +359,7 @@ SUBROUTINE diagnose_2d
USE futils, ONLY: append, getatt, attach, putarrnd
USE fields
USE array, ONLY: Ne00, Ni00, dens_e, dens_i, temp_e, temp_i
- USE grid, ONLY: ikrs,ikre, ikzs,ikze, nkr, nkz, local_nkr, ikr, ikz, ips_e, ips_i
+ USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx, ikx, iky, ips_e, ips_i
USE time_integration
USE diagnostics_par
USE prec_const
@@ -342,7 +367,7 @@ SUBROUTINE diagnose_2d
IMPLICIT NONE
- COMPLEX(dp) :: buffer(ikrs:ikre,ikzs:ikze)
+ COMPLEX(dp) :: buffer(ikxs:ikxe,ikys:ikye)
INTEGER :: i_, root, world_rank, world_size
CALL append(fidres, "/data/var2d/time", time,ionode=0)
@@ -351,63 +376,110 @@ SUBROUTINE diagnose_2d
iframe2d=iframe2d+1
CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
- IF (write_phi) CALL write_field2d(phi (:,:), 'phi')
+CONTAINS
+
+ SUBROUTINE write_field2d(field, text)
+ USE futils, ONLY: attach, putarr
+ USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx
+ USE prec_const
+ USE basic, ONLY : comm_kx, num_procs_p, rank_p
+ IMPLICIT NONE
+
+ COMPLEX(dp), DIMENSION(ikxs:ikxe, ikys:ikye), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ COMPLEX(dp) :: buffer_dist(ikxs:ikxe,ikys:ikye)
+ COMPLEX(dp) :: buffer_full(1:Nkx,1:Nky)
+ INTEGER :: scount, rcount
+ CHARACTER(LEN=50) :: dset_name
+
+ scount = (ikxe-ikxs+1) * (ikye-ikys+1)
+ rcount = scount
+
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var2d", TRIM(text), iframe2d
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr(fidres, dset_name, field(ikxs:ikxe, ikys:ikye), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ikxs:ikxe, ikys:ikye), (/1, 1/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+
+ END SUBROUTINE write_field2d
+
+END SUBROUTINE diagnose_2d
+
+SUBROUTINE diagnose_3d
+
+ USE basic
+ USE futils, ONLY: append, getatt, attach, putarrnd
+ USE fields
+ USE array, ONLY: Ne00, Ni00, dens_e, dens_i, temp_e, temp_i
+ USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx, ikx, iky, ips_e, ips_i
+ USE time_integration
+ USE diagnostics_par
+ USE prec_const
+ USE processing
+
+ IMPLICIT NONE
+
+ INTEGER :: i_, root, world_rank, world_size
+
+ CALL append(fidres, "/data/var3d/time", time,ionode=0)
+ CALL append(fidres, "/data/var3d/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidres, "/data/var3d/", "frames",iframe3d)
+ iframe3d=iframe3d+1
+ CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
+
+ IF (write_phi) CALL write_field3d(phi (:,:,:), 'phi')
IF (write_Na00) THEN
IF ( (ips_e .EQ. 1) .AND. (ips_i .EQ. 1) ) THEN
- Ne00(ikrs:ikre,ikzs:ikze) = moments_e(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
- Ni00(ikrs:ikre,ikzs:ikze) = moments_i(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
+ Ne00(ikxs:ikxe,ikys:ikye,izs:ize) = moments_e(ips_e,1,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel)
+ Ni00(ikxs:ikxe,ikys:ikye,izs:ize) = moments_i(ips_e,1,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel)
ENDIF
- CALL manual_2D_bcast(Ne00(ikrs:ikre,ikzs:ikze))
- CALL write_field2d(Ne00(ikrs:ikre,ikzs:ikze), 'Ne00')
+ CALL manual_3D_bcast(Ne00(ikxs:ikxe,ikys:ikye,izs:ize))
+ CALL write_field3d(Ne00(ikxs:ikxe,ikys:ikye,izs:ize), 'Ne00')
- CALL manual_2D_bcast(Ni00(ikrs:ikre,ikzs:ikze))
- CALL write_field2d(Ni00(ikrs:ikre,ikzs:ikze), 'Ni00')
+ CALL manual_3D_bcast(Ni00(ikxs:ikxe,ikys:ikye,izs:ize))
+ CALL write_field3d(Ni00(ikxs:ikxe,ikys:ikye,izs:ize), 'Ni00')
ENDIF
IF (write_dens) THEN
CALL compute_density
- CALL write_field2d(dens_e(ikrs:ikre,ikzs:ikze), 'dens_e')
- CALL write_field2d(dens_i(ikrs:ikre,ikzs:ikze), 'dens_i')
+ CALL write_field3d(dens_e(ikxs:ikxe,ikys:ikye,izs:ize), 'dens_e')
+ CALL write_field3d(dens_i(ikxs:ikxe,ikys:ikye,izs:ize), 'dens_i')
ENDIF
IF (write_temp) THEN
CALL compute_temperature
- CALL write_field2d(temp_e(ikrs:ikre,ikzs:ikze), 'temp_e')
- CALL write_field2d(temp_i(ikrs:ikre,ikzs:ikze), 'temp_i')
+ CALL write_field3d(temp_e(ikxs:ikxe,ikys:ikye,izs:ize), 'temp_e')
+ CALL write_field3d(temp_i(ikxs:ikxe,ikys:ikye,izs:ize), 'temp_i')
ENDIF
CONTAINS
- SUBROUTINE write_field2d(field, text)
+ SUBROUTINE write_field3d(field, text)
USE futils, ONLY: attach, putarr
- USE grid, ONLY: ikrs,ikre, ikzs,ikze, nkr, nkz, local_nkr
+ USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx
USE prec_const
- USE basic, ONLY : comm_kr, num_procs_p, rank_p
+ USE basic, ONLY : comm_kx, num_procs_p, rank_p
IMPLICIT NONE
- COMPLEX(dp), DIMENSION(ikrs:ikre, ikzs:ikze), INTENT(IN) :: field
+ COMPLEX(dp), DIMENSION(ikxs:ikxe, ikys:ikye, izs:ize), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
- COMPLEX(dp) :: buffer_dist(ikrs:ikre,ikzs:ikze)
- COMPLEX(dp) :: buffer_full(1:nkr,1:nkz)
- INTEGER :: scount, rcount
CHARACTER(LEN=50) :: dset_name
- scount = (ikre-ikrs+1) * (ikze-ikzs+1)
- rcount = scount
-
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var2d", TRIM(text), iframe2d
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
IF (num_procs .EQ. 1) THEN ! no data distribution
- CALL putarr(fidres, dset_name, field(ikrs:ikre, ikzs:ikze), ionode=0)
+ CALL putarr(fidres, dset_name, field(ikxs:ikxe, ikys:ikye, izs:ize), ionode=0)
ELSE
- CALL putarrnd(fidres, dset_name, field(ikrs:ikre, ikzs:ikze), (/1, 1/))
+ CALL putarrnd(fidres, dset_name, field(ikxs:ikxe, ikys:ikye, izs:ize), (/1, 1/))
ENDIF
CALL attach(fidres, dset_name, "time", time)
- END SUBROUTINE write_field2d
+ END SUBROUTINE write_field3d
-END SUBROUTINE diagnose_2d
+END SUBROUTINE diagnose_3d
SUBROUTINE diagnose_5d
@@ -429,33 +501,33 @@ SUBROUTINE diagnose_5d
CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
IF (write_Napj) THEN
- CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel), 'moments_e')
- CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel), 'moments_i')
+ CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,:,updatetlevel), 'moments_e')
+ CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,:,updatetlevel), 'moments_i')
ENDIF
IF (write_Sapj) THEN
- CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,:,:), 'Sepj')
- CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,:,:), 'Sipj')
+ CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,:,:,:), 'Sepj')
+ CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,:,:,:), 'Sipj')
ENDIF
CONTAINS
SUBROUTINE write_field5d_e(field, text)
USE futils, ONLY: attach, putarr, putarrnd
- USE grid, ONLY: ips_e,ipe_e, ijs_e,ije_e, ikrs,ikre, ikzs,ikze
+ USE grid, ONLY: ips_e,ipe_e, ijs_e,ije_e, ikxs,ikxe, ikys,ikye, izs,ize
USE prec_const
IMPLICIT NONE
- COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), INTENT(IN) :: field
+ COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikxs:ikxe,ikys:ikye,izs:ize), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
CHARACTER(LEN=50) :: dset_name
WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
IF (num_procs .EQ. 1) THEN
- CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), ionode=0)
+ CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikxs:ikxe,ikys:ikye,izs:ize), ionode=0)
ELSE
- CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), (/1,3/))
+ CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikxs:ikxe,ikys:ikye,izs:ize), (/1,3/))
ENDIF
CALL attach(fidres, dset_name, 'cstep', cstep)
CALL attach(fidres, dset_name, 'time', time)
@@ -468,20 +540,20 @@ SUBROUTINE diagnose_5d
SUBROUTINE write_field5d_i(field, text)
USE futils, ONLY: attach, putarr, putarrnd
- USE grid, ONLY: ips_i,ipe_i, ijs_i,ije_i, ikrs,ikre, ikzs,ikze
+ USE grid, ONLY: ips_i,ipe_i, ijs_i,ije_i, ikxs,ikxe, ikys,ikye, izs,ize
USE prec_const
IMPLICIT NONE
- COMPLEX(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), INTENT(IN) :: field
+ COMPLEX(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,ikxs:ikxe,ikys:ikye,izs:ize), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
CHARACTER(LEN=50) :: dset_name
WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
IF (num_procs .EQ. 1) THEN
- CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), ionode=0)
+ CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikxs:ikxe,ikys:ikye,izs:ize), ionode=0)
ELSE
- CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), (/1,3/))
+ CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikxs:ikxe,ikys:ikye,izs:ize), (/1,3/))
ENDIF
CALL attach(fidres, dset_name, 'cstep', cstep)
CALL attach(fidres, dset_name, 'time', time)
diff --git a/src/diagnostics_par_mod.F90 b/src/diagnostics_par_mod.F90
index 011e09ed..3e48810e 100644
--- a/src/diagnostics_par_mod.F90
+++ b/src/diagnostics_par_mod.F90
@@ -11,7 +11,7 @@ MODULE diagnostics_par
LOGICAL, PUBLIC, PROTECTED :: write_Napj, write_Sapj
LOGICAL, PUBLIC, PROTECTED :: write_dens, write_temp
- INTEGER, PUBLIC, PROTECTED :: nsave_0d , nsave_1d , nsave_2d , nsave_5d, nsave_cp
+ INTEGER, PUBLIC, PROTECTED :: nsave_0d, nsave_1d, nsave_2d, nsave_3d, nsave_5d, nsave_cp
! HDF5 file
CHARACTER(len=256), PUBLIC :: resfile0 = "results" ! Head of main result file name
@@ -34,7 +34,7 @@ CONTAINS
USE prec_const
IMPLICIT NONE
- NAMELIST /OUTPUT_PAR/ nsave_0d , nsave_1d , nsave_2d , nsave_5d, nsave_cp
+ NAMELIST /OUTPUT_PAR/ nsave_0d, nsave_1d, nsave_2d, nsave_3d, nsave_5d, nsave_cp
NAMELIST /OUTPUT_PAR/ write_doubleprecision, write_gamma, write_phi
NAMELIST /OUTPUT_PAR/ write_Na00, write_Napj, write_Sapj
NAMELIST /OUTPUT_PAR/ write_dens, write_temp
diff --git a/src/fields_mod.F90 b/src/fields_mod.F90
index 58075c2d..eac8c04f 100644
--- a/src/fields_mod.F90
+++ b/src/fields_mod.F90
@@ -3,13 +3,13 @@ MODULE fields
use prec_const
implicit none
!------------------MOMENTS Napj------------------
- ! Hermite-Moments: N_a^pj ! dimensions correspond to: p, j, kr, kz, updatetlevel.
- COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_e
- COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_i
+ ! Hermite-Moments: N_a^pj ! dimensions correspond to: p, j, kx, ky, z, updatetlevel.
+ COMPLEX(dp), DIMENSION(:,:,:,:,:,:), ALLOCATABLE :: moments_e
+ COMPLEX(dp), DIMENSION(:,:,:,:,:,:), ALLOCATABLE :: moments_i
!------------------ELECTROSTATIC POTENTIAL------------------
- ! Normalized electric potential: \hat{\phi} ! (kr,kz)
- COMPLEX(dp), DIMENSION(:,:), ALLOCATABLE :: phi
+ ! Normalized electric potential: \hat{\phi} ! (kx,ky,z)
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: phi
END MODULE fields
diff --git a/src/fourier_mod.F90 b/src/fourier_mod.F90
index 195b0493..3c5a232b 100644
--- a/src/fourier_mod.F90
+++ b/src/fourier_mod.F90
@@ -29,39 +29,39 @@ MODULE fourier
CONTAINS
- SUBROUTINE init_grid_distr_and_plans(Nr,Nz)
+ SUBROUTINE init_grid_distr_and_plans(Nx,Ny)
IMPLICIT NONE
- INTEGER, INTENT(IN) :: Nr,Nz
- NR_ = Nr; NZ_ = Nz
+ INTEGER, INTENT(IN) :: Nx,Ny
+ NR_ = Nx; NZ_ = Ny
NR_halved = NR_/2 + 1
! communicator = MPI_COMM_WORLD
- communicator = comm_kr
+ communicator = comm_kx
!! Complex arrays F, G
! Compute the room to allocate
- alloc_local_1 = fftw_mpi_local_size_2d(NR_halved, NZ_, communicator, local_nkr, local_nkr_offset)
+ alloc_local_1 = fftw_mpi_local_size_2d(NR_halved, NZ_, communicator, local_nkx, local_nkx_offset)
! Initalize pointers to this room
cdatac_f = fftw_alloc_complex(alloc_local_1)
cdatac_g = fftw_alloc_complex(alloc_local_1)
cdatac_c = fftw_alloc_complex(alloc_local_1)
! Initalize the arrays with the rooms pointed
- call c_f_pointer(cdatac_f, cmpx_data_f, [NZ_ ,local_nkr])
- call c_f_pointer(cdatac_g, cmpx_data_g, [NZ_ ,local_nkr])
- call c_f_pointer(cdatac_c, cmpx_data_c, [NZ_ ,local_nkr])
+ call c_f_pointer(cdatac_f, cmpx_data_f, [NZ_ ,local_nkx])
+ call c_f_pointer(cdatac_g, cmpx_data_g, [NZ_ ,local_nkx])
+ call c_f_pointer(cdatac_c, cmpx_data_c, [NZ_ ,local_nkx])
!! Real arrays iFFT(F), iFFT(G)
! Compute the room to allocate
- alloc_local_2 = fftw_mpi_local_size_2d(NZ_, NR_halved, communicator, local_nz, local_nz_offset)
+ alloc_local_2 = fftw_mpi_local_size_2d(NZ_, NR_halved, communicator, local_nky, local_nky_offset)
! Initalize pointers to this room
cdatar_f = fftw_alloc_real(2*alloc_local_2)
cdatar_g = fftw_alloc_real(2*alloc_local_2)
cdatar_c = fftw_alloc_real(2*alloc_local_2)
! Initalize the arrays with the rooms pointed
- call c_f_pointer(cdatar_f, real_data_f, [2*(NR_/2 + 1),local_nz])
- call c_f_pointer(cdatar_g, real_data_g, [2*(NR_/2 + 1),local_nz])
- call c_f_pointer(cdatar_c, real_data_c, [2*(NR_/2 + 1),local_nz])
+ call c_f_pointer(cdatar_f, real_data_f, [2*(NR_/2 + 1),local_nky])
+ call c_f_pointer(cdatar_g, real_data_g, [2*(NR_/2 + 1),local_nky])
+ call c_f_pointer(cdatar_c, real_data_c, [2*(NR_/2 + 1),local_nky])
! Plan Creation (out-of-place forward and backward FFT)
planf = fftw_mpi_plan_dft_r2c_2d(NZ_, NR_, real_data_f, cmpx_data_f, communicator, ior(FFTW_MEASURE, FFTW_MPI_TRANSPOSED_OUT))
@@ -80,13 +80,13 @@ MODULE fourier
SUBROUTINE convolve_2D_F2F( F_2D, G_2D, C_2D )
IMPLICIT NONE
- COMPLEX(C_DOUBLE_COMPLEX), DIMENSION(ikrs:ikre,ikzs:ikze), INTENT(IN) :: F_2D, G_2D ! input fields
- COMPLEX(C_DOUBLE_COMPLEX), DIMENSION(ikrs:ikre,ikzs:ikze), INTENT(OUT) :: C_2D ! output convolutioned field
+ COMPLEX(C_DOUBLE_COMPLEX), DIMENSION(ikxs:ikxe,ikys:ikye), INTENT(IN) :: F_2D, G_2D ! input fields
+ COMPLEX(C_DOUBLE_COMPLEX), DIMENSION(ikxs:ikxe,ikys:ikye), INTENT(OUT) :: C_2D ! output convolutioned field
- do ikr = ikrs, ikre
- do ikz = ikzs, ikze
- cmpx_data_f(ikz,ikr-local_nkr_offset) = F_2D(ikr,ikz)*AA_r(ikr)*AA_z(ikz)
- cmpx_data_g(ikz,ikr-local_nkr_offset) = G_2D(ikr,ikz)*AA_r(ikr)*AA_z(ikz)
+ do ikx = ikxs, ikxe
+ do iky = ikys, ikye
+ cmpx_data_f(iky,ikx-local_nkx_offset) = F_2D(ikx,iky)*AA_x(ikx)*AA_y(iky)
+ cmpx_data_g(iky,ikx-local_nkx_offset) = G_2D(ikx,iky)*AA_x(ikx)*AA_y(iky)
end do
end do
@@ -99,9 +99,9 @@ MODULE fourier
call fftw_mpi_execute_dft_r2c(planf, real_data_c, cmpx_data_c)
! Retrieve convolution in input format
- do ikr = ikrs, ikre
- do ikz = ikzs, ikze
- C_2D(ikr,ikz) = cmpx_data_c(ikz,ikr-local_nkr_offset)*AA_r(ikr)*AA_z(ikz)
+ do ikx = ikxs, ikxe
+ do iky = ikys, ikye
+ C_2D(ikx,iky) = cmpx_data_c(iky,ikx-local_nkx_offset)*AA_x(ikx)*AA_y(iky)
end do
end do
diff --git a/src/ghosts_mod.F90 b/src/ghosts_mod.F90
index 416b7a3c..1e428822 100644
--- a/src/ghosts_mod.F90
+++ b/src/ghosts_mod.F90
@@ -32,22 +32,22 @@ END SUBROUTINE update_ghosts
SUBROUTINE update_ghosts_p_e
IMPLICIT NONE
- count = (ijeg_e-ijsg_e+1)*(ikre-ikrs+1)*(ikze-ikzs+1)
+ count = (ijeg_e-ijsg_e+1)*(ikxe-ikxs+1)*(ikye-ikys+1)*(ize-izs+1)
!!!!!!!!!!! Send ghost to right neighbour !!!!!!!!!!!!!!!!!!!!!!
- CALL mpi_sendrecv(moments_e(ipe_e ,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 10, &
- moments_e(ips_e-1,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 10, &
+ CALL mpi_sendrecv(moments_e(ipe_e ,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 10, &
+ moments_e(ips_e-1,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 10, &
comm0, status, ierr)
- CALL mpi_sendrecv(moments_e(ipe_e-1,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 11, &
- moments_e(ips_e-2,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 11, &
+ CALL mpi_sendrecv(moments_e(ipe_e-1,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 11, &
+ moments_e(ips_e-2,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 11, &
comm0, status, ierr)
!!!!!!!!!!! Send ghost to left neighbour !!!!!!!!!!!!!!!!!!!!!!
- CALL mpi_sendrecv(moments_e(ips_e ,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 12, &
- moments_e(ipe_e+1,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 12, &
+ CALL mpi_sendrecv(moments_e(ips_e ,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 12, &
+ moments_e(ipe_e+1,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 12, &
comm0, status, ierr)
- CALL mpi_sendrecv(moments_e(ips_e+1,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 13, &
- moments_e(ipe_e+2,ijsg_e:ijeg_e,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 13, &
+ CALL mpi_sendrecv(moments_e(ips_e+1,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 13, &
+ moments_e(ipe_e+2,ijsg_e:ijeg_e,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 13, &
comm0, status, ierr)
END SUBROUTINE update_ghosts_p_e
@@ -57,23 +57,23 @@ SUBROUTINE update_ghosts_p_i
IMPLICIT NONE
- count = (ijeg_i-ijsg_i+1)*(ikre-ikrs+1)*(ikze-ikzs+1) ! Number of elements sent
+ count = (ijeg_i-ijsg_i+1)*(ikxe-ikxs+1)*(ikye-ikys+1)*(ize-izs+1) ! Number of elements sent
!!!!!!!!!!! Send ghost to right neighbour !!!!!!!!!!!!!!!!!!!!!!
- CALL mpi_sendrecv(moments_i(ipe_i ,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 14, &
- moments_i(ips_i-1,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 14, &
+ CALL mpi_sendrecv(moments_i(ipe_i ,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 14, &
+ moments_i(ips_i-1,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 14, &
comm0, status, ierr)
- CALL mpi_sendrecv(moments_i(ipe_i-1,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 15, &
- moments_i(ips_i-2,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 15, &
+ CALL mpi_sendrecv(moments_i(ipe_i-1,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 15, &
+ moments_i(ips_i-2,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 15, &
comm0, status, ierr)
!!!!!!!!!!! Send ghost to left neighbour !!!!!!!!!!!!!!!!!!!!!!
CALL mpi_cart_shift(comm0, 0, -1, source , dest , ierr)
- CALL mpi_sendrecv(moments_i(ips_i ,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 16, &
- moments_i(ipe_i+1,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 16, &
+ CALL mpi_sendrecv(moments_i(ips_i ,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 16, &
+ moments_i(ipe_i+1,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 16, &
comm0, status, ierr)
- CALL mpi_sendrecv(moments_i(ips_i+1,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 17, &
- moments_i(ipe_i+2,ijsg_i:ijeg_i,ikrs:ikre,ikzs:ikze,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 17, &
+ CALL mpi_sendrecv(moments_i(ips_i+1,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_L, 17, &
+ moments_i(ipe_i+2,ijsg_i:ijeg_i,ikxs:ikxe,ikys:ikye,izs:ize,updatetlevel), count, MPI_DOUBLE_COMPLEX, nbr_R, 17, &
comm0, status, ierr)
END SUBROUTINE update_ghosts_p_i
diff --git a/src/grid_mod.F90 b/src/grid_mod.F90
index 46d2ee30..eb57a255 100644
--- a/src/grid_mod.F90
+++ b/src/grid_mod.F90
@@ -12,32 +12,35 @@ MODULE grid
INTEGER, PUBLIC, PROTECTED :: pmaxi = 1 ! The maximal ion Hermite-moment computed
INTEGER, PUBLIC, PROTECTED :: jmaxi = 1 ! The maximal ion Laguerre-moment computed
INTEGER, PUBLIC, PROTECTED :: maxj = 1 ! The maximal ion Laguerre-moment computed
- INTEGER, PUBLIC, PROTECTED :: Nr = 16 ! Number of total internal grid points in r
- REAL(dp), PUBLIC, PROTECTED :: Lr = 1._dp ! horizontal length of the spatial box
- INTEGER, PUBLIC, PROTECTED :: Nz = 16 ! Number of total internal grid points in z
- REAL(dp), PUBLIC, PROTECTED :: Lz = 1._dp ! vertical length of the spatial box
- INTEGER, PUBLIC, PROTECTED :: Nkr = 8 ! Number of total internal grid points in kr
- REAL(dp), PUBLIC, PROTECTED :: Lkr = 1._dp ! horizontal length of the fourier box
- INTEGER, PUBLIC, PROTECTED :: Nkz = 16 ! Number of total internal grid points in kz
- REAL(dp), PUBLIC, PROTECTED :: Lkz = 1._dp ! vertical length of the fourier box
+ INTEGER, PUBLIC, PROTECTED :: Nx = 16 ! Number of total internal grid points in x
+ REAL(dp), PUBLIC, PROTECTED :: Lx = 1._dp ! horizontal length of the spatial box
+ INTEGER, PUBLIC, PROTECTED :: Ny = 16 ! Number of total internal grid points in y
+ REAL(dp), PUBLIC, PROTECTED :: Ly = 1._dp ! vertical length of the spatial box
+ INTEGER, PUBLIC, PROTECTED :: Nz = 1 ! Number of total perpendicular planes
+ REAL(dp), PUBLIC, PROTECTED :: q0 = 1._dp ! q factor
+ INTEGER, PUBLIC, PROTECTED :: Nkx = 8 ! Number of total internal grid points in kx
+ REAL(dp), PUBLIC, PROTECTED :: Lkx = 1._dp ! horizontal length of the fourier box
+ INTEGER, PUBLIC, PROTECTED :: Nky = 16 ! Number of total internal grid points in ky
+ REAL(dp), PUBLIC, PROTECTED :: Lky = 1._dp ! vertical length of the fourier box
REAL(dp), PUBLIC, PROTECTED :: kpar = 0_dp ! parallel wave vector component
! For Orszag filter
- REAL(dp), PUBLIC, PROTECTED :: two_third_krmax
- REAL(dp), PUBLIC, PROTECTED :: two_third_kzmax
+ REAL(dp), PUBLIC, PROTECTED :: two_third_kxmax
+ REAL(dp), PUBLIC, PROTECTED :: two_third_kymax
REAL(dp), PUBLIC, PROTECTED :: two_third_kpmax
! 1D Antialiasing arrays (2/3 rule)
- REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: AA_r
- REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: AA_z
+ REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: AA_x
+ REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: AA_y
! Grids containing position in physical space
- REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: rarray
+ REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: xarray
+ REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: yarray
REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: zarray
- REAL(dp), PUBLIC, PROTECTED :: deltar, deltaz
- INTEGER, PUBLIC, PROTECTED :: irs, ire, izs, ize
+ REAL(dp), PUBLIC, PROTECTED :: deltax, deltay, deltaz
+ INTEGER, PUBLIC, PROTECTED :: ixs, ixe, iys, iye, izs, ize
INTEGER, PUBLIC :: ir,iz ! counters
- integer(C_INTPTR_T), PUBLIC :: local_nkr, local_nz
- integer(C_INTPTR_T), PUBLIC :: local_nkr_offset, local_nz_offset
+ integer(C_INTPTR_T), PUBLIC :: local_nkx, local_nky
+ integer(C_INTPTR_T), PUBLIC :: local_nkx_offset, local_nky_offset
INTEGER, PUBLIC :: local_nkp
INTEGER, PUBLIC :: local_np_e, local_np_i
integer(C_INTPTR_T), PUBLIC :: local_np_e_offset, local_np_i_offset
@@ -45,15 +48,15 @@ MODULE grid
INTEGER, DIMENSION(:), ALLOCATABLE, PUBLIC :: displs_np_e, displs_np_i
! Grids containing position in fourier space
- REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: krarray
- REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: kzarray
+ REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: kxarray
+ REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: kyarray
REAL(dp), DIMENSION(:), ALLOCATABLE, PUBLIC :: kparray ! kperp array
- REAL(dp), PUBLIC, PROTECTED :: deltakr, deltakz, kr_max, kz_max, kp_max
- INTEGER, PUBLIC, PROTECTED :: ikrs, ikre, ikzs, ikze, ikps, ikpe
- INTEGER, PUBLIC, PROTECTED :: ikr_0, ikz_0, ikr_max, ikz_max ! Indices of k-grid origin and max
- INTEGER, PUBLIC :: ikr, ikz, ip, ij, ikp ! counters
- LOGICAL, PUBLIC, PROTECTED :: contains_kr0 = .false. ! rank of the proc containing kr=0 indices
- LOGICAL, PUBLIC, PROTECTED :: contains_krmax = .false. ! rank of the proc containing kr=max indices
+ REAL(dp), PUBLIC, PROTECTED :: deltakx, deltaky, kx_max, ky_max, kp_max
+ INTEGER, PUBLIC, PROTECTED :: ikxs, ikxe, ikys, ikye, ikps, ikpe
+ INTEGER, PUBLIC, PROTECTED :: ikx_0, iky_0, ikx_max, iky_max ! Indices of k-grid origin and max
+ INTEGER, PUBLIC :: ikx, iky, ip, ij, ikp ! counters
+ LOGICAL, PUBLIC, PROTECTED :: contains_kx0 = .false. ! rank of the proc containing kx=0 indices
+ LOGICAL, PUBLIC, PROTECTED :: contains_kxmax = .false. ! rank of the proc containing kx=max indices
! Grid containing the polynomials degrees
INTEGER, DIMENSION(:), ALLOCATABLE, PUBLIC :: parray_e
@@ -68,7 +71,7 @@ MODULE grid
! Public Functions
PUBLIC :: init_1Dgrid_distr
PUBLIC :: set_pgrid, set_jgrid
- PUBLIC :: set_krgrid, set_kzgrid, set_kpgrid
+ PUBLIC :: set_kxgrid, set_kygrid, set_kpgrid, set_zgrid
PUBLIC :: grid_readinputs, grid_outputinputs
PUBLIC :: bare, bari
@@ -79,12 +82,12 @@ CONTAINS
SUBROUTINE init_1Dgrid_distr
- ! write(*,*) Nr
- local_nkr = (Nr/2+1)/num_procs_kr
- ! write(*,*) local_nkr
- local_nkr_offset = rank_kr*local_nkr
+ ! write(*,*) Nx
+ local_nkx = (Nx/2+1)/num_procs_kx
+ ! write(*,*) local_nkx
+ local_nkx_offset = rank_kx*local_nkx
- if (rank_kr .EQ. num_procs_kr-1) local_nkr = (Nr/2+1)-local_nkr_offset
+ if (rank_kx .EQ. num_procs_kx-1) local_nkx = (Nx/2+1)-local_nkx_offset
END SUBROUTINE init_1Dgrid_distr
@@ -153,116 +156,136 @@ CONTAINS
END SUBROUTINE set_jgrid
- SUBROUTINE set_krgrid
+ SUBROUTINE set_kxgrid
USE prec_const
IMPLICIT NONE
INTEGER :: i_
- Nkr = Nr/2+1 ! Defined only on positive kr since fields are real
+ Nkx = Nx/2+1 ! Defined only on positive kx since fields are real
! Start and END indices of grid
- ikrs = local_nkr_offset + 1
- ikre = ikrs + local_nkr - 1
- ALLOCATE(krarray(ikrs:ikre))
+ ikxs = local_nkx_offset + 1
+ ikxe = ikxs + local_nkx - 1
+ ALLOCATE(kxarray(ikxs:ikxe))
! Grid spacings
- IF (Lr .EQ. 0) THEN
- deltakr = 1._dp
- kr_max = 0._dp
+ IF (Lx .EQ. 0) THEN
+ deltakx = 1._dp
+ kx_max = 0._dp
ELSE
- deltakr = 2._dp*PI/Lr
- kr_max = (Nr/2+1)*deltakr
+ deltakx = 2._dp*PI/Lx
+ kx_max = (Nx/2+1)*deltakx
ENDIF
! Creating a grid ordered as dk*(0 1 2 3)
- DO ikr = ikrs,ikre
- krarray(ikr) = REAL(ikr-1,dp) * deltakr
- ! Finding kr=0
- IF (krarray(ikr) .EQ. 0) THEN
- ikr_0 = ikr
- contains_kr0 = .true.
+ DO ikx = ikxs,ikxe
+ kxarray(ikx) = REAL(ikx-1,dp) * deltakx
+ ! Finding kx=0
+ IF (kxarray(ikx) .EQ. 0) THEN
+ ikx_0 = ikx
+ contains_kx0 = .true.
ENDIF
- ! Finding krmax idx
- IF (krarray(ikr) .EQ. kr_max) THEN
- ikr_max = ikr
- contains_krmax = .true.
+ ! Finding kxmax idx
+ IF (kxarray(ikx) .EQ. kx_max) THEN
+ ikx_max = ikx
+ contains_kxmax = .true.
ENDIF
END DO
! Orszag 2/3 filter
- two_third_krmax = 2._dp/3._dp*deltakr*Nkr
- ALLOCATE(AA_r(ikrs:ikre))
- DO ikr = ikrs,ikre
- IF ( (krarray(ikr) .LT. two_third_krmax) ) THEN
- AA_r(ikr) = 1._dp;
+ two_third_kxmax = 2._dp/3._dp*deltakx*Nkx
+ ALLOCATE(AA_x(ikxs:ikxe))
+ DO ikx = ikxs,ikxe
+ IF ( (kxarray(ikx) .LT. two_third_kxmax) ) THEN
+ AA_x(ikx) = 1._dp;
ELSE
- AA_r(ikr) = 0._dp;
+ AA_x(ikx) = 0._dp;
ENDIF
END DO
- END SUBROUTINE set_krgrid
+ END SUBROUTINE set_kxgrid
- SUBROUTINE set_kzgrid
+ SUBROUTINE set_kygrid
USE prec_const
IMPLICIT NONE
INTEGER :: i_, counter
- Nkz = Nz;
+ Nky = Ny;
! Start and END indices of grid
- ikzs = 1
- ikze = Nkz
- ALLOCATE(kzarray(ikzs:ikze))
-
- IF (Lz .EQ. 0) THEN ! 1D linear case
- deltakz = 1._dp
- kzarray(1) = 0
- ikz_0 = 1
- ikz_max = 1
+ ikys = 1
+ ikye = Nky
+ ALLOCATE(kyarray(ikys:ikye))
+
+ IF (Ly .EQ. 0) THEN ! 1D linear case
+ deltaky = 1._dp
+ kyarray(1) = 0
+ iky_0 = 1
+ iky_max = 1
ELSE
- deltakz = 2._dp*PI/Lz
- kz_max = (Nz/2)*deltakr
+ deltaky = 2._dp*PI/Ly
+ ky_max = (Ny/2)*deltakx
! Creating a grid ordered as dk*(0 1 2 3 -2 -1)
- DO ikz = ikzs,ikze
- kzarray(ikz) = deltakz*(MODULO(ikz-1,Nkz/2)-Nkz/2*FLOOR(2.*real(ikz-1)/real(Nkz)))
- if (ikz .EQ. Nz/2+1) kzarray(ikz) = -kzarray(ikz)
- ! Finding kz=0
- IF (kzarray(ikz) .EQ. 0) ikz_0 = ikz
- ! Finding kzmax
- IF (kzarray(ikr) .EQ. kz_max) ikr_max = ikr
+ DO iky = ikys,ikye
+ kyarray(iky) = deltaky*(MODULO(iky-1,Nky/2)-Nky/2*FLOOR(2.*real(iky-1)/real(Nky)))
+ if (iky .EQ. Ny/2+1) kyarray(iky) = -kyarray(iky)
+ ! Finding ky=0
+ IF (kyarray(iky) .EQ. 0) iky_0 = iky
+ ! Finding kymax
+ IF (kyarray(ikx) .EQ. ky_max) ikx_max = ikx
END DO
ENDIF
! Orszag 2/3 filter
- two_third_kzmax = 2._dp/3._dp*deltakz*(Nkz/2);
- ALLOCATE(AA_z(ikzs:ikze))
- DO ikz = ikzs,ikze
- IF ( (kzarray(ikz) .GT. -two_third_kzmax) .AND. (kzarray(ikz) .LT. two_third_kzmax) ) THEN
- AA_z(ikz) = 1._dp;
+ two_third_kymax = 2._dp/3._dp*deltaky*(Nky/2);
+ ALLOCATE(AA_y(ikys:ikye))
+ DO iky = ikys,ikye
+ IF ( (kyarray(iky) .GT. -two_third_kymax) .AND. (kyarray(iky) .LT. two_third_kymax) ) THEN
+ AA_y(iky) = 1._dp;
ELSE
- AA_z(ikz) = 0._dp;
+ AA_y(iky) = 0._dp;
ENDIF
END DO
- END SUBROUTINE set_kzgrid
+ END SUBROUTINE set_kygrid
SUBROUTINE set_kpgrid !Precompute the grid of kperp
IMPLICIT NONE
- INTEGER :: ikz_sym, tmp_, counter
+ INTEGER :: iky_sym, tmp_, counter
REAL(dp):: local_kp_min, local_kp_max
! Find the min and max kperp to load subsequent GK matrices
- local_kp_min = krarray(ikrs) !smallest local kperp is on the kr axis
- local_kp_max = SQRT(krarray(ikre)**2 + kzarray(Nkz/2+1)**2)
- ikps = ikrs
- ikpe = INT(CEILING(local_kp_max/deltakr))+2
+ local_kp_min = kxarray(ikxs) !smallest local kperp is on the kx axis
+ local_kp_max = SQRT(kxarray(ikxe)**2 + kyarray(Nky/2+1)**2)
+ ikps = ikxs
+ ikpe = INT(CEILING(local_kp_max/deltakx))+2
! local number of different kperp
local_nkp = ikpe - ikps + 1
! Allocate 1D array of kperp values and indices
ALLOCATE(kparray(ikps:ikpe))
DO ikp = ikps,ikpe
- kparray(ikp) = REAL(ikp-1,dp) * deltakr
+ kparray(ikp) = REAL(ikp-1,dp) * deltakx
ENDDO
- write(*,*) rank_kr, ': ikps = ', ikps, 'ikpe = ',ikpe
- two_third_kpmax = SQRT(two_third_krmax**2+two_third_kzmax**2)
+ write(*,*) rank_kx, ': ikps = ', ikps, 'ikpe = ',ikpe
+ two_third_kpmax = SQRT(two_third_kxmax**2+two_third_kymax**2)
kp_max = 3._dp/2._dp * two_third_kpmax
END SUBROUTINE
+ SUBROUTINE set_zgrid
+ USE prec_const
+ IMPLICIT NONE
+ INTEGER :: i_
+ ! Start and END indices of grid
+ izs = 1
+ ize = Nz
+ ALLOCATE(zarray(izs:ize))
+ IF (Nz .EQ. 1) THEN ! full perp case
+ deltaz = 1._dp
+ zarray(1) = 0
+ ELSE
+ deltaz = q0*2._dp*PI/REAL(Nz+1,dp)
+ DO iz = izs,ize
+ zarray(iz) = REAL((iz-1),dp)*deltaz
+ ENDDO
+ ENDIF
+ if(my_id.EQ.0) write(*,*) '#parallel planes = ', Nz
+ END SUBROUTINE set_zgrid
+
SUBROUTINE grid_readinputs
! Read the input parameters
USE prec_const
@@ -270,7 +293,7 @@ CONTAINS
INTEGER :: lu_in = 90 ! File duplicated from STDIN
NAMELIST /GRID/ pmaxe, jmaxe, pmaxi, jmaxi, &
- Nr, Lr, Nz, Lz, kpar
+ Nx, Lx, Ny, Ly, Nz, q0
READ(lu_in,grid)
END SUBROUTINE grid_readinputs
@@ -290,14 +313,16 @@ CONTAINS
CALL attach(fidres, TRIM(str), "jmaxe", jmaxe)
CALL attach(fidres, TRIM(str), "pmaxi", pmaxi)
CALL attach(fidres, TRIM(str), "jmaxi", jmaxi)
- CALL attach(fidres, TRIM(str), "nr", nr)
- CALL attach(fidres, TRIM(str), "Lr", Lr)
- CALL attach(fidres, TRIM(str), "nz", nz)
- CALL attach(fidres, TRIM(str), "Lz", Lz)
- CALL attach(fidres, TRIM(str), "nkr", nkr)
- CALL attach(fidres, TRIM(str), "Lkr", Lkr)
- CALL attach(fidres, TRIM(str), "nkz", nkz)
- CALL attach(fidres, TRIM(str), "Lkz", Lkz)
+ CALL attach(fidres, TRIM(str), "Nx", Nx)
+ CALL attach(fidres, TRIM(str), "Lx", Lx)
+ CALL attach(fidres, TRIM(str), "Ny", Ny)
+ CALL attach(fidres, TRIM(str), "Ly", Ly)
+ CALL attach(fidres, TRIM(str), "Nz", Nz)
+ CALL attach(fidres, TRIM(str), "q0", q0)
+ CALL attach(fidres, TRIM(str), "Nkx", Nkx)
+ CALL attach(fidres, TRIM(str), "Lkx", Lkx)
+ CALL attach(fidres, TRIM(str), "Nky", Nky)
+ CALL attach(fidres, TRIM(str), "Lky", Lky)
END SUBROUTINE grid_outputinputs
FUNCTION bare(p_,j_)
diff --git a/src/inital.F90 b/src/inital.F90
index dcb31a69..2dfd084e 100644
--- a/src/inital.F90
+++ b/src/inital.F90
@@ -7,43 +7,45 @@ SUBROUTINE inital
USE model, ONLY : CO, NON_LIN
USE initial_par
USE prec_const
- USE coeff
USE time_integration
USE array, ONLY : Sepj,Sipj
USE collision
USE closure
USE ghosts
USE restarts
-
- implicit none
+ IMPLICIT NONE
CALL set_updatetlevel(1)
- IF (my_id .EQ. 0) WRITE(*,*) 'Evaluate kernels'
- CALL evaluate_kernels
-
!!!!!! Set the moments arrays Nepj, Nipj and phi!!!!!!
+ ! through loading a previou state
IF ( RESTART ) THEN
IF (my_id .EQ. 0) WRITE(*,*) 'Load moments'
CALL load_moments ! get N_0
-
- IF (my_id .EQ. 0) WRITE(*,*) 'Init phi with Poisson'
CALL poisson ! compute phi_0=phi(N_0)
-
+ ! through initialization
ELSE
+ ! set phi with noise and set moments to 0
IF (INIT_NOISY_PHI) THEN
- IF (my_id .EQ. 0) WRITE(*,*) 'Init noisy phi'
- CALL init_phi ! init noisy phi_0, N_0 = 0
- ELSEIF (INIT_ZF .GT. 0) THEN
- IF (my_id .EQ. 0) WRITE(*,*) 'Init ZF phi'
- CALL init_phi ! init ZF
+ CALL init_phi
+
+ ! set moments_00 (GC density) with noise and compute phi afterwards
ELSE
- IF (my_id .EQ. 0) WRITE(*,*) 'Init noisy moments and ghosts'
+ IF (my_id .EQ. 0) WRITE(*,*) 'Init noisy moments'
CALL init_moments ! init noisy N_0
- IF (my_id .EQ. 0) WRITE(*,*) 'Init phi with Poisson'
CALL poisson ! get phi_0 = phi(N_0)
ENDIF
+ ENDIF
+ ! Option for wiping the turbulence and check growth of secondary inst.
+ IF ( WIPE_TURB ) THEN
+ IF (my_id .EQ. 0) WRITE(*,*) '-Wiping turbulence'
+ CALL wipe_turbulence
+ ENDIF
+ ! Option for initializing a gaussian blob on the zonal profile
+ IF ( INIT_BLOB ) THEN
+ IF (my_id .EQ. 0) WRITE(*,*) '--init a blob'
+ CALL put_blob
ENDIF
IF (my_id .EQ. 0) WRITE(*,*) 'Apply closure'
@@ -54,9 +56,6 @@ SUBROUTINE inital
!!!!!! Set Sepj, Sipj and dnjs coeff table !!!!!!
IF ( NON_LIN ) THEN;
- IF (my_id .EQ. 0) WRITE(*,*) 'Building Dnjs table'
- CALL build_dnjs_table
-
IF (my_id .EQ. 0) WRITE(*,*) 'Init Sapj'
CALL compute_Sapj ! compute S_0 = S(phi_0,N_0)
ENDIF
@@ -67,7 +66,6 @@ SUBROUTINE inital
! Compute collision
CALL compute_TColl ! compute C_0 = C(N_0)
ENDIF
-
END SUBROUTINE inital
!******************************************************************************!
@@ -85,7 +83,7 @@ SUBROUTINE init_moments
IMPLICIT NONE
REAL(dp) :: noise
- REAL(dp) :: kr, kz, sigma, gain, kz_shift
+ REAL(dp) :: kx, ky, sigma, gain, ky_shift
INTEGER, DIMENSION(12) :: iseedarr
! Seed random number generator
@@ -96,16 +94,18 @@ SUBROUTINE init_moments
DO ip=ips_e,ipe_e
DO ij=ijs_e,ije_e
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- CALL RANDOM_NUMBER(noise)
- moments_e( ip,ij, ikr,ikz, :) = (init_background + init_noiselvl*(noise-0.5_dp))
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ CALL RANDOM_NUMBER(noise)
+ moments_e(ip,ij,ikx,iky,iz,:) = (init_background + init_noiselvl*(noise-0.5_dp))
+ END DO
END DO
END DO
- IF ( contains_kr0 ) THEN
- DO ikz=2,Nkz/2 !symmetry at kr = 0
- moments_e( ip,ij,ikr_0,ikz, :) = moments_e( ip,ij,ikr_0,Nkz+2-ikz, :)
+ IF ( contains_kx0 ) THEN
+ DO iky=2,Nky/2 !symmetry at kx = 0 for all z
+ moments_e(ip,ij,ikx_0,iky,:,:) = moments_e( ip,ij,ikx_0,Nky+2-iky,:, :)
END DO
ENDIF
@@ -115,16 +115,18 @@ SUBROUTINE init_moments
DO ip=ips_i,ipe_i
DO ij=ijs_i,ije_i
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- CALL RANDOM_NUMBER(noise)
- moments_i( ip,ij, ikr,ikz, :) = (init_background + init_noiselvl*(noise-0.5_dp))
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ CALL RANDOM_NUMBER(noise)
+ moments_i(ip,ij,ikx,iky,iz,:) = (init_background + init_noiselvl*(noise-0.5_dp))
+ END DO
END DO
END DO
- IF ( contains_kr0 ) THEN
- DO ikz=2,Nkz/2 !symmetry at kr = 0
- moments_i( ip,ij,ikr_0,ikz, :) = moments_i( ip,ij,ikr_0,Nkz+2-ikz, :)
+ IF ( contains_kx0 ) THEN
+ DO iky=2,Nky/2 !symmetry at kx = 0 for all z
+ moments_i( ip,ij,ikx_0,iky,:,:) = moments_i( ip,ij,ikx_0,Nky+2-iky,:,:)
END DO
ENDIF
@@ -133,21 +135,19 @@ SUBROUTINE init_moments
! Putting to zero modes that are not in the 2/3 Orszag rule
IF (NON_LIN) THEN
- DO ip=ips_e,ipe_e
- DO ij=ijs_e,ije_e
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_e( ip,ij,ikr,ikz, :) = moments_e( ip,ij,ikr,ikz, :)*AA_r(ikr)*AA_z(ikz)
- ENDDO
- ENDDO
- ENDDO
- ENDDO
- DO ip=ips_i,ipe_i
- DO ij=ijs_i,ije_i
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_i( ip,ij,ikr,ikz, :) = moments_i( ip,ij,ikr,ikz, :)*AA_r(ikr)*AA_z(ikz)
- ENDDO
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ DO ip=ips_e,ipe_e
+ DO ij=ijs_e,ije_e
+ moments_e( ip,ij,ikx,iky,iz, :) = moments_e( ip,ij,ikx,iky,iz, :)*AA_x(ikx)*AA_y(iky)
+ ENDDO
+ ENDDO
+ DO ip=ips_i,ipe_i
+ DO ij=ijs_i,ije_i
+ moments_i( ip,ij,ikx,iky,iz, :) = moments_i( ip,ij,ikx,iky,iz, :)*AA_x(ikx)*AA_y(iky)
+ ENDDO
+ ENDDO
ENDDO
ENDDO
ENDDO
@@ -168,47 +168,50 @@ SUBROUTINE init_phi
IMPLICIT NONE
REAL(dp) :: noise
- REAL(dp) :: kr, kz, sigma, gain, kz_shift
+ REAL(dp) :: kx, ky, sigma, gain, ky_shift
INTEGER, DIMENSION(12) :: iseedarr
IF (INIT_NOISY_PHI) THEN
-
+ IF (my_id .EQ. 0) WRITE(*,*) 'Init noisy phi'
! Seed random number generator
iseedarr(:)=iseed
CALL RANDOM_SEED(PUT=iseedarr+my_id)
!**** noise initialization *******************************************
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- CALL RANDOM_NUMBER(noise)
- phi(ikr,ikz) = (init_background + init_noiselvl*(noise-0.5_dp))*AA_r(ikr)*AA_z(ikz)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ CALL RANDOM_NUMBER(noise)
+ phi(ikx,iky,iz) = (init_background + init_noiselvl*(noise-0.5_dp))*AA_x(ikx)*AA_y(iky)
+ ENDDO
END DO
END DO
- !symmetry at kr = 0 to keep real inverse transform
- IF ( contains_kr0 ) THEN
- DO ikz=2,Nkz/2
- phi(ikr_0,ikz) = phi(ikr_0,Nkz+2-ikz)
+ !symmetry at kx = 0 to keep real inverse transform
+ IF ( contains_kx0 ) THEN
+ DO iky=2,Nky/2
+ phi(ikx_0,iky,:) = phi(ikx_0,Nky+2-iky,:)
END DO
- phi(ikr_0,Nz/2) = REAL(phi(ikr_0,Nz/2)) !origin must be real
+ phi(ikx_0,Ny/2,:) = REAL(phi(ikx_0,Ny/2,:)) !origin must be real
ENDIF
- !**** Cancel previous moments initialization
+ !**** ensure no previous moments initialization
moments_e = 0._dp; moments_i = 0._dp
+ !**** Zonal Flow initialization *******************************************
+ ! put a mode at ikx = mode number + 1, symmetry is already included since kx>=0
IF(INIT_ZF .GT. 0) THEN
-
- !**** Zonal Flow initialization *******************************************
- ! put a mode at ikr = mode number + 1, symmetry is already included since kr>=0
- IF( (INIT_ZF+1 .GT. ikrs) .AND. (INIT_ZF+1 .LT. ikre) ) THEN
- phi(INIT_ZF+1,ikz_0) = ZF_AMP*(2._dp*PI)**2/deltakr/deltakz/2._dp
- moments_i(1,1,INIT_ZF+1,ikz_0,:) = krarray(INIT_ZF+1)**2*phi(INIT_ZF+1,ikz_0)
- moments_e(1,1,INIT_ZF+1,ikz_0,:) = 0._dp
+ IF (my_id .EQ. 0) WRITE(*,*) 'Init ZF phi'
+ IF( (INIT_ZF+1 .GT. ikxs) .AND. (INIT_ZF+1 .LT. ikxe) ) THEN
+ DO iz = izs,ize
+ phi(INIT_ZF+1,iky_0,iz) = ZF_AMP*(2._dp*PI)**2/deltakx/deltaky/2._dp * COS((iz-1)/Nz*2._dp*PI)
+ moments_i(1,1,INIT_ZF+1,iky_0,iz,:) = kxarray(INIT_ZF+1)**2*phi(INIT_ZF+1,iky_0,iz)* COS((iz-1)/Nz*2._dp*PI)
+ moments_e(1,1,INIT_ZF+1,iky_0,iz,:) = 0._dp
+ ENDDO
ENDIF
ENDIF
ELSE ! we compute phi from noisy moments and poisson
-
CALL poisson
ENDIF
@@ -216,224 +219,67 @@ END SUBROUTINE init_phi
!******************************************************************************!
!******************************************************************************!
-!!!!!!! Build the Laguerre-Laguerre coupling coefficient table for nonlin
+!!!!!!! Remove all ky!=0 modes to conserve only zonal modes in a restart
!******************************************************************************!
-SUBROUTINE build_dnjs_table
- USE basic
- USE array, Only : dnjs
- USE grid, Only : jmaxe, jmaxi
- USE coeff
+SUBROUTINE wipe_turbulence
+ USE fields
+ USE grid
IMPLICIT NONE
-
- INTEGER :: in, ij, is, J
- INTEGER :: n_, j_, s_
-
- J = max(jmaxe,jmaxi)
-
- DO in = 1,J+1 ! Nested dependent loops to make benefit from dnjs symmetry
- n_ = in - 1
- DO ij = in,J+1
- j_ = ij - 1
- DO is = ij,J+1
- s_ = is - 1
-
- dnjs(in,ij,is) = TO_DP(ALL2L(n_,j_,s_,0))
- ! By symmetry
- dnjs(in,is,ij) = dnjs(in,ij,is)
- dnjs(ij,in,is) = dnjs(in,ij,is)
- dnjs(ij,is,in) = dnjs(in,ij,is)
- dnjs(is,ij,in) = dnjs(in,ij,is)
- dnjs(is,in,ij) = dnjs(in,ij,is)
- ENDDO
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ DO ip=ips_e,ipe_e
+ DO ij=ijs_e,ije_e
+ IF( iky .NE. iky_0) THEN
+ moments_e( ip,ij,ikx,iky,iz, :) = 0e-3_dp*moments_e( ip,ij,ikx,iky,iz, :)
+ ELSE
+ moments_e( ip,ij,ikx,iky,iz, :) = 1e+0_dp*moments_e( ip,ij,ikx,iky,iz, :)
+ ENDIF
ENDDO
+ ENDDO
+ DO ip=ips_i,ipe_i
+ DO ij=ijs_i,ije_i
+ IF( iky .NE. iky_0) THEN
+ moments_i( ip,ij,ikx,iky,iz, :) = 0e-3_dp*moments_i( ip,ij,ikx,iky,iz, :)
+ ELSE
+ moments_i( ip,ij,ikx,iky,iz, :) = 1e+0_dp*moments_i( ip,ij,ikx,iky,iz, :)
+ ENDIF
+ ENDDO
+ ENDDO
+ ENDDO
ENDDO
-END SUBROUTINE build_dnjs_table
+ ENDDO
+END SUBROUTINE
!******************************************************************************!
!******************************************************************************!
-!!!!!!! Evaluate the kernels once for all
+!!!!!!! Initialize an ionic Gaussian blob on top of the preexisting modes
!******************************************************************************!
-SUBROUTINE evaluate_kernels
- USE basic
- USE array, Only : kernel_e, kernel_i
+SUBROUTINE put_blob
+ USE fields
USE grid
- use model, ONLY : tau_e, tau_i, sigma_e, sigma_i, q_e, q_i, lambdaD, CLOS, sigmae2_taue_o2, sigmai2_taui_o2
+ USE model, ONLY: sigmai2_taui_o2
IMPLICIT NONE
-
- REAL(dp) :: factj, j_dp, j_int
- REAL(dp) :: be_2, bi_2, alphaD
- REAL(dp) :: kr, kz, kperp2
-
- !!!!! Electron kernels !!!!!
- !Precompute species dependant factors
- factj = 1.0 ! Start of the recursive factorial
- DO ij = 1, jmaxe+1
- j_int = jarray_e(ij)
- j_dp = REAL(j_int,dp) ! REAL of degree
-
- ! Recursive factorial
- IF (j_dp .GT. 0) THEN
- factj = factj * j_dp
- ELSE
- factj = 1._dp
- ENDIF
-
- DO ikr = ikrs,ikre
- kr = krarray(ikr)
- DO ikz = ikzs,ikze
- kz = kzarray(ikz)
-
- be_2 = (kr**2 + kz**2) * sigmae2_taue_o2
-
- kernel_e(ij, ikr, ikz) = be_2**j_int * exp(-be_2)/factj
-
- ENDDO
- ENDDO
- ENDDO
- ! Kernels closure
- DO ikr = ikrs,ikre
- kr = krarray(ikr)
- DO ikz = ikzs,ikze
- kz = kzarray(ikz)
- be_2 = (kr**2 + kz**2) * sigmae2_taue_o2
- ! Kernel ghost + 1 with Kj+1 = y/(j+1) Kj (/!\ ij = j+1)
- kernel_e(ijeg_e,ikr,ikz) = be_2/(real(ijeg_e-1,dp))*kernel_e(ije_e,ikr,ikz)
- ! Kernel ghost - 1 with Kj-1 = j/y Kj(careful about the kperp=0)
- IF ( be_2 .NE. 0 ) THEN
- kernel_e(ijsg_e,ikr,ikz) = (real(ijsg_e,dp))/be_2*kernel_e(ijs_e,ikr,ikz)
- ELSE
- kernel_e(ijsg_e,ikr,ikz) = 0._dp
+ REAL(dp) ::kx, ky, sigma, gain
+ sigma = 0.5_dp
+ gain = 5e2_dp
+
+ DO ikx=ikxs,ikxe
+ kx = kxarray(ikx)
+ DO iky=ikys,ikye
+ ky = kyarray(iky)
+ DO iz=izs,ize
+ DO ip=ips_i,ipe_i
+ DO ij=ijs_i,ije_i
+ IF( (iky .NE. iky_0) .AND. (ip .EQ. 1) .AND. (ij .EQ. 1)) THEN
+ moments_i( ip,ij,ikx,iky,iz, :) = moments_i( ip,ij,ikx,iky,iz, :) &
+ + gain*sigma/SQRT2 * exp(-(kx**2+ky**2)*sigma**2/4._dp) &
+ * AA_x(ikx)*AA_y(iky)!&
+ ! * exp(sigmai2_taui_o2*(kx**2+ky**2))
ENDIF
ENDDO
- ENDDO
-
- !!!!! Ion kernels !!!!!
- factj = 1.0 ! Start of the recursive factorial
- DO ij = 1, jmaxi+1
- j_int = jarray_e(ij)
- j_dp = REAL(j_int,dp) ! REAL of degree
-
- ! Recursive factorial
- IF (j_dp .GT. 0) THEN
- factj = factj * j_dp
- ELSE
- factj = 1._dp
- ENDIF
-
- DO ikr = ikrs,ikre
- kr = krarray(ikr)
- DO ikz = ikzs,ikze
- kz = kzarray(ikz)
- bi_2 = (kr**2 + kz**2) * sigmai2_taui_o2
- kernel_i(ij, ikr, ikz) = bi_2**j_int * exp(-bi_2)/factj
-
- ENDDO
ENDDO
ENDDO
- ! Kernels closure
- DO ikr = ikrs,ikre
- kr = krarray(ikr)
- DO ikz = ikzs,ikze
- kz = kzarray(ikz)
- bi_2 = (kr**2 + kz**2) * sigmai2_taui_o2
- ! Kernel ghost + 1 with Kj+1 = y/(j+1) Kj
- kernel_i(ijeg_i,ikr,ikz) = bi_2/(real(ijeg_i-1,dp))*kernel_i(ije_i,ikr,ikz)
- ! Kernel ghost - 1 with Kj-1 = j/y Kj(careful about the kperp=0)
- IF ( bi_2 .NE. 0 ) THEN
- kernel_i(ijsg_i,ikr,ikz) = (real(ijsg_i,dp))/bi_2*kernel_i(ijs_i,ikr,ikz)
- ELSE
- kernel_i(ijsg_i,ikr,ikz) = 0._dp
- ENDIF
- ENDDO
ENDDO
-END SUBROUTINE evaluate_kernels
-! !******************************************************************************!
-! !!!!!!! Evaluate the kernels once for all
-! !******************************************************************************!
-! SUBROUTINE evaluate_kernels
-! USE basic
-! USE array, Only : kernel_e, kernel_i
-! USE grid
-! use model, ONLY : tau_e, tau_i, sigma_e, sigma_i, q_e, q_i, lambdaD, CLOS
-! IMPLICIT NONE
-!
-! REAL(dp) :: factj, j_dp, j_int
-! REAL(dp) :: sigmae2_taue_o2, sigmai2_taui_o2
-! REAL(dp) :: be_2, bi_2, alphaD
-! REAL(dp) :: kr, kz, kperp2
-!
-! !!!!! Electron kernels !!!!!
-! !Precompute species dependant factors
-! sigmae2_taue_o2 = sigma_e**2 * tau_e/2._dp ! factor of the Kernel argument
-!
-! factj = 1.0 ! Start of the recursive factorial
-! DO ij = 1, jmaxe+1
-! j_int = jarray_e(ij)
-! j_dp = REAL(j_int,dp) ! REAL of degree
-!
-! ! Recursive factorial
-! IF (j_dp .GT. 0) THEN
-! factj = factj * j_dp
-! ELSE
-! factj = 1._dp
-! ENDIF
-!
-! DO ikr = ikrs,ikre
-! kr = krarray(ikr)
-! DO ikz = ikzs,ikze
-! kz = kzarray(ikz)
-!
-! be_2 = (kr**2 + kz**2) * sigmae2_taue_o2
-!
-! kernel_e(ij, ikr, ikz) = be_2**j_int * exp(-be_2)/factj
-!
-! ENDDO
-! ENDDO
-! ENDDO
-! ! Kernels closure
-! DO ikr = ikrs,ikre
-! kr = krarray(ikr)
-! DO ikz = ikzs,ikze
-! kz = kzarray(ikz)
-! be_2 = (kr**2 + kz**2) * sigmae2_taue_o2
-! kernel_e(ijeg_e,ikr,ikz) = be_2/(real(ijeg_e,dp))*kernel_e(ije_e,ikr,ikz)
-! ENDDO
-! ENDDO
-!
-! !!!!! Ion kernels !!!!!
-! sigmai2_taui_o2 = sigma_i**2 * tau_i/2._dp ! (b_a/2)^2 = (kperp sqrt(2 tau_a) sigma_a/2)^2
-!
-! factj = 1.0 ! Start of the recursive factorial
-! DO ij = 1, jmaxi+1
-! j_int = jarray_e(ij)
-! j_dp = REAL(j_int,dp) ! REAL of degree
-!
-! ! Recursive factorial
-! IF (j_dp .GT. 0) THEN
-! factj = factj * j_dp
-! ELSE
-! factj = 1._dp
-! ENDIF
-!
-! DO ikr = ikrs,ikre
-! kr = krarray(ikr)
-! DO ikz = ikzs,ikze
-! kz = kzarray(ikz)
-!
-! bi_2 = (kr**2 + kz**2) * sigmai2_taui_o2
-!
-! kernel_i(ij, ikr, ikz) = bi_2**j_int * exp(-bi_2)/factj
-!
-! ENDDO
-! ENDDO
-! ENDDO
-! ! Kernels closure
-! DO ikr = ikrs,ikre
-! kr = krarray(ikr)
-! DO ikz = ikzs,ikze
-! kz = kzarray(ikz)
-! bi_2 = (kr**2 + kz**2) * sigmai2_taui_o2
-! kernel_i(ijeg_i,ikr,ikz) = bi_2/(real(ijeg_i,dp))*kernel_e(ije_i,ikr,ikz)
-! ENDDO
-! ENDDO
-! END SUBROUTINE evaluate_kernels
+ ENDDO
+END SUBROUTINE put_blob
!******************************************************************************!
diff --git a/src/initial_par_mod.F90 b/src/initial_par_mod.F90
index 1c619aa8..f0b3a7a1 100644
--- a/src/initial_par_mod.F90
+++ b/src/initial_par_mod.F90
@@ -10,6 +10,10 @@ MODULE initial_par
! Initialization through a zonal flow phi
INTEGER, PUBLIC, PROTECTED :: INIT_ZF = 0
REAL(DP), PUBLIC, PROTECTED :: ZF_AMP = 1E+3_dp
+ ! Wipe turbulence in the restart
+ LOGICAL, PUBLIC, PROTECTED :: WIPE_TURB = .false.
+ ! Init a Gaussian blob density in the middle
+ LOGICAL, PUBLIC, PROTECTED :: INIT_BLOB = .false.
! Initial background level
REAL(dp), PUBLIC, PROTECTED :: init_background=0._dp
! Initial noise amplitude
@@ -39,6 +43,8 @@ CONTAINS
NAMELIST /INITIAL_CON/ INIT_NOISY_PHI
NAMELIST /INITIAL_CON/ INIT_ZF
+ NAMELIST /INITIAL_CON/ WIPE_TURB
+ NAMELIST /INITIAL_CON/ INIT_BLOB
NAMELIST /INITIAL_CON/ init_background
NAMELIST /INITIAL_CON/ init_noiselvl
NAMELIST /INITIAL_CON/ iseed
diff --git a/src/lin_coeff_and_geometry.F90 b/src/lin_coeff_and_geometry.F90
index 110208ab..f2736623 100644
--- a/src/lin_coeff_and_geometry.F90
+++ b/src/lin_coeff_and_geometry.F90
@@ -5,7 +5,7 @@ SUBROUTINE lin_coeff_and_geometry
USE model, ONLY: taue_qe, taui_qi, sqrtTaue_qe, sqrtTaui_qi, eta_T, eta_n
USE prec_const
USE grid, ONLY: parray_e, parray_i, jarray_e, jarray_i, &
- ip,ij, ips_e,ip_e, ips_i,ipe_i, ijs_e,ije_e, ijs_i,ije_i,&
+ ip,ij, ips_e,ipe_e, ips_i,ipe_i, ijs_e,ije_e, ijs_i,ije_i,&
kxarray, kyarray, zarray, &
ikx,iky,iz, ikxs,ikxe, ikys,ikye, izs,ize
IMPLICIT NONE
@@ -34,8 +34,8 @@ SUBROUTINE lin_coeff_and_geometry
DO ij = ijs_e, ije_e
j_int= jarray_e(ij) ! Laguerre degree
j_dp = REAL(j_int,dp) ! REAL of Laguerre degree
- xnepjp1(ij) = -taui_qi * (j_dp + 1._dp)
- xnepjm1(ij) = -taui_qi * j_dp
+ xnepjp1(ij) = -taue_qe * (j_dp + 1._dp)
+ xnepjm1(ij) = -taue_qe * j_dp
ENDDO
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! Ions linear coefficients for moment RHS !!!!!!!!!!
@@ -72,10 +72,10 @@ SUBROUTINE lin_coeff_and_geometry
!! Electrostatic potential pj terms
IF (p_int .EQ. 0) THEN ! kronecker p0
xphij(ip,ij) = eta_n + 2.*j_dp*eta_T
- xphijp1(ip,ij) = eta_T*(j_dp+1._dp)
- xphijm1(ip,ij) = eta_T* j_dp
+ xphijp1(ip,ij) =-eta_T*(j_dp+1._dp)
+ xphijm1(ip,ij) =-eta_T* j_dp
ELSE IF (p_int .EQ. 2) THEN ! kronecker p2
- xphij(ip,ij) =-eta_T/SQRT2
+ xphij(ip,ij) = eta_T/SQRT2
xphijp1(ip,ij) = 0._dp; xphijm1(ip,ij) = 0._dp;
ELSE
xphij(ip,ij) = 0._dp; xphijp1(ip,ij) = 0._dp
diff --git a/src/memory.F90 b/src/memory.F90
index 4458499a..6c5f3fe1 100644
--- a/src/memory.F90
+++ b/src/memory.F90
@@ -12,43 +12,68 @@ SUBROUTINE memory
IMPLICIT NONE
!___________________ 2D ARRAYS __________________________
! Electrostatic potential
- CALL allocate_array(phi, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(phi, ikxs,ikxe, ikys,ikye, izs,ize)
!! Diagnostics arrays
! Gyrocenter density *for 2D output*
- CALL allocate_array(Ne00, ikrs,ikre, ikzs,ikze)
- CALL allocate_array(Ni00, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(Ne00, ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array(Ni00, ikxs,ikxe, ikys,ikye, izs,ize)
! particle density *for 2D output*
- CALL allocate_array(dens_e, ikrs,ikre, ikzs,ikze)
- CALL allocate_array(dens_i, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(dens_e, ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array(dens_i, ikxs,ikxe, ikys,ikye, izs,ize)
! particle temperature *for 2D output*
- CALL allocate_array(temp_e, ikrs,ikre, ikzs,ikze)
- CALL allocate_array(temp_i, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(temp_e, ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array(temp_i, ikxs,ikxe, ikys,ikye, izs,ize)
!___________________ 3D ARRAYS __________________________
!! FLR kernels functions
! Kernel evaluation from j= -1 to jmax+1 for truncation
- CALL allocate_array(Kernel_e, ijsg_e,ijeg_e, ikrs,ikre, ikzs,ikze)
- CALL allocate_array(Kernel_i, ijsg_i,ijeg_i, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(Kernel_e, ijsg_e,ijeg_e, ikxs,ikxe, ikys,ikye)
+ CALL allocate_array(Kernel_i, ijsg_i,ijeg_i, ikxs,ikxe, ikys,ikye)
!___________________ 5D ARRAYS __________________________
! Moments with ghost degrees for p+2 p-2, j+1, j-1 truncations
- CALL allocate_array( moments_e, ipsg_e,ipeg_e, ijsg_e,ijeg_e, ikrs,ikre, ikzs,ikze, 1,ntimelevel )
- CALL allocate_array( moments_i, ipsg_i,ipeg_i, ijsg_i,ijeg_i, ikrs,ikre, ikzs,ikze, 1,ntimelevel )
+ CALL allocate_array( moments_e, ipsg_e,ipeg_e, ijsg_e,ijeg_e, ikxs,ikxe, ikys,ikye, izs,ize, 1,ntimelevel )
+ CALL allocate_array( moments_i, ipsg_i,ipeg_i, ijsg_i,ijeg_i, ikxs,ikxe, ikys,ikye, izs,ize, 1,ntimelevel )
! Moments right-hand-side (contains linear part of hierarchy)
- CALL allocate_array( moments_rhs_e, ips_e,ipe_e, ijs_e,ije_e, ikrs,ikre, ikzs,ikze, 1,ntimelevel )
- CALL allocate_array( moments_rhs_i, ips_i,ipe_i, ijs_i,ije_i, ikrs,ikre, ikzs,ikze, 1,ntimelevel )
+ CALL allocate_array( moments_rhs_e, ips_e,ipe_e, ijs_e,ije_e, ikxs,ikxe, ikys,ikye, izs,ize, 1,ntimelevel )
+ CALL allocate_array( moments_rhs_i, ips_i,ipe_i, ijs_i,ije_i, ikxs,ikxe, ikys,ikye, izs,ize, 1,ntimelevel )
! Collision term
- CALL allocate_array( TColl_e, ips_e,ipe_e, ijs_e,ije_e , ikrs,ikre, ikzs,ikze)
- CALL allocate_array( TColl_i, ips_i,ipe_i, ijs_i,ije_i , ikrs,ikre, ikzs,ikze)
+ CALL allocate_array( TColl_e, ips_e,ipe_e, ijs_e,ije_e , ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array( TColl_i, ips_i,ipe_i, ijs_i,ije_i , ikxs,ikxe, ikys,ikye, izs,ize)
! Non linear terms and dnjs table
- CALL allocate_array( Sepj, ips_e,ipe_e, ijs_e,ije_e, ikrs,ikre, ikzs,ikze )
- CALL allocate_array( Sipj, ips_i,ipe_i, ijs_i,ije_i, ikrs,ikre, ikzs,ikze )
+ CALL allocate_array( Sepj, ips_e,ipe_e, ijs_e,ije_e, ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array( Sipj, ips_i,ipe_i, ijs_i,ije_i, ikxs,ikxe, ikys,ikye, izs,ize)
CALL allocate_array( dnjs, 1,maxj+1, 1,maxj+1, 1,maxj+1)
+ ! Linear coeff for moments rhs
+ ! electrons
+ CALL allocate_array( xnepj, ips_e,ipe_e, ijs_e,ije_e)
+ CALL allocate_array( xnepp2j, ips_e,ipe_e)
+ CALL allocate_array( xnepp1j, ips_e,ipe_e)
+ CALL allocate_array( xnepm1j, ips_e,ipe_e)
+ CALL allocate_array( xnepm2j, ips_e,ipe_e)
+ CALL allocate_array( xnepjp1, ijs_e,ije_e)
+ CALL allocate_array( xnepjm1, ijs_e,ije_e)
+ ! ions
+ CALL allocate_array( xnipj, ips_i,ipe_i, ijs_i,ije_i)
+ CALL allocate_array( xnipp2j, ips_i,ipe_i)
+ CALL allocate_array( xnipp1j, ips_i,ipe_i)
+ CALL allocate_array( xnipm1j, ips_i,ipe_i)
+ CALL allocate_array( xnipm2j, ips_i,ipe_i)
+ CALL allocate_array( xnipjp1, ijs_i,ije_i)
+ CALL allocate_array( xnipjm1, ijs_i,ije_i)
+ ! elect. pot.
+ CALL allocate_array( xphij, ips_i,ipe_i, ijs_i,ije_i)
+ CALL allocate_array( xphijp1, ips_i,ipe_i, ijs_i,ije_i)
+ CALL allocate_array( xphijm1, ips_i,ipe_i, ijs_i,ije_i)
+
+ ! Curvature and geometry
+ CALL allocate_array( Ckxky, ikxs,ikxe, ikys,ikye, izs,ize)
+
!___________________ 2x5D ARRAYS __________________________
!! Collision matrices
IF (CO .LT. -1) THEN !DK collision matrix (same for every k)
@@ -59,12 +84,12 @@ SUBROUTINE memory
CALL allocate_array( CiepjT, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxi+1)*(jmaxi+1), 1,1, 1,1)
CALL allocate_array( CiepjF, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxe+1)*(jmaxe+1), 1,1, 1,1)
ELSEIF (CO .GT. 1) THEN !GK collision matrices (one for each kperp)
- CALL allocate_array( Ceepj, 1,(pmaxe+1)*(jmaxe+1), 1,(pmaxe+1)*(jmaxe+1), ikrs,ikre, ikzs,ikze)
- CALL allocate_array( CeipjT, 1,(pmaxe+1)*(jmaxe+1), 1,(pmaxe+1)*(jmaxe+1), ikrs,ikre, ikzs,ikze)
- CALL allocate_array( CeipjF, 1,(pmaxe+1)*(jmaxe+1), 1,(pmaxi+1)*(jmaxi+1), ikrs,ikre, ikzs,ikze)
- CALL allocate_array( Ciipj, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxi+1)*(jmaxi+1), ikrs,ikre, ikzs,ikze)
- CALL allocate_array( CiepjT, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxi+1)*(jmaxi+1), ikrs,ikre, ikzs,ikze)
- CALL allocate_array( CiepjF, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxe+1)*(jmaxe+1), ikrs,ikre, ikzs,ikze)
+ CALL allocate_array( Ceepj, 1,(pmaxe+1)*(jmaxe+1), 1,(pmaxe+1)*(jmaxe+1), ikxs,ikxe, ikys,ikye)
+ CALL allocate_array( CeipjT, 1,(pmaxe+1)*(jmaxe+1), 1,(pmaxe+1)*(jmaxe+1), ikxs,ikxe, ikys,ikye)
+ CALL allocate_array( CeipjF, 1,(pmaxe+1)*(jmaxe+1), 1,(pmaxi+1)*(jmaxi+1), ikxs,ikxe, ikys,ikye)
+ CALL allocate_array( Ciipj, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxi+1)*(jmaxi+1), ikxs,ikxe, ikys,ikye)
+ CALL allocate_array( CiepjT, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxi+1)*(jmaxi+1), ikxs,ikxe, ikys,ikye)
+ CALL allocate_array( CiepjF, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxe+1)*(jmaxe+1), ikxs,ikxe, ikys,ikye)
ENDIF
END SUBROUTINE memory
diff --git a/src/model_mod.F90 b/src/model_mod.F90
index f06cf818..7ea6600d 100644
--- a/src/model_mod.F90
+++ b/src/model_mod.F90
@@ -25,8 +25,10 @@ MODULE model
REAL(dp), PUBLIC, PROTECTED :: eta_B = 1._dp ! Magnetic gradient
REAL(dp), PUBLIC, PROTECTED :: lambdaD = 1._dp ! Debye length
- REAL(dp), PUBLIC, PROTECTED :: taue_qe_etaB ! factor of the magnetic moment coupling
- REAL(dp), PUBLIC, PROTECTED :: taui_qi_etaB !
+ REAL(dp), PUBLIC, PROTECTED :: taue_qe ! factor of the magnetic moment coupling
+ REAL(dp), PUBLIC, PROTECTED :: taui_qi !
+ REAL(dp), PUBLIC, PROTECTED :: qi_taui !
+ REAL(dp), PUBLIC, PROTECTED :: qe_taue !
REAL(dp), PUBLIC, PROTECTED :: sqrtTaue_qe ! factor of parallel moment term
REAL(dp), PUBLIC, PROTECTED :: sqrtTaui_qi !
REAL(dp), PUBLIC, PROTECTED :: qe_sigmae_sqrtTaue ! factor of parallel phi term
@@ -54,16 +56,11 @@ CONTAINS
READ(lu_in,model_par)
- !Precompute species dependant factors
- IF( q_e .NE. 0._dp ) THEN
- taue_qe_etaB = tau_e/q_e * eta_B ! factor of the magnetic moment coupling
- sqrtTaue_qe = sqrt(tau_e)/q_e ! factor of parallel moment term
- ELSE
- taue_qe_etaB = 0._dp
- sqrtTaue_qe = 0._dp
- ENDIF
-
- taui_qi_etaB = tau_i/q_i * eta_B ! factor of the magnetic moment coupling
+ taue_qe = tau_e/q_e ! factor of the magnetic moment coupling
+ taui_qi = tau_i/q_i ! factor of the magnetic moment coupling
+ qe_taue = q_e/tau_e
+ qi_taui = q_i/tau_i
+ sqrtTaue_qe = sqrt(tau_e)/q_e ! factor of parallel moment term
sqrtTaui_qi = sqrt(tau_i)/q_i ! factor of parallel moment term
qe_sigmae_sqrtTaue = q_e/sigma_e/SQRT(tau_e) ! factor of parallel phi term
qi_sigmai_sqrtTaui = q_i/sigma_i/SQRT(tau_i)
@@ -79,7 +76,6 @@ CONTAINS
nu_ee = nu_e ! e-e coll. frequ.
nu_ie = nu_i ! i-e coll. frequ.
-
! Old normalization (MOLI Jorge/Frei)
! nu_e = 0.532_dp*nu ! electron-ion collision frequency (where already multiplied by 0.532)
! nu_i = 0.532_dp*nu*sigma_e*tau_e**(-3._dp/2._dp)/SQRT2 ! ion-ion collision frequ.
diff --git a/src/moments_eq_rhs.F90 b/src/moments_eq_rhs.F90
index d56a0bfe..9d41db73 100644
--- a/src/moments_eq_rhs.F90
+++ b/src/moments_eq_rhs.F90
@@ -13,168 +13,104 @@ SUBROUTINE moments_eq_rhs_e
USE grid
USE model
USE prec_const
- USE utility, ONLY : is_nan
USE collision
IMPLICIT NONE
- INTEGER :: ip2, ij2, il, p_int, j_int, p2_int, j2_int ! loops indices and polynom. degrees
- REAL(dp) :: p_dp, j_dp, l_dp
- REAL(dp) :: kr, kz, kperp2
- REAL(dp) :: kernelj, kerneljp1, kerneljm1 ! Kernel functions and variable
- REAL(dp) :: xNapj, xNapp1j, xNapm1j, xNapp2j, xNapm2j, xNapjp1, xNapjm1 ! Mom. factors depending on the pj loop
- REAL(dp) :: xphij, xphijp1, xphijm1, xphijpar ! ESpot. factors depending on the pj loop
- REAL(dp) :: xCapj, xCa20, xCa01, xCa10 ! Coll. factors depending on the pj loop
- COMPLEX(dp) :: TNapj, TNapp1j, TNapm1j, TNapp2j, TNapm2j, TNapjp1, TNapjm1, Tphi
- COMPLEX(dp) :: TColl, TColl20, TColl01, TColl10 ! terms of the rhs
- COMPLEX(dp) :: i_kz, Hyper_diff_p, Hyper_diff_j
+ INTEGER :: p_int, j_int ! loops indices and polynom. degrees
+ REAL(dp) :: kx, ky, kperp2
+ COMPLEX(dp) :: Tnepj, Tnepp2j, Tnepm2j, Tnepjp1, Tnepjm1, Tpare, Tphi
+ COMPLEX(dp) :: TColl ! terms of the rhs
+ COMPLEX(dp) :: i_ky
+ REAL(dp) :: delta_p0, delta_p1, delta_p2
+ INTEGER :: izprev,iznext ! indices of previous and next z slice
- ! Measuring execution time
+ ! Measuring execution time
CALL cpu_time(t0_rhs)
ploope : DO ip = ips_e, ipe_e ! loop over Hermite degree indices
p_int= parray_e(ip) ! Hermite polynom. degree
- p_dp = REAL(p_int,dp) ! REAL of the Hermite degree
-
- ! N_e^{p+1,j} coeff
- xNapp1j = sqrtTaue_qe * SQRT(p_dp + 1)
- ! N_e^{p-1,j} coeff
- xNapm1j = sqrtTaue_qe * SQRT(p_dp)
- ! N_e^{p+2,j} coeff
- xNapp2j = taue_qe_etaB * SQRT((p_dp + 1._dp) * (p_dp + 2._dp))
- ! N_e^{p-2,j} coeff
- xNapm2j = taue_qe_etaB * SQRT(p_dp * (p_dp - 1._dp))
+ delta_p0 = 0._dp; delta_p1 = 0._dp; delta_p2 = 0._dp
+ IF(p_int .EQ. 0) delta_p0 = 1._dp
+ IF(p_int .EQ. 1) delta_p1 = 1._dp
+ IF(p_int .EQ. 2) delta_p2 = 1._dp
jloope : DO ij = ijs_e, ije_e ! loop over Laguerre degree indices
- j_int= jarray_e(ij) ! Laguerre polynom. degree
- j_dp = REAL(j_int,dp) ! REAL of degree
-
- ! N_e^{p,j+1} coeff
- xNapjp1 = -taue_qe_etaB * (j_dp + 1._dp)
- ! N_e^{p,j-1} coeff
- xNapjm1 = -taue_qe_etaB * j_dp
- ! N_e^{pj} coeff
- xNapj = taue_qe_etaB * 2._dp*(p_dp + j_dp + 1._dp)
-
- !! Collision operator pj terms
- xCapj = -nu_ee*(p_dp + 2._dp*j_dp) !DK Lenard-Bernstein basis
- ! Dougherty part
- IF ( CO .EQ. -2) THEN
- IF ((p_int .EQ. 2) .AND. (j_int .EQ. 0)) THEN ! kronecker pj20
- xCa20 = nu_ee * 2._dp/3._dp
- xCa01 = -SQRT2 * xCa20
- xCa10 = 0._dp
- ELSEIF ((p_int .EQ. 0) .AND. (j_int .EQ. 1)) THEN ! kronecker pj01
- xCa20 = -nu_ee * SQRT2 * 2._dp/3._dp
- xCa01 = -SQRT2 * xCa20
- xCa10 = 0._dp
- ELSEIF ((p_int .EQ. 1) .AND. (j_int .EQ. 0)) THEN ! kronecker pj10
- xCa20 = 0._dp
- xCa01 = 0._dp
- xCa10 = nu_ee
- ELSE
- xCa20 = 0._dp; xCa01 = 0._dp; xCa10 = 0._dp
- ENDIF
- ENDIF
-
- !! Electrostatic potential pj terms
- IF (p_int .EQ. 0) THEN ! kronecker p0
- xphij = (eta_n + 2.*j_dp*eta_T - 2._dp*eta_B*(j_dp+1._dp) )
- xphijp1 = -(eta_T - eta_B)*(j_dp+1._dp)
- xphijm1 = -(eta_T - eta_B)* j_dp
- xphijpar= 0._dp
- ELSE IF (p_int .EQ. 1) THEN ! kronecker p1
- xphijpar = qe_sigmae_sqrtTaue
- xphij = 0._dp; xphijp1 = 0._dp; xphijm1 = 0._dp
- ELSE IF (p_int .EQ. 2) THEN ! kronecker p2
- xphij = (eta_T/SQRT2 - SQRT2*eta_B)
- xphijp1 = 0._dp; xphijm1 = 0._dp; xphijpar= 0._dp
- ELSE
- xphij = 0._dp; xphijp1 = 0._dp; xphijm1 = 0._dp; xphijpar= 0._dp
- ENDIF
-
! Loop on kspace
- krloope : DO ikr = ikrs,ikre
- kzloope : DO ikz = ikzs,ikze
- kr = krarray(ikr) ! Poloidal wavevector
- kz = kzarray(ikz) ! Toroidal wavevector
- i_kz = imagu * kz ! Ddz derivative
- IF (Nkz .EQ. 1) i_kz = imagu * krarray(ikr) ! If 1D simulation we put kr as kz
- kperp2 = kr**2 + kz**2 ! perpendicular wavevector
+ zloope : DO iz = izs,ize
+ ! Periodic BC for first order derivative
+ iznext = iz+1; izprev = iz-1;
+ IF(iz .EQ. 1) izprev = Nz
+ IF(iz .EQ. Nz) iznext = 1
+
+ kxloope : DO ikx = ikxs,ikxe
+ kx = kxarray(ikx) ! radial wavevector
+ kyloope : DO iky = ikys,ikye
+ ky = kyarray(iky) ! toroidal wavevector
+ i_ky = imagu * ky ! toroidal derivative
+ IF (Nky .EQ. 1) i_ky = imagu * kxarray(ikx) ! If 1D simulation we put kx as ky
+ kperp2 = kx**2 + ky**2 ! perpendicular wavevector
!! Compute moments mixing terms
- ! term propto N_e^{p,j}
- TNapj = xNapj * moments_e(ip,ij,ikr,ikz,updatetlevel)
- ! term propto N_e^{p+2,j}
- TNapp2j = xNapp2j * moments_e(ip+2,ij,ikr,ikz,updatetlevel)
- ! term propto N_e^{p-2,j}
- TNapm2j = xNapm2j * moments_e(ip-2,ij,ikr,ikz,updatetlevel)
- ! term propto N_e^{p,j+1}
- TNapjp1 = xNapjp1 * moments_e(ip,ij+1,ikr,ikz,updatetlevel)
- ! term propto N_e^{p,j-1}
- TNapjm1 = xNapjm1 * moments_e(ip,ij-1,ikr,ikz,updatetlevel)
-
- !! Collision
- IF (CO .EQ. 0) THEN ! Lenard Bernstein
- TColl = xCapj * moments_e(ip,ij,ikr,ikz,updatetlevel)
-
- ELSEIF (CO .EQ. -1) THEN ! DK Dougherty
- TColl20 = 0._dp; TColl01 = 0._dp; TColl10 = 0._dp
- IF ( (pmaxe .GE. 2) ) TColl20 = xCa20 * moments_e(3,1,ikr,ikz,updatetlevel)
- IF ( (jmaxe .GE. 1) ) TColl01 = xCa01 * moments_e(1,2,ikr,ikz,updatetlevel)
- IF ( (pmaxe .GE. 1) ) TColl10 = xCa10 * moments_e(2,1,ikr,ikz,updatetlevel)
- ! Total collisional term
- TColl = xCapj* moments_e(ip,ij,ikr,ikz,updatetlevel)&
- + TColl20 + TColl01 + TColl10
-
- ELSEIF (CO .EQ. 1) THEN ! GK Dougherty
- CALL DoughertyGK_e(ip,ij,ikr,ikz,TColl)
- ! CALL DoughertyGK(ip,ij,ikr,ikz,TColl,'e')
-
- ELSE ! COSOLver matrix
- TColl = TColl_e(ip,ij,ikr,ikz)
- ENDIF
+ ! Perpendicular dynamic
+ ! term propto n_e^{p,j}
+ Tnepj = xnepj(ip,ij) * (moments_e(ip,ij,ikx,iky,iz,updatetlevel) &
+ +kernel_e(ij,ikx,iky)*qe_taue*phi(ikx,iky,iz)*delta_p0)
+ ! term propto n_e^{p+2,j}
+ Tnepp2j = xnepp2j(ip) * moments_e(ip+2,ij,ikx,iky,iz,updatetlevel)
+ ! term propto n_e^{p-2,j}
+ Tnepm2j = xnepm2j(ip) * (moments_e(ip-2,ij,ikx,iky,iz,updatetlevel) &
+ +kernel_e(ij,ikx,iky)*qe_taue*phi(ikx,iky,iz)*delta_p2)
+ ! term propto n_e^{p,j+1}
+ Tnepjp1 = xnepjp1(ij) * (moments_e(ip,ij+1,ikx,iky,iz,updatetlevel) &
+ +kernel_e(ij+1,ikx,iky)*qe_taue*phi(ikx,iky,iz)*delta_p0)
+ ! term propto n_e^{p,j-1}
+ Tnepjm1 = xnepjm1(ij) * (moments_e(ip,ij-1,ikx,iky,iz,updatetlevel) &
+ +kernel_e(ij-1,ikx,iky)*qe_taue*phi(ikx,iky,iz)*delta_p0)
+ ! Parallel dynamic
+ ! term propto n_i^{p+1,j}, centered FDF
+ Tpare = xnepp1j(ip) * &
+ (moments_e(ip+1,ij,ikx,iky,iznext,updatetlevel)&
+ -moments_e(ip+1,ij,ikx,iky,izprev,updatetlevel)) &
+ +xnepm1j(ip) * &
+ (moments_e(ip-1,ij,ikx,iky,iznext,updatetlevel)+kernel_e(ij,ikx,iky)*qe_taue*phi(ikx,iky,iznext)*delta_p1&
+ -moments_e(ip-1,ij,ikx,iky,izprev,updatetlevel)-kernel_e(ij,ikx,iky)*qe_taue*phi(ikx,iky,izprev)*delta_p1)
!! Electrical potential term
IF ( p_int .LE. 2 ) THEN ! kronecker p0 p1 p2
- Tphi = phi(ikr,ikz) * (xphij*kernel_e(ij, ikr, ikz) &
- + xphijp1*kernel_e(ij+1, ikr, ikz) &
- + xphijm1*kernel_e(ij-1, ikr, ikz) )
+ Tphi = phi(ikx,iky,iz) * (xphij(ip,ij)*kernel_e(ij, ikx, iky) &
+ + xphijp1(ip,ij)*kernel_e(ij+1, ikx, iky) &
+ + xphijm1(ip,ij)*kernel_e(ij-1, ikx, iky) )
ELSE
Tphi = 0._dp
ENDIF
- !! Parallel kinetic hyperdiffusion (projection of d/dv^4 f on Hermite basis)
- Hyper_diff_p = 0._dp
- IF ( p_int .GE. 4 ) THEN
- Hyper_diff_p = 4._dp*SQRT(p_dp*(p_dp-1._dp)*(p_dp-2._dp)*(p_dp-3._dp)*(p_dp-4._dp))&
- *moments_e(ip-4,ij,ikr,ikz,updatetlevel)
- ENDIF
-
- !! Perpendicular kinetic hyperdiffusion (projection of d/dv^4 f on Laguerre basis)
- Hyper_diff_j = 0._dp
- IF ( j_int .GE. 4 ) THEN
- DO il = 1,(ij-4)
- l_dp = real(il-1,dp)
- Hyper_diff_j = Hyper_diff_j + (j_dp-(l_dp+1_dp))*moments_e(ip,il,ikr,ikz,updatetlevel)
- ENDDO
+ !! Collision
+ IF (CO .EQ. 0) THEN ! Lenhard Bernstein
+ TColl = -nu_ee*(ip+2*ij-3)*moments_e(ip,ij,ikx,iky,iz,updatetlevel)
+ ELSEIF (CO .EQ. 1) THEN ! GK Dougherty
+ CALL DoughertyGK_e(ip,ij,ikx,iky,iz,TColl)
+ ELSE ! COSOLver matrix
+ TColl = TColl_e(ip,ij,ikx,iky,iz)
ENDIF
- !! Sum of all linear terms
- moments_rhs_e(ip,ij,ikr,ikz,updatetlevel) = &
- - INV_LIN_SYS * i_kz * (TNapj + TNapp2j + TNapm2j + TNapjp1 + TNapjm1 - Tphi)&
- - mu*kperp2**2 * moments_e(ip,ij,ikr,ikz,updatetlevel) &
- + mu_p * Hyper_diff_p + mu_j * Hyper_diff_j &
- + INV_LIN_SYS * TColl
+ !! Sum of all linear terms (the sign is inverted to match RHS)
+ moments_rhs_e(ip,ij,ikx,iky,iz,updatetlevel) = &
+ - Ckxky(ikx,iky,iz) * (Tnepj + Tnepp2j + Tnepm2j + Tnepjp1 + Tnepjm1)&
+ - Tpare/2._dp/deltaz/q0 &
+ + i_ky * Tphi &
+ - mu*kperp2**2 * moments_e(ip,ij,ikx,iky,iz,updatetlevel) &
+ + TColl
!! Adding non linearity
IF ( NON_LIN ) THEN
- moments_rhs_e(ip,ij,ikr,ikz,updatetlevel) = &
- moments_rhs_e(ip,ij,ikr,ikz,updatetlevel) + Sepj(ip,ij,ikr,ikz)
+ moments_rhs_e(ip,ij,ikx,iky,iz,updatetlevel) = &
+ moments_rhs_e(ip,ij,ikx,iky,iz,updatetlevel) + Sepj(ip,ij,ikx,iky,iz)
ENDIF
- END DO kzloope
- END DO krloope
+ END DO kyloope
+ END DO kxloope
+ END DO zloope
END DO jloope
END DO ploope
@@ -199,167 +135,104 @@ SUBROUTINE moments_eq_rhs_i
USE grid
USE model
USE prec_const
- USE utility, ONLY : is_nan
USE collision
IMPLICIT NONE
- INTEGER :: ip2, ij2, il, p_int, j_int, p2_int, j2_int ! loops indices and polynom. degrees
- REAL(dp) :: p_dp, j_dp, l_dp
- REAL(dp) :: kr, kz, kperp2
- REAL(dp) :: kernelj, kerneljp1, kerneljm1 ! Kernel functions and variable
- REAL(dp) :: xNapj, xNapp1j, xNapm1j, xNapp2j, xNapm2j, xNapjp1, xNapjm1 ! Mom. factors depending on the pj loop
- REAL(dp) :: xphij, xphijp1, xphijm1, xphijpar ! ESpot. factors depending on the pj loop
- REAL(dp) :: xCapj, xCa20, xCa01, xCa10 ! Coll. factors depending on the pj loop
- COMPLEX(dp) :: TNapj, TNapp1j, TNapm1j, TNapp2j, TNapm2j, TNapjp1, TNapjm1, Tphi
- COMPLEX(dp) :: TColl, TColl20, TColl01, TColl10 ! terms of the rhs
- COMPLEX(dp) :: i_kz, Hyper_diff_p, Hyper_diff_j
-
- LOGICAL :: COPY_CLOS = .false. ! To test closures
- ! LOGICAL :: COPY_CLOS = .true. ! To test closures
+ INTEGER :: p_int, j_int ! loops indices and polynom. degrees
+ REAL(dp) :: kx, ky, kperp2
+ COMPLEX(dp) :: Tnipj, Tnipp2j, Tnipm2j, Tnipjp1, Tnipjm1, Tpari, Tphi
+ COMPLEX(dp) :: TColl ! terms of the rhs
+ COMPLEX(dp) :: i_ky
+ REAL(dp) :: delta_p0, delta_p1, delta_p2
+ INTEGER :: izprev,iznext ! indices of previous and next z slice
! Measuring execution time
CALL cpu_time(t0_rhs)
ploopi : DO ip = ips_i, ipe_i ! Hermite loop
p_int= parray_i(ip) ! Hermite degree
- p_dp = REAL(p_int,dp) ! REAL of Hermite degree
- ! N_i^{p+1,j} coeff
- xNapp1j = sqrtTaui_qi * SQRT(p_dp + 1)
- ! N_i^{p-1,j} coeff
- xNapm1j = sqrtTaui_qi * SQRT(p_dp)
- ! x N_i^{p+2,j} coeff
- xNapp2j = taui_qi_etaB * SQRT((p_dp + 1._dp) * (p_dp + 2._dp))
- ! x N_i^{p-2,j} coeff
- xNapm2j = taui_qi_etaB * SQRT(p_dp * (p_dp - 1._dp))
+ delta_p0 = 0._dp; delta_p1 = 0._dp; delta_p2 = 0._dp
+ IF(p_int .EQ. 0) delta_p0 = 1._dp
+ IF(p_int .EQ. 1) delta_p1 = 1._dp
+ IF(p_int .EQ. 2) delta_p2 = 1._dp
jloopi : DO ij = ijs_i, ije_i ! This loop is from 1 to jmaxi+1
- j_int= jarray_i(ij) ! REALof Laguerre degree
- j_dp = REAL(j_int,dp) ! REALof Laguerre degree
-
- ! x N_i^{p,j+1} coeff
- xNapjp1 = -taui_qi_etaB * (j_dp + 1._dp)
- ! x N_i^{p,j-1} coeff
- xNapjm1 = -taui_qi_etaB * j_dp
- ! x N_i^{pj} coeff
- xNapj = taui_qi_etaB * 2._dp*(p_dp + j_dp + 1._dp)
-
- !! Collision operator pj terms
- xCapj = -nu_i*(p_dp + 2._dp*j_dp) !DK Lenard-Bernstein basis
- ! Dougherty part
- IF ( CO .EQ. -2) THEN
- IF ((p_int .EQ. 2) .AND. (j_int .EQ. 0)) THEN ! kronecker pj20
- xCa20 = nu_i * 2._dp/3._dp
- xCa01 = -SQRT2 * xCa20
- xCa10 = 0._dp
- ELSEIF ((p_int .EQ. 0) .AND. (j_int .EQ. 1)) THEN ! kronecker pj01
- xCa20 = -nu_i * SQRT2 * 2._dp/3._dp
- xCa01 = -SQRT2 * xCa20
- xCa10 = 0._dp
- ELSEIF ((p_int .EQ. 1) .AND. (j_int .EQ. 0)) THEN ! kronecker pj10
- xCa20 = 0._dp
- xCa01 = 0._dp
- xCa10 = nu_i
- ELSE
- xCa20 = 0._dp; xCa01 = 0._dp; xCa10 = 0._dp
- ENDIF
- ENDIF
-
- !! Electrostatic potential pj terms
- IF (p_int .EQ. 0) THEN ! krokecker p0
- xphij = (eta_n + 2._dp*j_dp*eta_T - 2._dp*eta_B*(j_dp+1._dp))
- xphijp1 = -(eta_T - eta_B)*(j_dp+1._dp)
- xphijm1 = -(eta_T - eta_B)* j_dp
- xphijpar = 0._dp
- ELSE IF (p_int .EQ. 1) THEN ! kronecker p1
- xphijpar = qi_sigmai_sqrtTaui
- xphij = 0._dp; xphijp1 = 0._dp; xphijm1 = 0._dp
- ELSE IF (p_int .EQ. 2) THEN !krokecker p2
- xphij = (eta_T/SQRT2 - SQRT2*eta_B)
- xphijp1 = 0._dp; xphijm1 = 0._dp; xphijpar = 0._dp
- ELSE
- xphij = 0._dp; xphijp1 = 0._dp; xphijm1 = 0._dp; xphijpar = 0._dp
- ENDIF
-
! Loop on kspace
- krloopi : DO ikr = ikrs,ikre
- kzloopi : DO ikz = ikzs,ikze
- kr = krarray(ikr) ! Poloidal wavevector
- kz = kzarray(ikz) ! Toroidal wavevector
- i_kz = imagu * kz ! Ddz derivative
- IF (Nkz .EQ. 1) i_kz = imagu * krarray(ikr) ! If 1D simulation we put kr as kz
- kperp2 = kr**2 + kz**2 ! perpendicular wavevector
+ zloopi : DO iz = izs,ize
+ ! Periodic BC for first order derivative
+ iznext = iz+1; izprev = iz-1;
+ IF(iz .EQ. 1) izprev = Nz
+ IF(iz .EQ. Nz) iznext = 1
+
+ kxloopi : DO ikx = ikxs,ikxe
+ kx = kxarray(ikx) ! radial wavevector
+ kyloopi : DO iky = ikys,ikye
+ ky = kyarray(iky) ! toroidal wavevector
+ i_ky = imagu * ky ! toroidal derivative
+ IF (Nky .EQ. 1) i_ky = imagu * kxarray(ikx) ! If 1D simulation we put kx as ky
+ kperp2 = kx**2 + ky**2 ! perpendicular wavevector
!! Compute moments mixing terms
- ! term propto N_i^{p,j}
- TNapj = xNapj * moments_i(ip,ij,ikr,ikz,updatetlevel)
- ! term propto N_i^{p+2,j}
- TNapp2j = xNapp2j * moments_i(ip+2,ij,ikr,ikz,updatetlevel)
- ! term propto N_i^{p-2,j}
- TNapm2j = xNapm2j * moments_i(ip-2,ij,ikr,ikz,updatetlevel)
- ! term propto N_i^{p,j+1}
- TNapjp1 = xNapjp1 * moments_i(ip,ij+1,ikr,ikz,updatetlevel)
- ! term propto N_i^{p,j-1}
- TNapjm1 = xNapjm1 * moments_i(ip,ij-1,ikr,ikz,updatetlevel)
-
- !! Collision
- IF (CO .EQ. 0) THEN ! Lenard Bernstein
- TColl = xCapj * moments_i(ip,ij,ikr,ikz,updatetlevel)
-
- ELSEIF (CO .EQ. -1) THEN ! DK Dougherty
- TColl20 = 0._dp; TColl01 = 0._dp; TColl10 = 0._dp
- IF ( (pmaxi .GE. 2) ) TColl20 = xCa20 * moments_i(3,1,ikr,ikz,updatetlevel)
- IF ( (jmaxi .GE. 1) ) TColl01 = xCa01 * moments_i(1,2,ikr,ikz,updatetlevel)
- IF ( (pmaxi .GE. 1) ) TColl10 = xCa10 * moments_i(2,1,ikr,ikz,updatetlevel)
- ! Total collisional term
- TColl = xCapj* moments_i(ip,ij,ikr,ikz,updatetlevel)&
- + TColl20 + TColl01 + TColl10
-
- ELSEIF (CO .EQ. 1) THEN ! GK Dougherty
- CALL DoughertyGK_i(ip,ij,ikr,ikz,TColl)
- ! CALL DoughertyGK(ip,ij,ikr,ikz,TColl,'i')
- ELSE! COSOLver matrix (Sugama, Coulomb)
- TColl = TColl_i(ip,ij,ikr,ikz)
- ENDIF
+ ! Perpendicular dynamic
+ ! term propto n_i^{p,j}
+ Tnipj = xnipj(ip,ij) * (moments_i(ip,ij,ikx,iky,iz,updatetlevel) &
+ +kernel_i(ij,ikx,iky)*qi_taui*phi(ikx,iky,iz)*delta_p0)
+ ! term propto n_i^{p+2,j}
+ Tnipp2j = xnipp2j(ip) * moments_i(ip+2,ij,ikx,iky,iz,updatetlevel)
+ ! term propto n_i^{p-2,j}
+ Tnipm2j = xnipm2j(ip) * (moments_i(ip-2,ij,ikx,iky,iz,updatetlevel) &
+ +kernel_i(ij,ikx,iky)*qi_taui*phi(ikx,iky,iz)*delta_p2)
+ ! term propto n_e^{p,j+1}
+ Tnipjp1 = xnipjp1(ij) * (moments_i(ip,ij+1,ikx,iky,iz,updatetlevel) &
+ +kernel_i(ij+1,ikx,iky)*qi_taui*phi(ikx,iky,iz)*delta_p0)
+ ! term propto n_e^{p,j-1}
+ Tnipjm1 = xnipjm1(ij) * (moments_i(ip,ij-1,ikx,iky,iz,updatetlevel) &
+ +kernel_i(ij-1,ikx,iky)*qi_taui*phi(ikx,iky,iz)*delta_p0)
+ ! Parallel dynamic
+ ! term propto N_i^{p,j+1}, centered FDF
+ Tpari = xnipp1j(ip) * &
+ (moments_i(ip+1,ij,ikx,iky,iznext,updatetlevel)&
+ -moments_i(ip+1,ij,ikx,iky,izprev,updatetlevel)) &
+ +xnipm1j(ip) * &
+ (moments_i(ip-1,ij,ikx,iky,iznext,updatetlevel)+qi_taui*kernel_i(ij,ikx,iky)*phi(ikx,iky,iznext)*delta_p1&
+ -moments_i(ip-1,ij,ikx,iky,izprev,updatetlevel)-qi_taui*kernel_i(ij,ikx,iky)*phi(ikx,iky,izprev)*delta_p1)
!! Electrical potential term
IF ( p_int .LE. 2 ) THEN ! kronecker p0 p1 p2
- Tphi = phi(ikr,ikz) * (xphij*kernel_i(ij, ikr, ikz) &
- + xphijp1*kernel_i(ij+1, ikr, ikz) &
- + xphijm1*kernel_i(ij-1, ikr, ikz) )
+ Tphi = phi(ikx,iky,iz) * (xphij(ip,ij)*kernel_i(ij, ikx, iky) &
+ + xphijp1(ip,ij)*kernel_i(ij+1, ikx, iky) &
+ + xphijm1(ip,ij)*kernel_i(ij-1, ikx, iky) )
ELSE
Tphi = 0._dp
ENDIF
- !! Kinetic hyperdiffusion
- Hyper_diff_p = 0._dp
- IF ( p_int .GE. 4 ) THEN
- Hyper_diff_p = (2._dp*p_dp)**2 *moments_i(ip-4,ij,ikr,ikz,updatetlevel)
- ENDIF
-
- Hyper_diff_j = 0._dp
- IF ( j_int .GE. 2 ) THEN
- DO il = 1,(ij-2)
- l_dp = real(il-1,dp)
- Hyper_diff_j = Hyper_diff_j + (j_dp-(l_dp+1_dp))*moments_i(ip,il,ikr,ikz,updatetlevel)
- ENDDO
+ !! Collision
+ IF (CO .EQ. 0) THEN ! Lenhard Bernstein
+ TColl = -nu_i*(ip+2._dp*ij-3)*moments_i(ip,ij,ikx,iky,iz,updatetlevel)
+ ELSEIF (CO .EQ. 1) THEN ! GK Dougherty
+ CALL DoughertyGK_i(ip,ij,ikx,iky,iz,TColl)
+ ELSE! COSOLver matrix (Sugama, Coulomb)
+ TColl = TColl_i(ip,ij,ikx,iky,iz)
ENDIF
!! Sum of linear terms
- moments_rhs_i(ip,ij,ikr,ikz,updatetlevel) = &
- -INV_LIN_SYS * i_kz * (TNapj + TNapp2j + TNapm2j + TNapjp1 + TNapjm1 - Tphi)&
- - mu*kperp2**2 * moments_i(ip,ij,ikr,ikz,updatetlevel) &
- + mu_p * Hyper_diff_p + mu_j * Hyper_diff_j &
- +INV_LIN_SYS * TColl
+ moments_rhs_i(ip,ij,ikx,iky,iz,updatetlevel) = &
+ - Ckxky(ikx,iky,iz) * (Tnipj + Tnipp2j + Tnipm2j + Tnipjp1 + Tnipjm1)&
+ - Tpari/2._dp/deltaz/q0 &
+ + i_ky * Tphi &
+ - mu*kperp2**2 * moments_i(ip,ij,ikx,iky,iz,updatetlevel) &
+ + TColl
!! Adding non linearity
IF ( NON_LIN ) THEN
- moments_rhs_i(ip,ij,ikr,ikz,updatetlevel) = &
- moments_rhs_i(ip,ij,ikr,ikz,updatetlevel) + Sipj(ip,ij,ikr,ikz)
+ moments_rhs_i(ip,ij,ikx,iky,iz,updatetlevel) = &
+ moments_rhs_i(ip,ij,ikx,iky,iz,updatetlevel) + Sipj(ip,ij,ikx,iky,iz)
ENDIF
- END DO kzloopi
- END DO krloopi
+ END DO kyloopi
+ END DO kxloopi
+ END DO zloopi
END DO jloopi
END DO ploopi
diff --git a/src/numerics.F90 b/src/numerics.F90
new file mode 100644
index 00000000..b7870565
--- /dev/null
+++ b/src/numerics.F90
@@ -0,0 +1,150 @@
+MODULE numerics
+ USE basic
+ USE prec_const
+ USE grid
+ USE utility
+ USE coeff
+ implicit none
+
+ PUBLIC :: compute_derivatives, build_dnjs_table, evaluate_kernels
+
+CONTAINS
+
+! Compute the 2D particle temperature for electron and ions (sum over Laguerre)
+SUBROUTINE compute_derivatives
+
+END SUBROUTINE compute_derivatives
+
+!******************************************************************************!
+!!!!!!! Build the Laguerre-Laguerre coupling coefficient table for nonlin
+!******************************************************************************!
+SUBROUTINE build_dnjs_table
+ USE array, Only : dnjs
+ USE coeff
+ IMPLICIT NONE
+
+ INTEGER :: in, ij, is, J
+ INTEGER :: n_, j_, s_
+
+ J = max(jmaxe,jmaxi)
+
+ DO in = 1,J+1 ! Nested dependent loops to make benefit from dnjs symmetry
+ n_ = in - 1
+ DO ij = in,J+1
+ j_ = ij - 1
+ DO is = ij,J+1
+ s_ = is - 1
+
+ dnjs(in,ij,is) = TO_DP(ALL2L(n_,j_,s_,0))
+ ! By symmetry
+ dnjs(in,is,ij) = dnjs(in,ij,is)
+ dnjs(ij,in,is) = dnjs(in,ij,is)
+ dnjs(ij,is,in) = dnjs(in,ij,is)
+ dnjs(is,ij,in) = dnjs(in,ij,is)
+ dnjs(is,in,ij) = dnjs(in,ij,is)
+ ENDDO
+ ENDDO
+ ENDDO
+END SUBROUTINE build_dnjs_table
+!******************************************************************************!
+
+!******************************************************************************!
+!!!!!!! Evaluate the kernels once for all
+!******************************************************************************!
+SUBROUTINE evaluate_kernels
+ USE basic
+ USE array, Only : kernel_e, kernel_i
+ USE grid
+ use model, ONLY : tau_e, tau_i, sigma_e, sigma_i, q_e, q_i, lambdaD, CLOS, sigmae2_taue_o2, sigmai2_taui_o2
+ IMPLICIT NONE
+
+ REAL(dp) :: factj, j_dp, j_int
+ REAL(dp) :: be_2, bi_2, alphaD
+ REAL(dp) :: kx, ky, kperp2
+
+ !!!!! Electron kernels !!!!!
+ !Precompute species dependant factors
+ factj = 1.0 ! Start of the recursive factorial
+ DO ij = 1, jmaxe+1
+ j_int = jarray_e(ij)
+ j_dp = REAL(j_int,dp) ! REAL of degree
+
+ ! Recursive factorial
+ IF (j_dp .GT. 0) THEN
+ factj = factj * j_dp
+ ELSE
+ factj = 1._dp
+ ENDIF
+
+ DO ikx = ikxs,ikxe
+ kx = kxarray(ikx)
+ DO iky = ikys,ikye
+ ky = kyarray(iky)
+
+ be_2 = (kx**2 + ky**2) * sigmae2_taue_o2
+
+ kernel_e(ij, ikx, iky) = be_2**j_int * exp(-be_2)/factj
+
+ ENDDO
+ ENDDO
+ ENDDO
+ ! Kernels closure
+ DO ikx = ikxs,ikxe
+ kx = kxarray(ikx)
+ DO iky = ikys,ikye
+ ky = kyarray(iky)
+ be_2 = (kx**2 + ky**2) * sigmae2_taue_o2
+ ! Kernel ghost + 1 with Kj+1 = y/(j+1) Kj (/!\ ij = j+1)
+ kernel_e(ijeg_e,ikx,iky) = be_2/(real(ijeg_e-1,dp))*kernel_e(ije_e,ikx,iky)
+ ! Kernel ghost - 1 with Kj-1 = j/y Kj(careful about the kperp=0)
+ IF ( be_2 .NE. 0 ) THEN
+ kernel_e(ijsg_e,ikx,iky) = (real(ijsg_e,dp))/be_2*kernel_e(ijs_e,ikx,iky)
+ ELSE
+ kernel_e(ijsg_e,ikx,iky) = 0._dp
+ ENDIF
+ ENDDO
+ ENDDO
+
+ !!!!! Ion kernels !!!!!
+ factj = 1.0 ! Start of the recursive factorial
+ DO ij = 1, jmaxi+1
+ j_int = jarray_e(ij)
+ j_dp = REAL(j_int,dp) ! REAL of degree
+
+ ! Recursive factorial
+ IF (j_dp .GT. 0) THEN
+ factj = factj * j_dp
+ ELSE
+ factj = 1._dp
+ ENDIF
+
+ DO ikx = ikxs,ikxe
+ kx = kxarray(ikx)
+ DO iky = ikys,ikye
+ ky = kyarray(iky)
+ bi_2 = (kx**2 + ky**2) * sigmai2_taui_o2
+ kernel_i(ij, ikx, iky) = bi_2**j_int * exp(-bi_2)/factj
+
+ ENDDO
+ ENDDO
+ ENDDO
+ ! Kernels closure
+ DO ikx = ikxs,ikxe
+ kx = kxarray(ikx)
+ DO iky = ikys,ikye
+ ky = kyarray(iky)
+ bi_2 = (kx**2 + ky**2) * sigmai2_taui_o2
+ ! Kernel ghost + 1 with Kj+1 = y/(j+1) Kj
+ kernel_i(ijeg_i,ikx,iky) = bi_2/(real(ijeg_i-1,dp))*kernel_i(ije_i,ikx,iky)
+ ! Kernel ghost - 1 with Kj-1 = j/y Kj(careful about the kperp=0)
+ IF ( bi_2 .NE. 0 ) THEN
+ kernel_i(ijsg_i,ikx,iky) = (real(ijsg_i,dp))/bi_2*kernel_i(ijs_i,ikx,iky)
+ ELSE
+ kernel_i(ijsg_i,ikx,iky) = 0._dp
+ ENDIF
+ ENDDO
+ ENDDO
+END SUBROUTINE evaluate_kernels
+!******************************************************************************!
+
+END MODULE numerics
diff --git a/src/poisson.F90 b/src/poisson.F90
index b4d39180..6ec3a2fd 100644
--- a/src/poisson.F90
+++ b/src/poisson.F90
@@ -20,7 +20,7 @@ SUBROUTINE poisson
REAL(dp) :: gammaD
COMPLEX(dp) :: gammaD_phi
INTEGER :: count !! mpi integer to broadcast the electric potential at the end
- COMPLEX(dp) :: buffer(ikrs:ikre,ikzs:ikze)
+ COMPLEX(dp) :: buffer(ikxs:ikxe,ikys:ikye)
!! Poisson can be solved only for process containing ip=1
IF ( (ips_e .EQ. 1) .AND. (ips_i .EQ. 1) ) THEN
@@ -28,48 +28,50 @@ SUBROUTINE poisson
! Execution time start
CALL cpu_time(t0_poisson)
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
-
- !!!!!!!!!!!!! Electrons sum(Kernel * Ne0n) (skm) and sum(Kernel**2) (sk2)
- sum_kernel_mom_e = 0._dp
- sum_kernel2_e = 0._dp
- ! loop over n only if the max polynomial degree
- DO ine=1,jmaxe+1 ! ine = n+1
- Kne = kernel_e(ine, ikr, ikz)
- sum_kernel_mom_e = sum_kernel_mom_e + Kne * moments_e(1, ine, ikr, ikz, updatetlevel)
- sum_kernel2_e = sum_kernel2_e + Kne**2 ! ... sum recursively ...
- END DO
-
- !!!!!!!!!!!!!!!!! Ions sum(Kernel * Ni0n) (skm) and sum(Kernel**2) (sk2)
- sum_kernel_mom_i = 0
- sum_kernel2_i = 0
+ kxloop: DO ikx = ikxs,ikxe
+ kyloop: DO iky = ikys,ikye
+ zloop: DO iz = izs,ize
+
+ !!!!!!!!!!!!! Electrons sum(Kernel * Ne0n) (skm) and sum(Kernel**2) (sk2)
+ sum_kernel_mom_e = 0._dp
+ sum_kernel2_e = 0._dp
! loop over n only if the max polynomial degree
- DO ini=1,jmaxi+1
- Kni = kernel_i(ini, ikr, ikz)
- sum_kernel_mom_i = sum_kernel_mom_i + Kni * moments_i(1, ini, ikr, ikz, updatetlevel)
- sum_kernel2_i = sum_kernel2_i + Kni**2 ! ... sum recursively ...
+ DO ine=1,jmaxe+1 ! ine = n+1
+ Kne = kernel_e(ine, ikx, iky)
+ sum_kernel_mom_e = sum_kernel_mom_e + Kne * moments_e(1, ine, ikx, iky, iz, updatetlevel)
+ sum_kernel2_e = sum_kernel2_e + Kne**2 ! ... sum recursively ...
END DO
- !!!!!!!!!!!!!!! Assembling the poisson equation !!!!!!!!!!!!!!!!!!!!!!!!!!
- alphaD = (krarray(ikr)**2 + kzarray(ikz)**2) * lambdaD**2
- gammaD = alphaD + qe2_taue * (1._dp - sum_kernel2_e) & ! Called Poisson_ in MOLI
- + qi2_taui * (1._dp - sum_kernel2_i)
+ !!!!!!!!!!!!!!!!! Ions sum(Kernel * Ni0n) (skm) and sum(Kernel**2) (sk2)
+ sum_kernel_mom_i = 0._dp
+ sum_kernel2_i = 0._dp
+ ! loop over n only if the max polynomial degree
+ DO ini=1,jmaxi+1
+ Kni = kernel_i(ini, ikx, iky)
+ sum_kernel_mom_i = sum_kernel_mom_i + Kni * moments_i(1, ini, ikx, iky, iz, updatetlevel)
+ sum_kernel2_i = sum_kernel2_i + Kni**2 ! ... sum recursively ...
+ END DO
+
+ !!!!!!!!!!!!!!! Assembling the poisson equation !!!!!!!!!!!!!!!!!!!!!!!!!!
+ alphaD = (kxarray(ikx)**2 + kyarray(iky)**2) * lambdaD**2
+ gammaD = alphaD + qe2_taue * (1._dp - sum_kernel2_e) & ! Called Poisson_ in MOLI
+ + qi2_taui * (1._dp - sum_kernel2_i)
- gammaD_phi = q_e * sum_kernel_mom_e + q_i * sum_kernel_mom_i
+ gammaD_phi = q_e * sum_kernel_mom_e + q_i * sum_kernel_mom_i
- phi(ikr, ikz) = gammaD_phi/gammaD
+ phi(ikx, iky, iz) = gammaD_phi/gammaD
- END DO
- END DO
+ END DO zloop
+ END DO kyloop
+ END DO kxloop
! Cancel origin singularity
- IF ((ikr_0 .GE. ikrs) .AND. (ikr_0 .LE. ikre)) phi(ikr_0,ikz_0) = 0
+ IF ((ikx_0 .GE. ikxs) .AND. (ikx_0 .LE. ikxe)) phi(ikx_0,iky_0,izs:ize) = 0._dp
ENDIF
! Transfer phi to all the others process along p
- CALL manual_2D_bcast(phi(ikrs:ikre,ikzs:ikze))
+ CALL manual_3D_bcast(phi(ikxs:ikxe,ikys:ikye,izs:ize))
! Execution time end
CALL cpu_time(t1_poisson)
diff --git a/src/ppinit.F90 b/src/ppinit.F90
index 1364ea92..9b8382b6 100644
--- a/src/ppinit.F90
+++ b/src/ppinit.F90
@@ -7,7 +7,7 @@ SUBROUTINE ppinit
INTEGER :: version_prov=-1
! Variables for cartesian domain decomposition
- INTEGER, PARAMETER :: ndims=2 ! p and kr
+ INTEGER, PARAMETER :: ndims=2 ! p and kx
INTEGER, DIMENSION(ndims) :: dims=0, coords=0, coords_L=0, coords_R=0
LOGICAL :: periods(ndims) = .FALSE., reorder=.FALSE.
CHARACTER(len=32) :: str
@@ -40,12 +40,12 @@ SUBROUTINE ppinit
END IF
num_procs_p = dims(1) ! Number of processes along p
- num_procs_kr = dims(2) ! Number of processes along kr
+ num_procs_kx = dims(2) ! Number of processes along kx
!
!periodicity in p
periods(1)=.FALSE.
- !periodicity in kr
+ !periodicity in kx
periods(2)=.FALSE.
CALL MPI_CART_CREATE(MPI_COMM_WORLD, ndims, dims, periods, reorder, comm0, ierr)
@@ -58,10 +58,10 @@ SUBROUTINE ppinit
! Partitions 2-dim cartesian topology of comm0 into 1-dim cartesian subgrids
!
CALL MPI_CART_SUB (comm0, (/.TRUE.,.FALSE./), comm_p, ierr)
- CALL MPI_CART_SUB (comm0, (/.FALSE.,.TRUE./), comm_kr, ierr)
+ CALL MPI_CART_SUB (comm0, (/.FALSE.,.TRUE./), comm_kx, ierr)
! Find id inside the sub communicators
CALL MPI_COMM_RANK(comm_p, rank_p, ierr)
- CALL MPI_COMM_RANK(comm_kr, rank_kr, ierr)
+ CALL MPI_COMM_RANK(comm_kx, rank_kx, ierr)
! Find neighbours
CALL MPI_CART_SHIFT(comm0, 0, 1, nbr_L, nbr_R, ierr)
CALL MPI_CART_SHIFT(comm0, 1, 1, nbr_B, nbr_T, ierr)
diff --git a/src/processing_mod.F90 b/src/processing_mod.F90
index 0cf497c7..129a4c17 100644
--- a/src/processing_mod.F90
+++ b/src/processing_mod.F90
@@ -19,41 +19,44 @@ SUBROUTINE compute_radial_ion_transport
USE time_integration, ONLY : updatetlevel
IMPLICIT NONE
COMPLEX(dp) :: pflux_local, gflux_local
- REAL(dp) :: kz_, buffer(1:2)
+ REAL(dp) :: ky_, buffer(1:2)
INTEGER :: i_, world_rank, world_size, root
pflux_local = 0._dp ! particle flux
gflux_local = 0._dp ! gyrocenter flux
IF(ips_i .EQ. 1) THEN
- ! Loop to compute gamma_kr = sum_kz sum_j -i k_z Kernel_j Ni00 * phi
- DO ikz = ikzs,ikze
- kz_ = kzarray(ikz)
- DO ikr = ikrs,ikre
- gflux_local = gflux_local - &
- imagu * kz_ * moments_i(1,1,ikr,ikz,updatetlevel) * CONJG(phi(ikr,ikz))
- DO ij = ijs_i, ije_i
- pflux_local = pflux_local - &
- imagu * kz_ * kernel_i(ij,ikr,ikz) * moments_i(1,ij,ikr,ikz,updatetlevel) * CONJG(phi(ikr,ikz))
- ENDDO
- ENDDO
+ ! Loop to compute gamma_kx = sum_ky sum_j -i k_z Kernel_j Ni00 * phi
+ DO iz = izs,ize
+ DO iky = ikys,ikye
+ ky_ = kyarray(iky)
+ DO ikx = ikxs,ikxe
+ gflux_local = gflux_local - &
+ imagu * ky_ * moments_i(1,1,ikx,iky,iz,updatetlevel) * CONJG(phi(ikx,iky,iz))
+ DO ij = ijs_i, ije_i
+ pflux_local = pflux_local - &
+ imagu * ky_ * kernel_i(ij,ikx,iky) * moments_i(1,ij,ikx,iky,iz,updatetlevel) * CONJG(phi(ikx,iky,iz))
+ ENDDO
+ ENDDO
+ ENDDO
ENDDO
+ gflux_local = gflux_local/Nz ! Average over parallel planes
+ pflux_local = pflux_local/Nz
buffer(1) = REAL(gflux_local)
buffer(2) = REAL(pflux_local)
-
root = 0
!Gather manually among the rank_p=0 processes and perform the sum
gflux_ri = 0
pflux_ri = 0
- IF (num_procs_kr .GT. 1) THEN
+ IF (num_procs_kx .GT. 1) THEN
!! Everyone sends its local_sum to root = 0
- IF (rank_kr .NE. root) THEN
- CALL MPI_SEND(buffer, 2 , MPI_DOUBLE_PRECISION, root, 1234, comm_kr, ierr)
+ IF (rank_kx .NE. root) THEN
+ CALL MPI_SEND(buffer, 2 , MPI_DOUBLE_PRECISION, root, 1234, comm_kx, ierr)
ELSE
! Recieve from all the other processes
- DO i_ = 0,num_procs_kr-1
- IF (i_ .NE. rank_kr) &
- CALL MPI_RECV(buffer, 2 , MPI_DOUBLE_PRECISION, i_, 1234, comm_kr, MPI_STATUS_IGNORE, ierr)
+ DO i_ = 0,num_procs_kx-1
+ IF (i_ .NE. rank_kx) &
+ CALL MPI_RECV(buffer, 2 , MPI_DOUBLE_PRECISION, i_, 1234, comm_kx, MPI_STATUS_IGNORE, ierr)
gflux_ri = gflux_ri + buffer(1)
pflux_ri = pflux_ri + buffer(2)
ENDDO
@@ -72,25 +75,27 @@ SUBROUTINE compute_density
IF( (ips_i .EQ. 1) .AND. (ips_e .EQ. 1) ) THEN
! Loop to compute dens_i = sum_j kernel_j Ni0j at each k
- DO ikz = ikzs,ikze
- DO ikr = ikrs,ikre
- ! electron density
- dens_e(ikr,ikz) = 0._dp
- DO ij = ijs_e, ije_e
- dens_e(ikr,ikz) = dens_e(ikr,ikz) + kernel_e(ij,ikr,ikz) * &
- (moments_e(1,ij,ikr,ikz,updatetlevel)+q_e/tau_e*kernel_e(ij,ikr,ikz)*phi(ikr,ikz))
- ENDDO
- ! ion density
- dens_i(ikr,ikz) = 0._dp
- DO ij = ijs_i, ije_i
- dens_i(ikr,ikz) = dens_i(ikr,ikz) + kernel_i(ij,ikr,ikz) * &
- (moments_i(1,ij,ikr,ikz,updatetlevel)+q_i/tau_i*kernel_i(ij,ikr,ikz)*phi(ikr,ikz))
+ DO iky = ikys,ikye
+ DO ikx = ikxs,ikxe
+ DO iz = izs,ize
+ ! electron density
+ dens_e(ikx,iky,iz) = 0._dp
+ DO ij = ijs_e, ije_e
+ dens_e(ikx,iky,iz) = dens_e(ikx,iky,iz) + kernel_e(ij,ikx,iky) * &
+ (moments_e(1,ij,ikx,iky,iz,updatetlevel)+q_e/tau_e*kernel_e(ij,ikx,iky)*phi(ikx,iky,iz))
+ ENDDO
+ ! ion density
+ dens_i(ikx,iky,iz) = 0._dp
+ DO ij = ijs_i, ije_i
+ dens_i(ikx,iky,iz) = dens_i(ikx,iky,iz) + kernel_i(ij,ikx,iky) * &
+ (moments_i(1,ij,ikx,iky,iz,updatetlevel)+q_i/tau_i*kernel_i(ij,ikx,iky)*phi(ikx,iky,iz))
+ ENDDO
ENDDO
ENDDO
ENDDO
ENDIF
- CALL manual_2D_bcast(dens_e(ikrs:ikre,ikzs:ikze))
- CALL manual_2D_bcast(dens_i(ikrs:ikre,ikzs:ikze))
+ CALL manual_3D_bcast(dens_e(ikxs:ikxe,ikys:ikye,izs:ize))
+ CALL manual_3D_bcast(dens_i(ikxs:ikxe,ikys:ikye,izs:ize))
END SUBROUTINE compute_density
! Compute the 2D particle temperature for electron and ions (sum over Laguerre)
@@ -105,32 +110,34 @@ SUBROUTINE compute_temperature
IF( ((ips_i .EQ. 1) .AND. (ips_e .EQ. 1)) ) THEN
! Loop to compute T = 1/3*(Tpar + 2Tperp)
- DO ikz = ikzs,ikze
- DO ikr = ikrs,ikre
- ! electron temperature
- temp_e(ikr,ikz) = 0._dp
- DO ij = ijs_e, ije_e
- j_dp = REAL(ij-1,dp)
- temp_e(ikr,ikz) = temp_e(ikr,ikz) + &
- 2._dp/3._dp * (2._dp*j_dp*kernel_e(ij,ikr,ikz) - (j_dp+1)*kernel_e(ij+1,ikr,ikz) - j_dp*kernel_e(ij-1,ikr,ikz))&
- * (moments_e(1,ij,ikr,ikz,updatetlevel)+q_e/tau_e*kernel_e(ij,ikr,ikz)*phi(ikr,ikz)) + &
- SQRT2/3._dp * kernel_e(ij,ikr,ikz) * moments_e(3,ij,ikr,ikz,updatetlevel)
- ENDDO
+ DO iky = ikys,ikye
+ DO ikx = ikxs,ikxe
+ DO iz = izs,ize
+ ! electron temperature
+ temp_e(ikx,iky,iz) = 0._dp
+ DO ij = ijs_e, ije_e
+ j_dp = REAL(ij-1,dp)
+ temp_e(ikx,iky,iz) = temp_e(ikx,iky,iz) + &
+ 2._dp/3._dp * (2._dp*j_dp*kernel_e(ij,ikx,iky) - (j_dp+1)*kernel_e(ij+1,ikx,iky) - j_dp*kernel_e(ij-1,ikx,iky))&
+ * (moments_e(1,ij,ikx,iky,iz,updatetlevel)+q_e/tau_e*kernel_e(ij,ikx,iky)*phi(ikx,iky,iz)) + &
+ SQRT2/3._dp * kernel_e(ij,ikx,iky) * moments_e(3,ij,ikx,iky,iz,updatetlevel)
+ ENDDO
- ! ion temperature
- temp_i(ikr,ikz) = 0._dp
- DO ij = ijs_i, ije_i
- j_dp = REAL(ij-1,dp)
- temp_i(ikr,ikz) = temp_i(ikr,ikz) + &
- 2._dp/3._dp * (2._dp*j_dp*kernel_i(ij,ikr,ikz) - (j_dp+1)*kernel_i(ij+1,ikr,ikz) - j_dp*kernel_i(ij-1,ikr,ikz))&
- * (moments_i(1,ij,ikr,ikz,updatetlevel)+q_i/tau_i*kernel_i(ij,ikr,ikz)*phi(ikr,ikz)) + &
- SQRT2/3._dp * kernel_i(ij,ikr,ikz) * moments_i(3,ij,ikr,ikz,updatetlevel)
+ ! ion temperature
+ temp_i(ikx,iky,iz) = 0._dp
+ DO ij = ijs_i, ije_i
+ j_dp = REAL(ij-1,dp)
+ temp_i(ikx,iky,iz) = temp_i(ikx,iky,iz) + &
+ 2._dp/3._dp * (2._dp*j_dp*kernel_i(ij,ikx,iky) - (j_dp+1)*kernel_i(ij+1,ikx,iky) - j_dp*kernel_i(ij-1,ikx,iky))&
+ * (moments_i(1,ij,ikx,iky,iz,updatetlevel)+q_i/tau_i*kernel_i(ij,ikx,iky)*phi(ikx,iky,iz)) + &
+ SQRT2/3._dp * kernel_i(ij,ikx,iky) * moments_i(3,ij,ikx,iky,iz,updatetlevel)
+ ENDDO
ENDDO
ENDDO
ENDDO
ENDIF
- CALL manual_2D_bcast(temp_e(ikrs:ikre,ikzs:ikze))
- CALL manual_2D_bcast(temp_i(ikrs:ikre,ikzs:ikze))
+ CALL manual_3D_bcast(temp_e(ikxs:ikxe,ikys:ikye,izs:ize))
+ CALL manual_3D_bcast(temp_i(ikxs:ikxe,ikys:ikye,izs:ize))
END SUBROUTINE compute_temperature
END MODULE processing
diff --git a/src/restarts_mod.F90 b/src/restarts_mod.F90
index f3f14e9d..f1c3e293 100644
--- a/src/restarts_mod.F90
+++ b/src/restarts_mod.F90
@@ -12,8 +12,8 @@ INTEGER :: rank, sz_, n_
INTEGER :: dims(1) = (/0/)
CHARACTER(LEN=50) :: dset_name
INTEGER :: pmaxe_cp, jmaxe_cp, pmaxi_cp, jmaxi_cp, n0
-COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: moments_e_cp
-COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: moments_i_cp
+COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_e_cp
+COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_i_cp
PUBLIC :: load_moments
@@ -68,9 +68,9 @@ CONTAINS
! Read state of system from checkpoint file
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_
- CALL getarrnd(fidrst, dset_name, moments_e(ips_e:ipe_e, ijs_e:ije_e, ikrs:ikre, ikzs:ikze, 1),(/1,3/))
+ CALL getarrnd(fidrst, dset_name, moments_e(ips_e:ipe_e, ijs_e:ije_e, ikxs:ikxe, ikys:ikye, izs:ize, 1),(/1,3/))
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_i", n_
- CALL getarrnd(fidrst, dset_name, moments_i(ips_i:ipe_i, ijs_i:ije_i, ikrs:ikre, ikzs:ikze, 1),(/1,3/))
+ CALL getarrnd(fidrst, dset_name, moments_i(ips_i:ipe_i, ijs_i:ije_i, ikxs:ikxe, ikys:ikye, izs:ize, 1),(/1,3/))
CALL closef(fidrst)
@@ -103,8 +103,8 @@ CONTAINS
CALL getatt(fidrst,"/data/input/" , "start_iframe5d", n0)
! Allocate the required size to load checkpoints moments
- CALL allocate_array(moments_e_cp, 1,pmaxe_cp+1, 1,jmaxe_cp+1, ikrs,ikre, ikzs,ikze)
- CALL allocate_array(moments_i_cp, 1,pmaxi_cp+1, 1,jmaxi_cp+1, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(moments_e_cp, 1,pmaxe_cp+1, 1,jmaxe_cp+1, ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array(moments_i_cp, 1,pmaxi_cp+1, 1,jmaxi_cp+1, ikxs,ikxe, ikys,ikye, izs,ize)
! Find the last results of the checkpoint file by iteration
n_ = n0+1
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_ ! start with moments_e/000001
@@ -116,18 +116,20 @@ CONTAINS
! Read state of system from checkpoint file and load every moment to change the distribution
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_
- CALL getarrnd(fidrst, dset_name, moments_e_cp(1:pmaxe_cp+1, 1:jmaxe_cp+1, ikrs:ikre, ikzs:ikze),(/1,3/))
+ CALL getarrnd(fidrst, dset_name, moments_e_cp(1:pmaxe_cp+1, 1:jmaxe_cp+1, ikxs:ikxe, ikys:ikye, izs:ize),(/1,3/))
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_i", n_
- CALL getarrnd(fidrst, dset_name, moments_i_cp(1:pmaxi_cp+1, 1:jmaxi_cp+1, ikrs:ikre, ikzs:ikze),(/1,3/))
+ CALL getarrnd(fidrst, dset_name, moments_i_cp(1:pmaxi_cp+1, 1:jmaxi_cp+1, ikxs:ikxe, ikys:ikye, izs:ize),(/1,3/))
! Initialize simulation moments array with checkpoints ones
! (they may have a larger number of polynomials, set to 0 at the begining)
moments_e = 0._dp; moments_i = 0._dp
DO ip=ips_e,ipe_e
DO ij=ijs_e,ije_e
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_e(ip,ij,ikr,ikz,:) = moments_e_cp(ip,ij,ikr,ikz)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz = izs,ize
+ moments_e(ip,ij,ikx,iky,iz,:) = moments_e_cp(ip,ij,ikx,iky,iz)
+ ENDDO
ENDDO
ENDDO
ENDDO
@@ -135,9 +137,11 @@ CONTAINS
DO ip=1,pmaxi_cp+1
DO ij=1,jmaxi_cp+1
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_i(ip,ij,ikr,ikz,:) = moments_i_cp(ip,ij,ikr,ikz)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz = izs,ize
+ moments_i(ip,ij,ikx,iky,iz,:) = moments_i_cp(ip,ij,ikx,iky,iz)
+ ENDDO
ENDDO
ENDDO
ENDDO
@@ -183,8 +187,8 @@ CONTAINS
IF (my_id .EQ. 0) WRITE(*,*) "Je_cp = ", jmaxe_cp
! Allocate the required size to load checkpoints moments
- CALL allocate_array(moments_e_cp, 1,pmaxe_cp+1, 1,jmaxe_cp+1, ikrs,ikre, ikzs,ikze)
- CALL allocate_array(moments_i_cp, 1,pmaxi_cp+1, 1,jmaxi_cp+1, ikrs,ikre, ikzs,ikze)
+ CALL allocate_array(moments_e_cp, 1,pmaxe_cp+1, 1,jmaxe_cp+1, ikxs,ikxe, ikys,ikye, izs,ize)
+ CALL allocate_array(moments_i_cp, 1,pmaxi_cp+1, 1,jmaxi_cp+1, ikxs,ikxe, ikys,ikye, izs,ize)
! Find the last results of the checkpoint file by iteration
n_ = 0
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/moments_e", n_ ! start with moments_e/000000
@@ -196,20 +200,22 @@ CONTAINS
! Read state of system from checkpoint file
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/moments_e", n_
- CALL getarr(fidrst, dset_name, moments_e_cp(1:pmaxe_cp+1, 1:jmaxe_cp+1, ikrs:ikre, ikzs:ikze),pardim=3)
+ CALL getarr(fidrst, dset_name, moments_e_cp(1:pmaxe_cp+1, 1:jmaxe_cp+1, ikxs:ikxe, ikys:ikye, izs:ize),pardim=3)
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/moments_i", n_
- CALL getarr(fidrst, dset_name, moments_i_cp(1:pmaxi_cp+1, 1:jmaxi_cp+1, ikrs:ikre, ikzs:ikze),pardim=3)
+ CALL getarr(fidrst, dset_name, moments_i_cp(1:pmaxi_cp+1, 1:jmaxi_cp+1, ikxs:ikxe, ikys:ikye, izs:ize),pardim=3)
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/phi", n_
- CALL getarr(fidrst, dset_name, phi(ikrs:ikre,ikzs:ikze),pardim=1)
+ CALL getarr(fidrst, dset_name, phi(ikxs:ikxe,ikys:ikye,izs:ize),pardim=1)
! Initialize simulation moments array with checkpoints ones
! (they may have a larger number of polynomials, set to 0 at the begining)
moments_e = 0._dp; moments_i = 0._dp
DO ip=1,pmaxe_cp+1
DO ij=1,jmaxe_cp+1
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_e(ip,ij,ikr,ikz,:) = moments_e_cp(ip,ij,ikr,ikz)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz = izs,ize
+ moments_e(ip,ij,ikx,iky,iz,:) = moments_e_cp(ip,ij,ikx,iky,iz)
+ ENDDO
ENDDO
ENDDO
ENDDO
@@ -217,9 +223,11 @@ CONTAINS
DO ip=1,pmaxi_cp+1
DO ij=1,jmaxi_cp+1
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_i(ip,ij,ikr,ikz,:) = moments_i_cp(ip,ij,ikr,ikz)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz = izs,ize
+ moments_i(ip,ij,ikx,iky,iz,:) = moments_i_cp(ip,ij,ikx,iky,iz)
+ ENDDO
ENDDO
ENDDO
ENDDO
diff --git a/src/stepon.F90 b/src/stepon.F90
index 2ef08caa..2f2d8a7e 100644
--- a/src/stepon.F90
+++ b/src/stepon.F90
@@ -56,19 +56,19 @@ SUBROUTINE stepon
! Execution time start
CALL cpu_time(t0_checkfield)
- IF ( (ikrs .EQ. 1) .AND. (NON_LIN) ) CALL enforce_symetry() ! Enforcing symmetry on kr = 0
+ IF ( (ikxs .EQ. 1) .AND. (NON_LIN) ) CALL enforce_symetry() ! Enforcing symmetry on kx = 0
mlend=.FALSE.
IF(.NOT.nlend) THEN
mlend=mlend .or. checkfield(phi,' phi')
DO ip=ips_e,ipe_e
DO ij=ijs_e,ije_e
- mlend=mlend .or. checkfield(moments_e(ip,ij,:,:,updatetlevel),' moments_e')
+ mlend=mlend .or. checkfield(moments_e(ip,ij,:,:,:,updatetlevel),' moments_e')
ENDDO
ENDDO
DO ip=ips_i,ipe_i
DO ij=ijs_i,ije_i
- mlend=mlend .or. checkfield(moments_i(ip,ij,:,:,updatetlevel),' moments_i')
+ mlend=mlend .or. checkfield(moments_i(ip,ij,:,:,:,updatetlevel),' moments_i')
ENDDO
ENDDO
CALL MPI_ALLREDUCE(mlend, nlend, 1, MPI_LOGICAL, MPI_LOR, MPI_COMM_WORLD, ierr)
@@ -82,18 +82,22 @@ SUBROUTINE stepon
SUBROUTINE anti_aliasing
DO ip=ips_e,ipe_e
DO ij=ijs_e,ije_e
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_e( ip,ij,ikr,ikz,:) = AA_r(ikr)* AA_z(ikz) * moments_e( ip,ij,ikr,ikz,:)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ moments_e( ip,ij,ikx,iky,iz,:) = AA_x(ikx)* AA_y(iky) * moments_e( ip,ij,ikx,iky,iz,:)
+ END DO
END DO
END DO
END DO
END DO
DO ip=ips_i,ipe_i
DO ij=ijs_i,ije_i
- DO ikr=ikrs,ikre
- DO ikz=ikzs,ikze
- moments_i( ip,ij,ikr,ikz,:) = AA_r(ikr)* AA_z(ikz) * moments_i( ip,ij,ikr,ikz,:)
+ DO ikx=ikxs,ikxe
+ DO iky=ikys,ikye
+ DO iz=izs,ize
+ moments_i( ip,ij,ikx,iky,iz,:) = AA_x(ikx)* AA_y(iky) * moments_i( ip,ij,ikx,iky,iz,:)
+ END DO
END DO
END DO
END DO
@@ -101,33 +105,37 @@ SUBROUTINE stepon
END SUBROUTINE anti_aliasing
SUBROUTINE enforce_symetry ! Force X(k) = X(N-k)* complex conjugate symmetry
- IF ( contains_kr0 ) THEN
+ IF ( contains_kx0 ) THEN
! Electron moments
DO ip=ips_e,ipe_e
DO ij=ijs_e,ije_e
- DO ikz=2,Nkz/2 !symmetry at kr = 0
- moments_e( ip,ij,ikr_0,ikz, :) = CONJG(moments_e( ip,ij,ikr_0,Nkz+2-ikz, :))
+ DO iz=izs,ize
+ DO iky=2,Nky/2 !symmetry at kx = 0
+ moments_e( ip,ij,ikx_0,iky,iz, :) = CONJG(moments_e( ip,ij,ikx_0,Nky+2-iky,iz, :))
+ END DO
+ ! must be real at origin
+ moments_e(ip,ij, ikx_0,iky_0,iz, :) = REAL(moments_e(ip,ij, ikx_0,iky_0,iz, :))
END DO
- ! must be real at origin
- moments_e(ip,ij, ikr_0,ikz_0, :) = REAL(moments_e(ip,ij, ikr_0,ikz_0, :))
END DO
END DO
! Ion moments
DO ip=ips_i,ipe_i
DO ij=ijs_i,ije_i
- DO ikz=2,Nkz/2 !symmetry at kr = 0
- moments_i( ip,ij,ikr_0,ikz, :) = CONJG(moments_i( ip,ij,ikr_0,Nkz+2-ikz, :))
+ DO iz=izs,ize
+ DO iky=2,Nky/2 !symmetry at kx = 0
+ moments_i( ip,ij,ikx_0,iky,iz, :) = CONJG(moments_i( ip,ij,ikx_0,Nky+2-iky,iz, :))
+ END DO
+ ! must be real at origin and top right
+ moments_i(ip,ij, ikx_0,iky_0,iz, :) = REAL(moments_i(ip,ij, ikx_0,iky_0,iz, :))
END DO
- ! must be real at origin and top right
- moments_i(ip,ij, ikr_0,ikz_0, :) = REAL(moments_i(ip,ij, ikr_0,ikz_0, :))
END DO
END DO
! Phi
- DO ikz=2,Nkz/2 !symmetry at kr = 0
- phi(ikr_0,ikz) = phi(ikr_0,Nkz+2-ikz)
+ DO iky=2,Nky/2 !symmetry at kx = 0
+ phi(ikx_0,iky,:) = phi(ikx_0,Nky+2-iky,:)
END DO
! must be real at origin
- phi(ikr_0,ikz_0) = REAL(phi(ikr_0,ikz_0))
+ phi(ikx_0,iky_0,:) = REAL(phi(ikx_0,iky_0,:))
ENDIF
END SUBROUTINE enforce_symetry
diff --git a/src/utility_mod.F90 b/src/utility_mod.F90
index b044ce6d..a295575e 100644
--- a/src/utility_mod.F90
+++ b/src/utility_mod.F90
@@ -4,7 +4,7 @@ MODULE utility
use prec_const
IMPLICIT NONE
- PUBLIC :: manual_2D_bcast
+ PUBLIC :: manual_2D_bcast, manual_3D_bcast
CONTAINS
@@ -59,7 +59,7 @@ CONTAINS
use prec_const
IMPLICIT NONE
- COMPLEX(dp), DIMENSION(ikrs:ikre,ikzs:ikze), INTENT(IN) :: field
+ COMPLEX(dp), DIMENSION(ikxs:ikxe,ikys:ikye), INTENT(IN) :: field
CHARACTER(LEN=*), INTENT(IN) :: str
LOGICAL :: mlend
COMPLEX(dp) :: sumfield
@@ -75,8 +75,8 @@ CONTAINS
SUBROUTINE manual_2D_bcast(field_)
USE grid
IMPLICIT NONE
- COMPLEX(dp), INTENT(INOUT) :: field_(ikrs:ikre,ikzs:ikze)
- COMPLEX(dp) :: buffer(ikrs:ikre,ikzs:ikze)
+ COMPLEX(dp), INTENT(INOUT) :: field_(ikxs:ikxe,ikys:ikye)
+ COMPLEX(dp) :: buffer(ikxs:ikxe,ikys:ikye)
INTEGER :: i_, root, world_rank, world_size
root = 0;
CALL MPI_COMM_RANK(comm_p,world_rank,ierr)
@@ -85,27 +85,68 @@ CONTAINS
!! Broadcast phi to the other processes on the same k range (communicator along p)
IF (world_rank .EQ. root) THEN
! Fill the buffer
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- buffer(ikr,ikz) = field_(ikr,ikz)
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ buffer(ikx,iky) = field_(ikx,iky)
ENDDO
ENDDO
! Send it to all the other processes
DO i_ = 0,num_procs_p-1
IF (i_ .NE. world_rank) &
- CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, comm_p, ierr)
+ CALL MPI_SEND(buffer, local_nkx * Nky , MPI_DOUBLE_COMPLEX, i_, 0, comm_p, ierr)
ENDDO
ELSE
! Recieve buffer from root
- CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, comm_p, MPI_STATUS_IGNORE, ierr)
+ CALL MPI_RECV(buffer, local_nkx * Nky , MPI_DOUBLE_COMPLEX, root, 0, comm_p, MPI_STATUS_IGNORE, ierr)
! Write it in phi
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- field_(ikr,ikz) = buffer(ikr,ikz)
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ field_(ikx,iky) = buffer(ikx,iky)
ENDDO
ENDDO
ENDIF
ENDIF
END SUBROUTINE manual_2D_bcast
+ !!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
+SUBROUTINE manual_3D_bcast(field_)
+ USE grid
+ IMPLICIT NONE
+ COMPLEX(dp), INTENT(INOUT) :: field_(ikxs:ikxe,ikys:ikye,izs:ize)
+ COMPLEX(dp) :: buffer(ikxs:ikxe,ikys:ikye,izs:ize)
+ INTEGER :: i_, root, world_rank, world_size
+ root = 0;
+ CALL MPI_COMM_RANK(comm_p,world_rank,ierr)
+ CALL MPI_COMM_SIZE(comm_p,world_size,ierr)
+ IF (world_size .GT. 1) THEN
+ !! Broadcast phi to the other processes on the same k range (communicator along p)
+ IF (world_rank .EQ. root) THEN
+ ! Fill the buffer
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ DO iz = izs,ize
+ buffer(ikx,iky,iz) = field_(ikx,iky,iz)
+ ENDDO
+ ENDDO
+ ENDDO
+ ! Send it to all the other processes
+ DO i_ = 0,num_procs_p-1
+ IF (i_ .NE. world_rank) &
+ CALL MPI_SEND(buffer, local_nkx * Nky * Nz, MPI_DOUBLE_COMPLEX, i_, 0, comm_p, ierr)
+ ENDDO
+ ELSE
+ ! Recieve buffer from root
+ CALL MPI_RECV(buffer, local_nkx * Nky * Nz, MPI_DOUBLE_COMPLEX, root, 0, comm_p, MPI_STATUS_IGNORE, ierr)
+ ! Write it in phi
+ DO ikx = ikxs,ikxe
+ DO iky = ikys,ikye
+ DO iz = izs,ize
+ field_(ikx,iky,iz) = buffer(ikx,iky,iz)
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDIF
+ ENDIF
+END SUBROUTINE manual_3D_bcast
+
END MODULE utility
diff --git a/wk/HD_study.m b/wk/HD_study.m
deleted file mode 100644
index 14951e8d..00000000
--- a/wk/HD_study.m
+++ /dev/null
@@ -1,88 +0,0 @@
-% bursts simulations
-b_=[...
- 5e-1, 5e+0;...
- 1e-1, 1e-1;...
- 1e-1, 3e-2;...
- 1e-1, 2e-2;...
- 1e-1, 1e-2;...
- 5e-2, 3e-3;...
- 5e-2, 2e-3;...
- 1e-2, 3e-3;...
- 1e-3, 2e-2;...
- ];
-% converged plateau simulations
-cp_=[...
- 1e+0, 1e-2;...
- 1e+0, 3e-3;...
- 1e+0, 2e-3;...
- 1e-1, 2e-3;...
- 1e-1, 1e-3;...
- ];
-% moving plateau
-dp_=[...
- 1e+0, 5e+0;...
- 1e+0, 2e+0;...
- 1e+0, 1e+0;...
- 1e-3, 2e-2;...
- 1e-3, 1e-2;...
- 1e-3, 5e-3;...
- 1e-3, 2.5e-3,...
- ];
-% not sure
-rp_=[...
- 5e-2, 1e-3;...
- 1e-2, 1e-3;...
- 1e-2, 1e-4;...
- ];
-figure; set(gcf, 'Position', [100, 100, 900, 400])
-grid on; xlim([5e-4,5e0]); ylim([5e-5,5e+0]);
-set(gca, 'XScale', 'log'); set(gca, 'YScale', 'log');
-xlabel('$\nu_{DGGK}$'); ylabel('$\mu_{HD}$'); hold on;
-
-% Trajectory of simulations
-
-% HD_study/200x100_L_200_P_2_J_1_eta_0.6_nu_1e+00_DGGK_CLOS_0_mu_1e-02/
-mu_ = [0 1 2 5 5];
-nu_ = [1 1 1 1 0.5];
-plot(nu_,mu_,'x--','DisplayName','N=200, L=050, P,J=2,1');
-
-% HD_study/300x150_L_200_P_2_J_1_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_1e-02/
-mu_ = [1e-2 1e-3];
-nu_ = [1e-1 1e-1];
-plot(nu_,mu_,'x--','DisplayName','N=300, L=100, P,J=2,1');
-
-% Trajectory of simulations
-% HD_study/100x50_L_50_P_2_J_1_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_1e-02/
-mu_ = [1e-2 5e-3 2e-3];
-nu_ = [1e-1 1e-1 1e-1];
-plot(nu_,mu_,'x-','DisplayName','N=100, L=050, P,J=2,1');
-
-% HD_study/150x75_L_100_P_2_J_1_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_3e-02/
-mu_ = [3e-2 1e-3 0];
-nu_ = [1e-1 1e-1 1e-1];
-plot(nu_,mu_,'x--','DisplayName','N=150, L=100, P,J=2,1');
-
-% HD_study/150x75_L_100_P_2_J_1_eta_0.6_nu_1e-02_DGGK_CLOS_0_mu_3e-02/
-mu_ = [3e-3 1e-3 1e-4];
-nu_ = [1e-2 1e-2 1e-2];
-plot(nu_,mu_,'x--','DisplayName','N=150, L=100, P,J=2,1');
-
-% HD_study/150x75_L_100_P_2_J_1_eta_0.6_nu_5e-02_DGGK_CLOS_0_mu_3e-02/
-mu_ = [3e-3 1e-3];
-nu_ = [5e-2 5e-2];
-plot(nu_,mu_,'x--','DisplayName','N=150, L=100, P,J=2,1');
-
-scatter( b_(:,1), b_(:,2),'o',...
- 'MarkerFaceColor',[0.6350 0.0780 0.1840],'MarkerEdgeColor',[0 0 0],'SizeData',50,...
- 'DisplayName','Bursts');
-scatter(cp_(:,1),cp_(:,2),'s',...
- 'MarkerFaceColor',[0.4660 0.6740 0.1880],'MarkerEdgeColor',[0 0 0],'SizeData',50,...
- 'DisplayName','Converged Plateau');
-scatter(dp_(:,1),dp_(:,2),'v',...
- 'MarkerFaceColor',[0.4660 0.6740 0.1880],'MarkerEdgeColor',[0 0 0],'SizeData',50,...
- 'DisplayName','Moving Plateau');
-scatter(rp_(:,1),rp_(:,2),'h',...
- 'MarkerFaceColor',[0.9290 0.6940 0.1250],'MarkerEdgeColor',[0 0 0],'SizeData',50,...
- 'DisplayName','not sure');
-% plot([1 1],[5e-5 5e-1],'--','Color',[0.4660 0.6740 0.1880]);
-legend('show','Location','Eastoutside')
\ No newline at end of file
diff --git a/wk/ZF_fourier_analysis.m b/wk/ZF_fourier_analysis.m
index d5833371..da4cf878 100644
--- a/wk/ZF_fourier_analysis.m
+++ b/wk/ZF_fourier_analysis.m
@@ -9,7 +9,7 @@ set(gcf, 'Position', [100, 100, 800, 400])
% Time series analysis (burst period and time frequencies spectrum)
subplot(121)
samplerate = Ts0D(2)-Ts0D(1);
- Y = log(PGAMMA_RI(its0D:ite0D)*(2*pi/Nr/Nz)^2);
+ Y = log(PGAMMA_RI(its0D:ite0D)*(2*pi/Nx/Ny)^2);
[n,~] = size(Y);
Yy= fft(Y);
Pot = Yy .* conj(Yy) / n;
@@ -35,13 +35,20 @@ set(gcf, 'Position', [100, 100, 800, 400])
[amax, ikZF] = max(mean(Pot,2));
% pclr = pcolor(NN(1:nmax,:),TT(1:nmax,:),Pot(1:nmax,:)); set(pclr, 'edgecolor','none'); hold on;
plot(0:nmax,mean(Pot(1:nmax+1,:),2)/amax,'DisplayName','$\langle\partial_r\phi\rangle_z (k_r)$'); hold on;
- plot([ikZF-1,ikZF-1],[0,1],'--k', 'DisplayName',['$L_z=',num2str(2*pi/kr(ikZF)),'\rho_s$']);
+ plot([ikZF-1,ikZF-1],[0,1],'--k', 'DisplayName',['$L_z=',num2str(2*pi/kx(ikZF)),'\rho_s$']);
grid on; box on;
title('ZF spatial spectrum')
xlabel('radial mode number'); yticks([]); legend('show')
save_figure
%% Pred-Pray phase space (A Zonal Flow review, Diamond 2005, Fig 15, Kobayashi 2015)
+
+E_turb = zeros(1,Ns2D); % Time evol. of the turbulence energy (Pred in Kobayashi 2015)
+E_ZF = zeros(1,Ns2D); % Time evol. of the ZF energy (Pray in Kobayashi 2015)
+for it = 1:numel(Ts2D)
+ E_turb(it) = sum(sum((1+kx.^2+ky.^2).*abs(PHI(:,:,it)).^2))- sum((1+kx.^2).*abs(PHI(:,1,it)).^2);
+ E_ZF(it) = kx(ikZF)^2*abs(PHI(ikZF,1,it)).^2;
+end
fig = figure; FIGNAME = ['phi_shear_phase_space_',PARAMS];
set(gcf, 'Position', [100, 100, 700, 500])
scatter(E_ZF*SCALE,E_turb*SCALE,35,Ts2D,'.',...
@@ -75,10 +82,10 @@ end
PHI_NZ = PHI;
PHI_NZ(ikZF-1:ikZF+1,:,:) = 0;
-phi_nz = zeros(Nr,Nz,Ns2D);
+phi_nz = zeros(Nx,Ny,Ns2D);
for it = 1:numel(Ts2D)
PH_ = PHI_NZ(:,:,it);
- phi_nz (:,:,it) = real(fftshift(ifft2((PH_),Nr,Nz)));
+ phi_nz (:,:,it) = real(fftshift(ifft2((PH_),Nx,Ny)));
end
%%
t0 = 1000;
@@ -91,6 +98,6 @@ if 0
%% Phi non zonal real space
GIFNAME = ['phi_nz',sprintf('_%.2d',JOBNUM),'_',PARAMS];INTERP = 0;
FIELD = real(phi_nz); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
-FIELDNAME = '$\phi_{NZ}$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
+FIELDNAME = '$\phi_{Ny}$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
create_gif
end
\ No newline at end of file
diff --git a/wk/analysis_1D.m b/wk/analysis_1D.m
index 9076e856..bcfffa57 100644
--- a/wk/analysis_1D.m
+++ b/wk/analysis_1D.m
@@ -9,30 +9,30 @@ Ts2D = Ts2D';
Ns = numel(Ts2D);
dt_samp = mean(diff(Ts2D));
% Build grids
-Nkr = numel(kr); Nkz = numel(kz);
-[KZ,KR] = meshgrid(kz,kr);
-Lkr = max(kr)-min(kr); Lkz = max(kz)-min(kz);
-dkr = Lkr/(Nkr-1); dkz = Lkz/(Nkz-1);
-Lk = max(Lkr,Lkz);
+Nkx = numel(kx); Nky = numel(ky);
+[ky,kx] = meshgrid(ky,kx);
+Lkx = max(kx)-min(kx); Lky = max(ky)-min(ky);
+dkx = Lkx/(Nkx-1); dky = Lky/(Nky-1);
+Lk = max(Lkx,Lky);
dr = 2*pi/Lk; dz = 2*pi/Lk;
-Nr = max(Nkr,Nkz) * (Nkr > 1) + (Nkr == 1); Nz = Nkz;
-r = dr*(-Nr/2:(Nr/2-1)); Lr = max(r)-min(r);
-z = dz*(-Nz/2:(Nz/2-1)); Lz = max(z)-min(z);
+Nx = max(Nkx,Nky) * (Nkx > 1) + (Nkx == 1); Ny = Nky;
+r = dr*(-Nx/2:(Nx/2-1)); Lx = max(r)-min(r);
+z = dz*(-Ny/2:(Ny/2-1)); Ly = max(z)-min(z);
[YY,XX] = meshgrid(z,r);
% Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% IFFT
-ne00 = zeros(Nz, Ns);
-ni00 = zeros(Nz, Ns);
-phi = zeros(Nz, Ns);
+ne00 = zeros(Ny, Ns);
+ni00 = zeros(Ny, Ns);
+phi = zeros(Ny, Ns);
for it = 1:numel(Ts2D)
NE_ = Ne00(:,it); NN_ = Ni00(:,it); PH_ = PHI(:,it);
- F_ = (ifft((NE_),Nz));
+ F_ = (ifft((NE_),Ny));
ne00(:,it)= real(fftshift(F_));
- F_ = (ifft((NN_),Nz));
+ F_ = (ifft((NN_),Ny));
ni00(:,it) = real(fftshift(F_));
- F_ = (ifft((PH_),Nz));
+ F_ = (ifft((PH_),Ny));
phi(:,it) = real(fftshift(F_));
end
@@ -44,9 +44,9 @@ E_pot = zeros(1,Ns); % Potential energy n^2
E_kin = zeros(1,Ns); % Kinetic energy grad(phi)^2
ExB = zeros(1,Ns); % ExB drift intensity \propto |\grad \phi|
CFL = zeros(1,Ns); % CFL time step
-Ddz = 1i*kz;
+Ddz = 1i*ky;
[~,iz0] = min(abs(z)); % index of z==0
-[~,ikz1] = min(abs(kz-round(1/dkz)*dkz)); % index of kz==1
+[~,iky1] = min(abs(ky-round(1/dky)*dky)); % index of ky==1
for it = 1:numel(Ts2D)
NE_ = squeeze(Ne00(:,it)); NN_ = squeeze(Ni00(:,it)); PH_ = squeeze(PHI(:,it));
@@ -56,23 +56,23 @@ for it = 1:numel(Ts2D)
phi_00(it) = phi(iz0,it);
- E_pot(it) = pi/Lz*sum(abs(NN_).^2)/Nkz; % integrate through Parseval id
- E_kin(it) = pi/Lz*sum(abs(Ddz.*PH_).^2)/Nkz;
+ E_pot(it) = pi/Ly*sum(abs(NN_).^2)/Nky; % integrate through Parseval id
+ E_kin(it) = pi/Ly*sum(abs(Ddz.*PH_).^2)/Nky;
ExB(it) = max(abs(phi(3:end,it)-phi(1:end-2,it))'/(2*dz));
end
-E_kin_KZ = abs(Ddz.*PHI(:,it)).^2;
+E_kin_KY = abs(Ddz.*PHI(:,it)).^2;
dEdt = diff(E_pot+E_kin)./diff(Ts2D);
%% Compute growth rate
-gamma_Ne = zeros(1,Nkz);
-gamma_Ni = zeros(1,Nkz);
-gamma_PH = zeros(1,Nkz);
+gamma_Ne = zeros(1,Nky);
+gamma_Ni = zeros(1,Nky);
+gamma_PH = zeros(1,Nky);
tend = Ts2D(end); tstart = 0.6*tend;
plt = @(x) squeeze(abs(x));
-for ikz = 1:Nkz
- gamma_Ne(ikz) = LinearFit_s(Ts2D,plt(Ne00(ikz,:)),tstart,tend);
- gamma_Ni(ikz) = LinearFit_s(Ts2D,plt(Ni00(ikz,:)),tstart,tend);
- gamma_PH(ikz) = LinearFit_s(Ts2D,plt(PHI(ikz,:)),tstart,tend);
+for iky = 1:Nky
+ gamma_Ne(iky) = LinearFit_s(Ts2D,plt(Ne00(iky,:)),tstart,tend);
+ gamma_Ni(iky) = LinearFit_s(Ts2D,plt(Ni00(iky,:)),tstart,tend);
+ gamma_PH(iky) = LinearFit_s(Ts2D,plt(PHI(iky,:)),tstart,tend);
end
gamma_Ne = real(gamma_Ne .* (gamma_Ne>=0.0));
gamma_Ni = real(gamma_Ni .* (gamma_Ni>=0.0));
@@ -98,15 +98,15 @@ end
if 1
%% Growth rate
fig = figure; FIGNAME = ['growth_rate',sprintf('_%.2d',JOBNUM)];
-plt = @(x) circshift(x,Nkz/2-1);
+plt = @(x) circshift(x,Nky/2-1);
subplot(221)
- plot(plt(kz),plt(gamma_Ne),'-'); hold on; xlim([0.0,max(kz)+dkz]);
+ plot(plt(ky),plt(gamma_Ne),'-'); hold on; xlim([0.0,max(ky)+dky]);
grid on; xlabel('$k_z$'); ylabel('$\gamma(N_e^{00})$');
subplot(222)
- plot(plt(kz),plt(gamma_Ni),'-'); hold on; xlim([0.0,max(kz)+dkz]);
+ plot(plt(ky),plt(gamma_Ni),'-'); hold on; xlim([0.0,max(ky)+dky]);
grid on; xlabel('$k_z$'); ylabel('$\gamma(N_i^{00})$');
subplot(223)
- plot(plt(kz),plt(gamma_PH),'-'); hold on; xlim([0.0,max(kz)+dkz]);
+ plot(plt(ky),plt(gamma_PH),'-'); hold on; xlim([0.0,max(ky)+dky]);
grid on; xlabel('$k_z$'); ylabel('$\gamma(\tilde\phi)$'); legend('show');
FMT = '.fig'; save_figure
end
@@ -137,9 +137,9 @@ XMIN = -L/2-2; XMAX = L/2+1; YMIN = -1.1; YMAX = 1.1;
create_gif_1D
%% Density electron frequency
GIFNAME = ['Ni',sprintf('_%.2d',JOBNUM)];
-FIELD = (abs(Ni00)); X = (kz); T = Ts2D;
+FIELD = (abs(Ni00)); X = (ky); T = Ts2D;
FIELDNAME = '$|N_i^{00}|$'; XNAME = '$k_z$';
-XMIN = min(kz)-0.5; XMAX = max(kz)+.5; YMIN = -0.1; YMAX = 1.1;
+XMIN = min(ky)-0.5; XMAX = max(ky)+.5; YMIN = -0.1; YMAX = 1.1;
create_gif_1D
end
@@ -159,28 +159,28 @@ subplot(223)% density
xlabel('$z\,(r=0)$'); ylabel('$t$'); title('$\phi$');
FMT = '.fig'; save_figure
-%% Space-Time diagrams at kr=0
+%% Space-Time diagrams at kx=0
plt = @(x) abs(x);
-fig = figure; FIGNAME = ['kz_space_time_diag',sprintf('_%.2d',JOBNUM)];
- [TY,TX] = meshgrid(Ts2D,kz);
+fig = figure; FIGNAME = ['ky_space_time_diag',sprintf('_%.2d',JOBNUM)];
+ [TY,TX] = meshgrid(Ts2D,ky);
subplot(221)% density
pclr = pcolor(TX,TY,(plt(Ne00))); set(pclr, 'edgecolor','none'); colorbar;
- xlabel('$kz$'); ylabel('$t$'); title('$\textrm{Re}(N_e^{00})|_{k_r=0}$');
+ xlabel('$ky$'); ylabel('$t$'); title('$\textrm{Re}(N_e^{00})|_{k_r=0}$');
subplot(222)% density
pclr = pcolor(TX,TY,(plt(Ni00))); set(pclr, 'edgecolor','none'); colorbar;
- xlabel('$kz$'); ylabel('$t$'); title('$\textrm{Re}(N_i^{00})|_{k_r=0}$');
+ xlabel('$ky$'); ylabel('$t$'); title('$\textrm{Re}(N_i^{00})|_{k_r=0}$');
subplot(223)% density
pclr = pcolor(TX,TY,(plt(PH))); set(pclr, 'edgecolor','none'); colorbar;
- xlabel('$kz$'); ylabel('$t$'); title('$\textrm{Re}(\tilde\phi)|_{k_r=0}$');
+ xlabel('$ky$'); ylabel('$t$'); title('$\textrm{Re}(\tilde\phi)|_{k_r=0}$');
FMT = '.fig'; save_figure
end
if 0
%% Mode time evolution
-[~,ik05] = min(abs(kz-0.50));
-[~,ik10] = min(abs(kz-1.00));
-[~,ik15] = min(abs(kz-1.50));
-[~,ik20] = min(abs(kz-2.00));
+[~,ik05] = min(abs(ky-0.50));
+[~,ik10] = min(abs(ky-1.00));
+[~,ik15] = min(abs(ky-1.50));
+[~,ik20] = min(abs(ky-2.00));
fig = figure; FIGNAME = ['frame',sprintf('_%.2d',JOBNUM)];
subplot(221); plt = @(x) abs(squeeze(x));
@@ -221,13 +221,13 @@ if 0
it = min(70,numel(Ts2D));
fig = figure; FIGNAME = ['frame',sprintf('_%.2d',JOBNUM)];
subplot(221); plt = @(x) (abs(x));
- plot(kz,plt(PH(:,it)))
+ plot(ky,plt(PH(:,it)))
xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('t=%.3d',Ts2D(it))); legend('$\hat\phi$');
subplot(222); plt = @(x) (abs(x));
- plot(kz,plt(Ni00(:,it)))
+ plot(ky,plt(Ni00(:,it)))
xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('t=%.3d',Ts2D(it))); legend('$\hat n_i^{00}$');
subplot(223); plt = @(x) (abs(x));
- plot(kz,plt(Ne00(:,it)))
+ plot(ky,plt(Ne00(:,it)))
xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('t=%.3d',Ts2D(it))); legend('$\hat n_e^{00}$');
FMT = '.fig'; save_figure
end
\ No newline at end of file
diff --git a/wk/analysis_2D.m b/wk/analysis_2D.m
index b52f4554..50a40384 100644
--- a/wk/analysis_2D.m
+++ b/wk/analysis_2D.m
@@ -2,23 +2,21 @@ addpath(genpath('../matlab')) % ... add
for i_ = 1
% for ETA_ =[0.6:0.1:0.9]
%% Load results
-if 1% Local results
+if 0% Local results
outfile ='';
outfile ='';
outfile ='';
outfile ='';
-outfile ='HD_study/300x150_L_100_P_2_J_1_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_1e-03';
-% outfile ='test_3D/50x25_L_50_lin_P_2_J_1_eta_0.5_nu_1e-01_LBDK_CLOS_0_mu_0e+00';
+outfile ='v2.8_kobayashi/100x50_L_50_P_6_J_3_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00';
BASIC.RESDIR = ['../results/',outfile,'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/results/',outfile,'/'];
CMD = ['cp ', BASIC.RESDIR,'outputs* ',BASIC.MISCDIR]; disp(CMD);
system(CMD);
-else% Marconi results
-outfile ='';
-outfile ='';
+end
+if 1% Marconi results
outfile ='';
outfile ='';
-outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/300x150_L_100_P_10_J_5_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00/out.txt';
+outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-02_SGGK_CLOS_0_mu_1e-02/out.txt';
% outfile = outcl{i_};
% load_marconi(outfile);
BASIC.RESDIR = ['../',outfile(46:end-8),'/'];
@@ -39,69 +37,63 @@ Ts5D = Ts5D';
Ts2D = Ts2D';
%% Build grids
-Nkr = numel(kr); Nkz = numel(kz);
-[KZ,KR] = meshgrid(kz,kr);
-Lkr = max(kr)-min(kr); Lkz = max(kz)-min(kz);
-dkr = Lkr/(Nkr-1); dkz = Lkz/(Nkz-1);
-KPERP2 = KZ.^2+KR.^2;
-[~,ikr0] = min(abs(kr)); [~,ikz0] = min(abs(kz));
+Nkx = numel(kx); Nky = numel(ky);
+[ky,kx] = meshgrid(ky,kx);
+Lkx = max(kx)-min(kx); Lky = max(ky)-min(ky);
+dkx = Lkx/(Nkx-1); dky = Lky/(Nky-1);
+KPERP2 = ky.^2+kx.^2;
+[~,ikx0] = min(abs(kx)); [~,iky0] = min(abs(ky));
-Lk = max(Lkr,Lkz);
+Lk = max(Lkx,Lky);
dr = 2*pi/Lk; dz = 2*pi/Lk;
-Nr = max(Nkr,Nkz); Nz = Nr;
-r = dr*(-Nr/2:(Nr/2-1)); Lr = max(r)-min(r);
-z = dz*(-Nz/2:(Nz/2-1)); Lz = max(z)-min(z);
+Nx = max(Nkx,Nky); Ny = Nx;
+r = dr*(-Nx/2:(Nx/2-1)); Lx = max(r)-min(r);
+z = dz*(-Ny/2:(Ny/2-1)); Ly = max(z)-min(z);
[ZZ,RR] = meshgrid(z,r);
%% Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp('Analysis :')
disp('- iFFT')
% IFFT (Lower case = real space, upper case = frequency space)
-ne00 = zeros(Nr,Nz,Ns2D); % Gyrocenter density
-ni00 = zeros(Nr,Nz,Ns2D);
-dzTe = zeros(Nr,Nz,Ns2D);
-dzTi = zeros(Nr,Nz,Ns2D);
-dzni = zeros(Nr,Nz,Ns2D);
-np_i = zeros(Nr,Nz,Ns5D); % Ion particle density
-si00 = zeros(Nr,Nz,Ns5D);
-phi = zeros(Nr,Nz,Ns2D);
-dens_e = zeros(Nr,Nz,Ns2D);
-dens_i = zeros(Nr,Nz,Ns2D);
-temp_e = zeros(Nr,Nz,Ns2D);
-temp_i = zeros(Nr,Nz,Ns2D);
-drphi = zeros(Nr,Nz,Ns2D);
-dzphi = zeros(Nr,Nz,Ns2D);
-dr2phi = zeros(Nr,Nz,Ns2D);
-E_turb = zeros(1,Ns2D); % Time evol. of the turbulence energy (Pred in Kobayashi 2015)
-E_ZF = zeros(1,Ns2D); % Time evol. of the ZF energy (Pray in Kobayashi 2015)
-for it = 1:numel(Ts2D)
+ne00 = zeros(Nx,Ny,Ns2D); % Gyrocenter density
+ni00 = zeros(Nx,Ny,Ns2D);
+dzTe = zeros(Nx,Ny,Ns2D);
+dzTi = zeros(Nx,Ny,Ns2D);
+dzni = zeros(Nx,Ny,Ns2D);
+np_i = zeros(Nx,Ny,Ns5D); % Ion particle density
+si00 = zeros(Nx,Ny,Ns5D);
+phi = zeros(Nx,Ny,Ns2D);
+dens_e = zeros(Nx,Ny,Ns2D);
+dens_i = zeros(Nx,Ny,Ns2D);
+temp_e = zeros(Nx,Ny,Ns2D);
+temp_i = zeros(Nx,Ny,Ns2D);
+drphi = zeros(Nx,Ny,Ns2D);
+dzphi = zeros(Nx,Ny,Ns2D);
+dr2phi = zeros(Nx,Ny,Ns2D);
-end
for it = 1:numel(Ts2D)
NE_ = Ne00(:,:,it); NI_ = Ni00(:,:,it); PH_ = PHI(:,:,it);
- ne00(:,:,it) = real(fftshift(ifft2((NE_),Nr,Nz)));
- ni00(:,:,it) = real(fftshift(ifft2((NI_),Nr,Nz)));
- phi (:,:,it) = real(fftshift(ifft2((PH_),Nr,Nz)));
- drphi(:,:,it) = real(fftshift(ifft2(1i*KR.*(PH_),Nr,Nz)));
- dr2phi(:,:,it)= real(fftshift(ifft2(-KR.^2.*(PH_),Nr,Nz)));
- dzphi(:,:,it) = real(fftshift(ifft2(1i*KZ.*(PH_),Nr,Nz)));
- E_turb(it) = sum(sum((1+KR.^2+KZ.^2).*abs(PHI(:,:,it)).^2))- sum((1+kr.^2).*abs(PHI(:,1,it)).^2);
- E_ZF(it) = sum(kr.^2.*abs(PHI(:,1,it)).^2);
+ ne00(:,:,it) = real(fftshift(ifft2((NE_),Nx,Ny)));
+ ni00(:,:,it) = real(fftshift(ifft2((NI_),Nx,Ny)));
+ phi (:,:,it) = real(fftshift(ifft2((PH_),Nx,Ny)));
+ drphi(:,:,it) = real(fftshift(ifft2(1i*kx.*(PH_),Nx,Ny)));
+ dr2phi(:,:,it)= real(fftshift(ifft2(-kx.^2.*(PH_),Nx,Ny)));
+ dzphi(:,:,it) = real(fftshift(ifft2(1i*ky.*(PH_),Nx,Ny)));
if(W_DENS && W_TEMP)
DENS_E_ = DENS_E(:,:,it); DENS_I_ = DENS_I(:,:,it);
TEMP_E_ = TEMP_E(:,:,it); TEMP_I_ = TEMP_I(:,:,it);
- dzni(:,:,it) = real(fftshift(ifft2(1i*KZ.*(DENS_I_),Nr,Nz)));
- dzTe(:,:,it) = real(fftshift(ifft2(1i*KZ.*(TEMP_E_),Nr,Nz)));
- dzTi(:,:,it) = real(fftshift(ifft2(1i*KZ.*(TEMP_I_),Nr,Nz)));
- dens_e (:,:,it) = real(fftshift(ifft2((DENS_E_),Nr,Nz)));
- dens_i (:,:,it) = real(fftshift(ifft2((DENS_I_),Nr,Nz)));
- temp_e (:,:,it) = real(fftshift(ifft2((TEMP_E_),Nr,Nz)));
- temp_i (:,:,it) = real(fftshift(ifft2((TEMP_I_),Nr,Nz)));
+ dzni(:,:,it) = real(fftshift(ifft2(1i*ky.*(DENS_I_),Nx,Ny)));
+ dzTe(:,:,it) = real(fftshift(ifft2(1i*ky.*(TEMP_E_),Nx,Ny)));
+ dzTi(:,:,it) = real(fftshift(ifft2(1i*ky.*(TEMP_I_),Nx,Ny)));
+ dens_e (:,:,it) = real(fftshift(ifft2((DENS_E_),Nx,Ny)));
+ dens_i (:,:,it) = real(fftshift(ifft2((DENS_I_),Nx,Ny)));
+ temp_e (:,:,it) = real(fftshift(ifft2((TEMP_E_),Nx,Ny)));
+ temp_i (:,:,it) = real(fftshift(ifft2((TEMP_I_),Nx,Ny)));
end
end
% Building a version of phi only 5D sampling times
-PHI_Ts5D = zeros(Nkr,Nkz,Ns5D);
+PHI_Ts5D = zeros(Nkx,Nky,Ns5D);
err = 0;
for it = 1:numel(Ts5D) % Loop over 5D arrays
[shift, it2D] = min(abs(Ts2D-Ts5D(it)));
@@ -110,7 +102,7 @@ for it = 1:numel(Ts5D) % Loop over 5D arrays
end
if err > 0; disp('WARNING Ts2D and Ts5D are shifted'); end;
-Np_i = zeros(Nkr,Nkz,Ns5D); % Ion particle density in Fourier space
+Np_i = zeros(Nkx,Nky,Ns5D); % Ion particle density in Fourier space
for it = 1:numel(Ts5D)
[~, it2D] = min(abs(Ts2D-Ts5D(it)));
@@ -120,7 +112,7 @@ for it = 1:numel(Ts5D)
Np_i(:,:,it) = Np_i(:,:,it) + Kn.*squeeze(Nipj(1,ij,:,:,it));
end
- np_i(:,:,it) = real(fftshift(ifft2(squeeze(Np_i(:,:,it)),Nr,Nz)));
+ np_i(:,:,it) = real(fftshift(ifft2(squeeze(Np_i(:,:,it)),Nx,Ny)));
end
% Post processing
@@ -132,8 +124,8 @@ GFlux_re = zeros(1,Ns2D); % Gyrocenter flux Gamma = <ne drphi>
GFlux_ze = zeros(1,Ns2D); % Gyrocenter flux Gamma = <ne dzphi>
PFlux_ri = zeros(1,Ns5D); % Particle flux
% gyrocenter and particle flux from fourier coefficients
-GFLUX_RI = real(squeeze(sum(sum(-1i*KZ.*Ni00.*conj(PHI),1),2)))*(2*pi/Nr/Nz)^2;
-PFLUX_RI = real(squeeze(sum(sum(-1i*KZ.*Np_i.*conj(PHI_Ts5D),1),2)))*(2*pi/Nr/Nz)^2;
+GFLUX_RI = real(squeeze(sum(sum(-1i*ky.*Ni00.*conj(PHI),1),2)))*(2*pi/Nx/Ny)^2;
+PFLUX_RI = real(squeeze(sum(sum(-1i*ky.*Np_i.*conj(PHI_Ts5D),1),2)))*(2*pi/Nx/Ny)^2;
% Heat flux
Q_RI = -squeeze(mean(mean(dzphi.*temp_i,1),2))';
% Hermite energy spectrum
@@ -153,17 +145,17 @@ shear_avgr_avgz = zeros(1,Ns2D); % Time evol. of the norm of shear
Ne_norm = zeros(Pe_max,Je_max,Ns5D); % Time evol. of the norm of Napj
Ni_norm = zeros(Pi_max,Ji_max,Ns5D); % .
-Ddr = 1i*KR; Ddz = 1i*KZ; lapl = Ddr.^2 + Ddz.^2;
+Ddr = 1i*kx; Ddz = 1i*ky; lapl = Ddr.^2 + Ddz.^2;
% Kperp spectrum interpolation
%full kperp points
-kperp = reshape(sqrt(KR.^2+KZ.^2),[numel(KR),1]);
+kperp = reshape(sqrt(kx.^2+ky.^2),[numel(kx),1]);
% interpolated kperps
-nk_noAA = floor(2/3*numel(kr));
-kp_ip = kr;
+nk_noAA = floor(2/3*numel(kx));
+kp_ip = kx;
[thg, rg] = meshgrid(linspace(0,pi,2*nk_noAA),kp_ip);
[xn,yn] = pol2cart(thg,rg);
-[kz_s, sortIdx] = sort(kz);
-[xc,yc] = meshgrid(kz_s,kr);
+[ky_s, sortIdx] = sort(ky);
+[xc,yc] = meshgrid(ky_s,kx);
phi_kp_t = zeros(numel(kp_ip),Ns2D);
%
for it = 1:numel(Ts2D) % Loop over 2D arrays
@@ -178,10 +170,10 @@ for it = 1:numel(Ts2D) % Loop over 2D arrays
shear_maxr_avgz(it) = mean( max(squeeze(-(dr2phi(:,:,it)))));
shear_avgr_avgz(it) = mean(mean(squeeze(-(dr2phi(:,:,it)))));
- GFlux_ri(it) = sum(sum(ni00(:,:,it).*dzphi(:,:,it)))*dr*dz/Lr/Lz;
- GFlux_zi(it) = sum(sum(-ni00(:,:,it).*drphi(:,:,it)))*dr*dz/Lr/Lz;
- GFlux_re(it) = sum(sum(ne00(:,:,it).*dzphi(:,:,it)))*dr*dz/Lr/Lz;
- GFlux_ze(it) = sum(sum(-ne00(:,:,it).*drphi(:,:,it)))*dr*dz/Lr/Lz;
+ GFlux_ri(it) = sum(sum(ni00(:,:,it).*dzphi(:,:,it)))*dr*dz/Lx/Ly;
+ GFlux_zi(it) = sum(sum(-ni00(:,:,it).*drphi(:,:,it)))*dr*dz/Lx/Ly;
+ GFlux_re(it) = sum(sum(ne00(:,:,it).*dzphi(:,:,it)))*dr*dz/Lx/Ly;
+ GFlux_ze(it) = sum(sum(-ne00(:,:,it).*drphi(:,:,it)))*dr*dz/Lx/Ly;
Z_rth = interp2(xc,yc,squeeze(mean((abs(PHI(:,sortIdx,it))).^2,3)),xn,yn);
phi_kp_t(:,it) = mean(Z_rth,2);
@@ -189,50 +181,50 @@ end
%
for it = 1:numel(Ts5D) % Loop over 5D arrays
[~, it2D] = min(abs(Ts2D-Ts5D(it)));
- Ne_norm(:,:,it)= sum(sum(abs(Nepj(:,:,:,:,it)),3),4)/Nkr/Nkz;
- Ni_norm(:,:,it)= sum(sum(abs(Nipj(:,:,:,:,it)),3),4)/Nkr/Nkz;
+ Ne_norm(:,:,it)= sum(sum(abs(Nepj(:,:,:,:,it)),3),4)/Nkx/Nky;
+ Ni_norm(:,:,it)= sum(sum(abs(Nipj(:,:,:,:,it)),3),4)/Nkx/Nky;
epsilon_e_pj(:,:,it) = sqrt(pi)/2*sum(sum(abs(Nepj(:,:,:,:,it)).^2,3),4);
epsilon_i_pj(:,:,it) = sqrt(pi)/2*sum(sum(abs(Nipj(:,:,:,:,it)).^2,3),4);
% Particle flux
- PFlux_ri(it) = sum(sum(np_i(:,:,it).*dzphi(:,:,it2D)))*dr*dz/Lr/Lz;
+ PFlux_ri(it) = sum(sum(np_i(:,:,it).*dzphi(:,:,it2D)))*dr*dz/Lx/Ly;
end
%% Compute primary instability growth rate
disp('- growth rate')
% Find max value of transport (end of linear mode)
-[tmp,tmax] = max(GGAMMA_RI*(2*pi/Nr/Nz)^2);
+[tmp,tmax] = max(GGAMMA_RI*(2*pi/Nx/Ny)^2);
[~,itmax] = min(abs(Ts2D-tmax));
tstart = 0.1 * Ts2D(itmax); tend = 0.5 * Ts2D(itmax);
[~,its2D_lin] = min(abs(Ts2D-tstart));
[~,ite2D_lin] = min(abs(Ts2D-tend));
-g_I = zeros(Nkr,Nkz);
-for ikr = 1:Nkr
- for ikz = 1:Nkz
- [g_I(ikr,ikz), ~] = LinearFit_s(Ts2D(its2D_lin:ite2D_lin),squeeze(abs(Ni00(ikr,ikz,its2D_lin:ite2D_lin))));
+g_I = zeros(Nkx,Nky);
+for ikx = 1:Nkx
+ for iky = 1:Nky
+ [g_I(ikx,iky), ~] = LinearFit_s(Ts2D(its2D_lin:ite2D_lin),squeeze(abs(Ni00(ikx,iky,its2D_lin:ite2D_lin))));
end
end
[gmax_I,ikmax_I] = max(g_I(1,:));
-kmax_I = abs(kz(ikmax_I));
+kmax_I = abs(ky(ikmax_I));
Bohm_transport = ETAB/ETAN*gmax_I/kmax_I^2;
%% Compute secondary instability growth rate
disp('- growth rate')
% Find max value of transport (end of linear mode)
-% [tmp,tmax] = max(GGAMMA_RI*(2*pi/Nr/Nz)^2);
+% [tmp,tmax] = max(GGAMMA_RI*(2*pi/Nx/Ny)^2);
% [~,itmax] = min(abs(Ts2D-tmax));
% tstart = Ts2D(itmax); tend = 1.5*Ts2D(itmax);
[~,its2D_lin] = min(abs(Ts2D-tstart));
[~,ite2D_lin] = min(abs(Ts2D-tend));
-g_II = zeros(Nkr,Nkz);
-for ikr = 1:Nkr
- for ikz = 1
- [g_II(ikr,ikz), ~] = LinearFit_s(Ts2D(its2D_lin:ite2D_lin),squeeze(abs(Ni00(ikr,ikz,its2D_lin:ite2D_lin))));
+g_II = zeros(Nkx,Nky);
+for ikx = 1:Nkx
+ for iky = 1
+ [g_II(ikx,iky), ~] = LinearFit_s(Ts2D(its2D_lin:ite2D_lin),squeeze(abs(Ni00(ikx,iky,its2D_lin:ite2D_lin))));
end
end
[gmax_II,ikmax_II] = max(g_II(1,:));
-kmax_II = abs(kr(ikmax_II));
+kmax_II = abs(kx(ikmax_II));
%% PLOTS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
default_plots_options
@@ -244,8 +236,8 @@ if 1
fig = figure; FIGNAME = ['t_evolutions',sprintf('_%.2d',JOBNUM),'_',PARAMS];
set(gcf, 'Position', [100, 100, 900, 800])
subplot(111);
- suptitle(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
- ', $L=',num2str(L),'$, $N=',num2str(Nr),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+ suptitle(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+ ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
' $\mu_{hd}=$',num2str(MU)]);
subplot(421);
for ip = 1:Pe_max
@@ -272,20 +264,20 @@ subplot(111);
end
grid on; ylabel('$\sum_{k_r,k_z}|N_i^{pj}|$'); xlabel('$t c_s/R$')
subplot(222)
- plot(Ts0D,GGAMMA_RI*(2*pi/Nr/Nz)^2); hold on;
+ plot(Ts0D,GGAMMA_RI*(2*pi/Nx/Ny)^2); hold on;
% plot(Ts2D,GFLUX_RI)
- plot(Ts0D,PGAMMA_RI*(2*pi/Nr/Nz)^2);
+ plot(Ts0D,PGAMMA_RI*(2*pi/Nx/Ny)^2);
% plot(Ts5D,PFLUX_RI,'--');
legend(['Gyro. flux';'Part. flux']);
grid on; xlabel('$t c_s/R$'); ylabel('$\Gamma_{r,i}$')
% ylim([0,2.0]);
- if(0)
+ if(1)
subplot(223)
- plot(kz,g_I(1,:),'-','DisplayName','Primar. instability'); hold on;
- plot(kr,g_II(:,1),'x-','DisplayName','Second. instability'); hold on;
- plot([max(kz)*2/3,max(kz)*2/3],[0,10],'--k', 'DisplayName','2/3 Orszag AA');
+ plot(ky,g_I(1,:),'-','DisplayName','Primar. instability'); hold on;
+ plot(kx,g_II(:,1),'x-','DisplayName','Second. instability'); hold on;
+ plot([max(ky)*2/3,max(ky)*2/3],[0,10],'--k', 'DisplayName','2/3 Orszag AA');
grid on; xlabel('$k\rho_s$'); ylabel('$\gamma R/c_s$'); legend('show');
- ylim([0,max(g_I(1,:))]); xlim([0,max(kz)]);
+ ylim([0,max(g_I(1,:))]); xlim([0,max(ky)]);
shearplot = 426; phiplot = 428;
else
shearplot = 223; phiplot = 224;
@@ -311,12 +303,12 @@ end
if 1
%% Space time diagramm (fig 11 Ivanov 2020)
-TAVG = 1000; % Averaging time duration
+TAVG = 5000; % Averaging time duration
%Compute steady radial transport
tend = Ts0D(end); tstart = tend - TAVG;
[~,its0D] = min(abs(Ts0D-tstart));
[~,ite0D] = min(abs(Ts0D-tend));
-SCALE = (2*pi/Nr/Nz)^2;
+SCALE = (2*pi/Nx/Ny)^2;
gamma_infty_avg = mean(PGAMMA_RI(its0D:ite0D))*SCALE;
gamma_infty_std = std (PGAMMA_RI(its0D:ite0D))*SCALE;
% Compute steady shearing rate
@@ -330,28 +322,33 @@ Q_infty_std = std(Q_RI(its2D:ite2D))*SCALE;
% plots
fig = figure; FIGNAME = ['ZF_transport_drphi','_',PARAMS];set(gcf, 'Position', [100, 100, 1200, 600])
subplot(311)
- yyaxis left
+% yyaxis left
plot(Ts0D,PGAMMA_RI*SCALE,'DisplayName','$\langle n_i d\phi/dz \rangle_z$'); hold on;
plot(Ts0D(its0D:ite0D),ones(ite0D-its0D+1,1)*gamma_infty_avg, '-k',...
'DisplayName',['$\Gamma^{\infty} = $',num2str(gamma_infty_avg),'$\pm$',num2str(gamma_infty_std)]);
grid on; set(gca,'xticklabel',[]); ylabel('$\Gamma_r$')
ylim([0,5*abs(gamma_infty_avg)]); xlim([0,Ts0D(end)]);
- title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
- ', $L=',num2str(L),'$, $N=',num2str(Nr),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+ title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+ ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
' $\mu_{hd}=$',num2str(MU)]);
- yyaxis right
+% yyaxis right
+% plot(Ts2D,Q_RI*SCALE,'.','DisplayName','$\langle T_i d\phi/dz \rangle_z$'); hold on;
+% ylim([0,5*Q_infty_avg]); xlim([0,Ts0D(end)]); ylabel('$Q_r$')
+% plot(Ts0D(its0D:ite0D),ones(ite0D-its0D+1,1)*Q_infty_avg, '--k',...
+% 'DisplayName',['$Q^{\infty} = $',num2str(Q_infty_avg),'$\pm$',num2str(Q_infty_std)]);
+% legend('show','Location','west')
+ %
+ subplot(312)
+ clr = line_colors(1,:);
+ lstyle = line_styles(1);
+ plot(Ts2D,shear_maxr_maxz,'DisplayName','$\max_{r,z}(s_\phi)$'); hold on;
plot(Ts2D,shear_maxr_avgz,'DisplayName','$\max_{r}\langle s_\phi\rangle_z$'); hold on;
+ plot(Ts2D,shear_avgr_maxz,'DisplayName','$\max_{z}\langle s_\phi\rangle_r$'); hold on;
+ plot(Ts2D,shear_avgr_avgz,'DisplayName','$\langle s_\phi\rangle_{r,z}$'); hold on;
plot(Ts2D(its2D:ite2D),ones(ite2D-its2D+1,1)*shear_infty_avg, '-k',...
'DisplayName',['$s^{\infty} = $',num2str(shear_infty_avg),'$\pm$',num2str(shear_infty_std)]);
ylim([0,shear_infty_avg*5.0]); xlim([0,Ts0D(end)]);
grid on; ylabel('Shear amp.');set(gca,'xticklabel',[]);% legend('show');
- subplot(312)
- yyaxis left
- plot(Ts2D,SCALE*E_ZF);xlim([0,Ts0D(end)]);
- ylabel('ZF energy'); ylim([0;1.2*max(SCALE*E_ZF(floor(0.5*numel(Ts2D)):end))]);
- yyaxis right
- plot(Ts2D,SCALE*E_turb);xlim([0,Ts0D(end)]);
- ylabel('Turb. energy'); ylim([0;1.2*max(SCALE*E_turb(floor(0.5*numel(Ts2D)):end))]);
subplot(313)
[TY,TX] = meshgrid(r,Ts2D);
% pclr = pcolor(TX,TY,squeeze(mean(drphi(:,:,:),2))'); set(pclr, 'edgecolor','none'); legend('$\langle \partial_r\phi\rangle_z$') %colorbar;
@@ -360,7 +357,7 @@ fig = figure; FIGNAME = ['ZF_transport_drphi','_',PARAMS];set(gcf, 'Position',
save_figure
end
-if 0
+if 1
%% Space time diagramms
tstart = 0; tend = Ts2D(end);
[~,itstart] = min(abs(Ts2D-tstart));
@@ -369,20 +366,32 @@ trange = itstart:itend;
[TY,TX] = meshgrid(r,Ts2D(trange));
fig = figure; FIGNAME = ['space_time','_',PARAMS];set(gcf, 'Position', [100, 100, 1200, 600])
subplot(211)
+% pclr = pcolor(TX,TY,squeeze(mean(dens_i(:,:,trange).*dzphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
pclr = pcolor(TX,TY,squeeze(mean(ni00(:,:,trange).*dzphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
shading interp
colormap hot;
caxis([0.0,0.05*max(max(mean(ni00(:,:,its2D:ite2D).*dzphi(:,:,its2D:ite2D),2)))]);
- caxis([0.0,0.05]); c = colorbar; c.Label.String ='\langle n_i\partial_z\phi\rangle_z';
+ caxis([0.0,0.01]); c = colorbar; c.Label.String ='\langle n_i\partial_z\phi\rangle_z';
xticks([]); ylabel('$r/\rho_s$')
- title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
- ', $L=',num2str(L),'$, $N=',num2str(Nr),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+% legend('Radial part. transport $\langle n_i\partial_z\phi\rangle_z$')
+ title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+ ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
' $\mu_{hd}=$',num2str(MU)]);
+% subplot(312)
+% pclr = pcolor(TX,TY,squeeze(mean(temp_i(:,:,trange).*dzphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
+% shading interp
+% % colormap(bluewhitered(256));
+% xticks([]); ylabel('$r/\rho_s$')
+% legend('Radial part. transport $\langle T_i\partial_z\phi\rangle_z$')
+% title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
+% ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+% ' $\mu_{hd}=$',num2str(MU)]);
subplot(212)
pclr = pcolor(TX,TY,squeeze(mean(drphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
fieldmax = max(max(mean(abs(drphi(:,:,its2D:ite2D)),2)));
caxis([-fieldmax,fieldmax]); c = colorbar; c.Label.String ='\langle \partial_r\phi\rangle_z';
xlabel('$t c_s/R$'), ylabel('$r/\rho_s$')
+% legend('Zonal flow $\langle \partial_r\phi\rangle_z$')
save_figure
end
@@ -403,20 +412,20 @@ end
if 1
%% |phi_k|^2 spectra (Kobayashi 2015 fig 3)
-tstart = 3000; tend = 5000;
+tstart = 0.8*Ts2D(end); tend = Ts2D(end);
[~,itstart] = min(abs(Ts2D-tstart));
[~,itend] = min(abs(Ts2D-tend));
trange = itstart:itend;
%full kperp points
-phi_k_2 = reshape(mean((abs(PHI(:,:,trange))).^2,3),[numel(KR),1]);
-kperp = reshape(sqrt(KR.^2+KZ.^2),[numel(KR),1]);
+phi_k_2 = reshape(mean((abs(PHI(:,:,trange))).^2,3),[numel(kx),1]);
+kperp = reshape(sqrt(kx.^2+ky.^2),[numel(kx),1]);
% interpolated kperps
-nk_noAA = floor(2/3*numel(kr));
-kp_ip = kr;
+nk_noAA = floor(2/3*numel(kx));
+kp_ip = kx;
[thg, rg] = meshgrid(linspace(0,pi,2*nk_noAA),kp_ip);
[xn,yn] = pol2cart(thg,rg);
-[kz_s, sortIdx] = sort(kz);
-[xc,yc] = meshgrid(kz_s,kr);
+[ky_s, sortIdx] = sort(ky);
+[xc,yc] = meshgrid(ky_s,kx);
Z_rth = interp2(xc,yc,squeeze(mean((abs(PHI(:,sortIdx,trange))).^2,3)),xn,yn);
phi_kp = mean(Z_rth,2);
Z_rth = interp2(xc,yc,squeeze(mean((abs(Ni00(:,sortIdx,trange))).^2,3)),xn,yn);
@@ -426,7 +435,7 @@ ne00_kp = mean(Z_rth,2);
%for theorical trends
a1 = phi_kp(2)*kp_ip(2).^(13/3);
a2 = phi_kp(2)*kp_ip(2).^(3)./(1+kp_ip(2).^2).^(-2);
-fig = figure; FIGNAME = ['cascade_',num2str(tstart),'to',num2str(tend),PARAMS];set(gcf, 'Position', [100, 100, 500, 500])
+fig = figure; FIGNAME = ['cascade','_',PARAMS];set(gcf, 'Position', [100, 100, 500, 500])
% scatter(kperp,phi_k_2,'.k','MarkerEdgeAlpha',0.4,'DisplayName','$|\phi_k|^2$'); hold on; grid on;
plot(kp_ip,phi_kp,'^','DisplayName','$\langle|\phi_k|^2\rangle_{k_\perp}$'); hold on;
plot(kp_ip,ni00_kp, '^','DisplayName','$\langle|N_{i,k}^{00}|^2\rangle_{k_\perp}$'); hold on;
@@ -435,19 +444,19 @@ plot(kp_ip,a1*kp_ip.^(-13/3),'-','DisplayName','$k^{-13/3}$');
plot(kp_ip,a2/100*kp_ip.^(-3)./(1+kp_ip.^2).^2,'-','DisplayName','$k^{-3}/(1+k^2)^2$');
set(gca, 'XScale', 'log');set(gca, 'YScale', 'log'); grid on
xlabel('$k_\perp \rho_s$'); legend('show','Location','southwest')
-title({['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
-', $L=',num2str(L),'$, $N=',num2str(Nr),'$'];[' $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
-' $\mu_{hd}=$',num2str(MU),', $',num2str(tstart),'<t<',num2str(tend),'$']});
+title({['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+', $L=',num2str(L),'$, $N=',num2str(Nx),'$'];[' $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+' $\mu_{hd}=$',num2str(MU)]});
xlim([0.1,10]);
save_figure
clear Z_rth phi_kp ni_kp Ti_kp
end
%%
-t0 =000;
+t0 =00;
[~, it02D] = min(abs(Ts2D-t0));
[~, it05D] = min(abs(Ts5D-t0));
-skip_ = 5;
+skip_ = 4;
DELAY = 1e-3*skip_;
FRAMES_2D = it02D:skip_:numel(Ts2D);
FRAMES_5D = it05D:skip_:numel(Ts5D);
@@ -543,48 +552,48 @@ if 0
%% phi kperp spectrum
GIFNAME = ['phi2_kp',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0; SCALING = 0;
FIELD =log10(phi_kp_t); linestyle = '-'; FRAMES = FRAMES_2D;
-X = kp_ip; T = Ts2D; YMIN = -20; YMAX = 10; XMIN = min(kr); XMAX = max(kr);
+X = kp_ip; T = Ts2D; YMIN = -20; YMAX = 10; XMIN = min(kx); XMAX = max(kx);
FIELDNAME = '$\log_{10}|\tilde\phi_k|^2$'; XNAME = '$k_r\rho_s$';
create_gif_1D
end
if 0
%% Density ion frequency
GIFNAME = ['Ni00',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0; FRAMES = FRAMES_2D;
-FIELD =ifftshift((abs(Ni00)),2); X = fftshift(KR,2); Y = fftshift(KZ,2); T = Ts2D;
+FIELD =ifftshift((abs(Ni00)),2); X = fftshift(kx,2); Y = fftshift(ky,2); T = Ts2D;
FIELDNAME = '$N_i^{00}$'; XNAME = '$k_r\rho_s$'; YNAME = '$k_z\rho_s$';
create_gif
end
if 0
%% Density electron frequency
GIFNAME = ['Ne00',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0; FRAMES = FRAMES_2D;
-FIELD =ifftshift((abs(Ne00)),2); X = fftshift(KR,2); Y = fftshift(KZ,2); T = Ts2D;
+FIELD =ifftshift((abs(Ne00)),2); X = fftshift(kx,2); Y = fftshift(ky,2); T = Ts2D;
FIELDNAME = '$N_e^{00}$'; XNAME = '$k_r\rho_s$'; YNAME = '$k_z\rho_s$';
create_gif
end
if 0
-%% kr vs P Si
-GIFNAME = ['Sip0_kr',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
+%% kx vs P Si
+GIFNAME = ['Sip0_kx',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
plt = @(x) squeeze(max((abs(x)),[],4));
-FIELD =plt(Sipj(:,1,:,:,:)); X = kr'; Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
+FIELD =plt(Sipj(:,1,:,:,:)); X = kx'; Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
FIELDNAME = '$N_i^{p0}$'; XNAME = '$k_{max}\rho_s$'; YNAME = '$P$, $\sum_z$';
create_gif_imagesc
end
if 0
-%% maxkz, kr vs p, for all Nipj over time
-GIFNAME = ['Nipj_kr',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
+%% maxky, kx vs p, for all Nipj over time
+GIFNAME = ['Nipj_kx',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
plt = @(x) squeeze(sum((abs(x)),4));
-FIELD = plt(Nipj); X = kr'; Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
+FIELD = plt(Nipj); X = kx'; Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
FIELDNAME = 'N_i'; XNAME = '$k_r\rho_s$'; YNAME = '$P$';
create_gif_5D
end
if 0
-%% maxkr, kz vs p, for all Nipj over time
-GIFNAME = ['Nipj_kz',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
+%% maxkx, ky vs p, for all Nipj over time
+GIFNAME = ['Nipj_ky',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
plt = @(x) fftshift(squeeze(sum((abs(x)),3)),3);
-FIELD = plt(Nipj); X = sort(kz'); Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
+FIELD = plt(Nipj); X = sort(ky'); Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
FIELDNAME = 'N_i'; XNAME = '$k_z\rho_s$'; YNAME = '$P$, $\sum_r$';
create_gif_5D
end
%%
-% ZF_fourier_analysis
+ZF_fourier_analysis
end
\ No newline at end of file
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
new file mode 100644
index 00000000..6fc1d667
--- /dev/null
+++ b/wk/analysis_3D.m
@@ -0,0 +1,510 @@
+addpath(genpath('../matlab')) % ... add
+for i_ = 1
+% for ETA_ =[0.6:0.1:0.9]
+%% Load results
+if 1% Local results
+outfile ='';
+outfile ='Blob_diffusion/100x50_L_60_P_2_J_1_eta_Inf_nu_1e-01_DGGK_mu_0e+00';
+% outfile ='test_3D/100x50x10_L_60_q0_1_P_2_J_1_eta_0.6_nu_1e-01_DGGK_mu_2e-03';
+% outfile ='test_3D/100x50_L_60_P_2_J_1_eta_0.6_nu_1e-01_DGGK_mu_0e+00';
+ BASIC.RESDIR = ['../results/',outfile,'/'];
+ BASIC.MISCDIR = ['/misc/HeLaZ_outputs/results/',outfile,'/'];
+ CMD = ['cp ', BASIC.RESDIR,'outputs* ',BASIC.MISCDIR]; disp(CMD);
+ system(CMD);
+end
+if 0% Marconi results
+outfile ='';
+outfile ='';
+outfile ='';
+outfile ='';
+outfile ='';
+outfile ='';
+BASIC.RESDIR = ['../',outfile(46:end-8),'/'];
+BASIC.MISCDIR = ['/misc/HeLaZ_outputs/',outfile(46:end-8),'/'];
+end
+
+%%
+JOBNUMMIN = 00; JOBNUMMAX = 20;
+compile_results_3D %Compile the results from first output found to JOBNUMMAX if existing
+
+%% Retrieving max polynomial degree and sampling info
+Npe = numel(Pe); Nje = numel(Je); [JE,PE] = meshgrid(Je,Pe);
+Npi = numel(Pi); Nji = numel(Ji); [JI,PI] = meshgrid(Ji,Pi);
+Ns5D = numel(Ts5D);
+Ns3D = numel(Ts3D);
+% renaming and reshaping quantity of interest
+Ts5D = Ts5D';
+Ts3D = Ts3D';
+
+%% Build grids
+Nkx = numel(kx); Nky = numel(ky);
+[KY,KX] = meshgrid(ky,kx);
+Lkx = max(kx)-min(kx); Lky = max(ky)-min(ky);
+dkx = Lkx/(Nkx-1); dky = Lky/(Nky-1);
+KPERP2 = KY.^2+KX.^2;
+[~,ikx0] = min(abs(kx)); [~,iky0] = min(abs(ky));
+
+Lk = max(Lkx,Lky);
+Nx = max(Nkx,Nky); Ny = Nx; Nz = numel(z);
+dx = 2*pi/Lk; dy = 2*pi/Lk; dz = q0*2*pi/Nz;
+x = dx*(-Nx/2:(Nx/2-1)); Lx = max(x)-min(x);
+y = dy*(-Ny/2:(Ny/2-1)); Ly = max(y)-min(y);
+z = dz * (1:Nz);
+[Y_XY,X_XY] = meshgrid(y,x);
+[Z_XZ,X_XZ] = meshgrid(z,x);
+[Z_YZ,Y_YZ] = meshgrid(z,y);
+
+%% Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+disp('Analysis :')
+disp('- iFFT')
+% IFFT (Lower case = real space, upper case = frequency space)
+ne00 = zeros(Nx,Ny,Nz,Ns3D); % Gyrocenter density
+ni00 = zeros(Nx,Ny,Nz,Ns3D);
+dzTe = zeros(Nx,Ny,Nz,Ns3D);
+dzTi = zeros(Nx,Ny,Nz,Ns3D);
+dzni = zeros(Nx,Ny,Nz,Ns3D);
+np_i = zeros(Nx,Ny,Nz,Ns5D); % Ion particle density
+si00 = zeros(Nx,Ny,Nz,Ns5D);
+phi = zeros(Nx,Ny,Nz,Ns3D);
+dens_e = zeros(Nx,Ny,Nz,Ns3D);
+dens_i = zeros(Nx,Ny,Nz,Ns3D);
+temp_e = zeros(Nx,Ny,Nz,Ns3D);
+temp_i = zeros(Nx,Ny,Nz,Ns3D);
+drphi = zeros(Nx,Ny,Nz,Ns3D);
+dzphi = zeros(Nx,Ny,Nz,Ns3D);
+dr2phi = zeros(Nx,Ny,Nz,Ns3D);
+
+for it = 1:numel(Ts3D)
+ for iz = 1:numel(z)
+ NE_ = Ne00(:,:,iz,it); NI_ = Ni00(:,:,iz,it); PH_ = PHI(:,:,iz,it);
+ ne00(:,:,iz,it) = real(fftshift(ifft2((NE_),Nx,Ny)));
+ ni00(:,:,iz,it) = real(fftshift(ifft2((NI_),Nx,Ny)));
+ phi (:,:,iz,it) = real(fftshift(ifft2((PH_),Nx,Ny)));
+ drphi(:,:,iz,it) = real(fftshift(ifft2(1i*KX.*(PH_),Nx,Ny)));
+ dr2phi(:,:,iz,it)= real(fftshift(ifft2(-KX.^2.*(PH_),Nx,Ny)));
+ dzphi(:,:,iz,it) = real(fftshift(ifft2(1i*KY.*(PH_),Nx,Ny)));
+ if(W_DENS && W_TEMP)
+ DENS_E_ = DENS_E(:,:,iz,it); DENS_I_ = DENS_I(:,:,iz,it);
+ TEMP_E_ = TEMP_E(:,:,iz,it); TEMP_I_ = TEMP_I(:,:,iz,it);
+ dzni(:,:,iz,it) = real(fftshift(ifft2(1i*KY.*(DENS_I_),Nx,Ny)));
+ dzTe(:,:,iz,it) = real(fftshift(ifft2(1i*KY.*(TEMP_E_),Nx,Ny)));
+ dzTi(:,:,iz,it) = real(fftshift(ifft2(1i*KY.*(TEMP_I_),Nx,Ny)));
+ dens_e (:,:,iz,it) = real(fftshift(ifft2((DENS_E_),Nx,Ny)));
+ dens_i (:,:,iz,it) = real(fftshift(ifft2((DENS_I_),Nx,Ny)));
+ temp_e (:,:,iz,it) = real(fftshift(ifft2((TEMP_E_),Nx,Ny)));
+ temp_i (:,:,iz,it) = real(fftshift(ifft2((TEMP_I_),Nx,Ny)));
+ end
+ end
+end
+
+Np_i = zeros(Nkx,Nky,Ns5D); % Ion particle density in Fourier space
+
+for it = 1:numel(Ts5D)
+ [~, it2D] = min(abs(Ts3D-Ts5D(it)));
+ Np_i(:,:,it) = 0;
+ for ij = 1:Nji
+ Kn = (KPERP2/2.).^(ij-1) .* exp(-KPERP2/2)/(factorial(ij-1));
+ Np_i(:,:,it) = Np_i(:,:,it) + Kn.*squeeze(Nipj(1,ij,:,:,it));
+ end
+
+ np_i(:,:,it) = real(fftshift(ifft2(squeeze(Np_i(:,:,it)),Nx,Ny)));
+end
+
+% Post processing
+disp('- post processing')
+% gyrocenter and particle flux from real space
+GFlux_xi = zeros(1,Ns3D); % Gyrocenter flux Gamma = <ni drphi>
+GFlux_yi = zeros(1,Ns3D); % Gyrocenter flux Gamma = <ni dzphi>
+GFlux_xe = zeros(1,Ns3D); % Gyrocenter flux Gamma = <ne drphi>
+GFlux_ye = zeros(1,Ns3D); % Gyrocenter flux Gamma = <ne dzphi>
+% Hermite energy spectrum
+epsilon_e_pj = zeros(Pe_max,Je_max,Ns5D);
+epsilon_i_pj = zeros(Pi_max,Ji_max,Ns5D);
+
+phi_maxx_maxy = zeros(Nz,Ns3D); % Time evol. of the norm of phi
+phi_avgx_maxy = zeros(Nz,Ns3D); % Time evol. of the norm of phi
+phi_maxx_avg = zeros(Nz,Ns3D); % Time evol. of the norm of phi
+phi_avgx_avgy = zeros(Nz,Ns3D); % Time evol. of the norm of phi
+
+shear_maxx_maxy = zeros(Nz,Ns3D); % Time evol. of the norm of shear
+shear_avgx_maxy = zeros(Nz,Ns3D); % Time evol. of the norm of shear
+shear_maxx_avgy = zeros(Nz,Ns3D); % Time evol. of the norm of shear
+shear_avgx_avgy = zeros(Nz,Ns3D); % Time evol. of the norm of shear
+
+Ne_norm = zeros(Pe_max,Je_max,Ns5D); % Time evol. of the norm of Napj
+Ni_norm = zeros(Pi_max,Ji_max,Ns5D); % .
+
+% Kperp spectrum interpolation
+%full kperp points
+kperp = reshape(sqrt(KX.^2+KY.^2),[numel(KX),1]);
+% interpolated kperps
+nk_noAA = floor(2/3*numel(kx));
+kp_ip = kx;
+[thg, rg] = meshgrid(linspace(0,pi,2*nk_noAA),kp_ip);
+[xn,yn] = pol2cart(thg,rg);
+[ky_s, sortIdx] = sort(ky);
+[xc,yc] = meshgrid(ky_s,kx);
+phi_kp_t = zeros(numel(kp_ip),Nz,Ns3D);
+%
+for it = 1:numel(Ts3D) % Loop over 2D aX_XYays
+ for iz = 1:numel(z)
+ NE_ = Ne00(:,:,iz,it); NI_ = Ni00(:,:,iz,it); PH_ = PHI(:,:,iz,it);
+ phi_maxx_maxy(iz,it) = max( max(squeeze(phi(:,:,iz,it))));
+ phi_avgx_maxy(iz,it) = max(mean(squeeze(phi(:,:,iz,it))));
+ phi_maxx_avgy(iz,it) = mean( max(squeeze(phi(:,:,iz,it))));
+ phi_avgx_avgy(iz,it) = mean(mean(squeeze(phi(:,:,iz,it))));
+
+ shear_maxx_maxy(iz,it) = max( max(squeeze(-(dr2phi(:,:,iz,it)))));
+ shear_avgx_maxy(iz,it) = max(mean(squeeze(-(dr2phi(:,:,iz,it)))));
+ shear_maxx_avgy(iz,it) = mean( max(squeeze(-(dr2phi(:,:,iz,it)))));
+ shear_avgx_avgy(iz,it) = mean(mean(squeeze(-(dr2phi(:,:,iz,it)))));
+
+ GFlux_xi(iz,it) = sum(sum(ni00(:,:,iz,it).*dzphi(:,:,iz,it)))*dx*dy/Lx/Ly;
+ GFlux_yi(iz,it) = sum(sum(-ni00(:,:,iz,it).*drphi(:,:,iz,it)))*dx*dy/Lx/Ly;
+ GFlux_xe(iz,it) = sum(sum(ne00(:,:,iz,it).*dzphi(:,:,iz,it)))*dx*dy/Lx/Ly;
+ GFlux_ye(iz,it) = sum(sum(-ne00(:,:,iz,it).*drphi(:,:,iz,it)))*dx*dy/Lx/Ly;
+
+ Z_rth = interp2(xc,yc,squeeze(mean((abs(PHI(:,sortIdx,iz,it))).^2,3)),xn,yn);
+ phi_kp_t(:,iz,it) = mean(Z_rth,2);
+ end
+end
+%
+for it = 1:numel(Ts5D) % Loop over 5D aX_XYays
+ [~, it2D] = min(abs(Ts3D-Ts5D(it)));
+ Ne_norm(:,:,it)= sum(sum(abs(Nepj(:,:,:,:,it)),3),4)/Nkx/Nky;
+ Ni_norm(:,:,it)= sum(sum(abs(Nipj(:,:,:,:,it)),3),4)/Nkx/Nky;
+ epsilon_e_pj(:,:,it) = sqrt(pi)/2*sum(sum(abs(Nepj(:,:,:,:,it)).^2,3),4);
+ epsilon_i_pj(:,:,it) = sqrt(pi)/2*sum(sum(abs(Nipj(:,:,:,:,it)).^2,3),4);
+end
+
+%% Compute primary instability growth rate
+disp('- growth rate')
+% Find max value of transport (end of linear mode)
+[tmp,tmax] = max(GGAMMA_RI*(2*pi/Nx/Ny)^2);
+[~,itmax] = min(abs(Ts3D-tmax));
+tstart = 0.1 * Ts3D(itmax); tend = 0.5 * Ts3D(itmax);
+[~,its3D_lin] = min(abs(Ts3D-tstart));
+[~,ite3D_lin] = min(abs(Ts3D-tend));
+
+g_I = zeros(Nkx,Nky,Nz);
+for ikx = 1:Nkx
+ for iky = 1:Nky
+ for iz = 1:Nz
+ [g_I(ikx,iky,iz), ~] = LinearFit_s(Ts3D(its3D_lin:ite3D_lin),squeeze(abs(Ni00(ikx,iky,iz,its3D_lin:ite3D_lin))));
+ end
+ end
+end
+[gmax_I,ikmax_I] = max(max(g_I(1,:,:),[],2),[],3);
+kmax_I = abs(ky(ikmax_I));
+Bohm_transport = ETAB/ETAN*gmax_I/kmax_I^2;
+
+%% Compute secondary instability growth rate
+disp('- growth rate')
+% Find max value of transport (end of linear mode)
+% [tmp,tmax] = max(GGAMMA_RI*(2*pi/Nx/Ny)^2);
+% [~,itmax] = min(abs(Ts2D-tmax));
+% tstart = Ts2D(itmax); tend = 1.5*Ts2D(itmax);
+[~,its3D_lin] = min(abs(Ts3D-tstart));
+[~,ite3D_lin] = min(abs(Ts3D-tend));
+
+g_II = zeros(Nkx,Nky);
+for ikx = 1:Nkx
+ for iky = 1
+ for iz = 1:Nz
+ [g_II(ikx,iky,iz), ~] = LinearFit_s(Ts3D(its3D_lin:ite3D_lin),squeeze(abs(Ni00(ikx,iky,iz,its3D_lin:ite3D_lin))));
+ end
+ end
+end
+[gmax_II,ikmax_II] = max(max(g_II(1,:,:),[],2),[],3);
+kmax_II = abs(kx(ikmax_II));
+
+%% PLOTS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+default_plots_options
+disp('Plots')
+FMT = '.fig';
+
+if 1
+%% Time evolutions and growth rate
+fig = figure; FIGNAME = ['t_evolutions',sprintf('_%.2d',JOBNUM),'_',PARAMS];
+set(gcf, 'Position', [100, 100, 900, 800])
+subplot(111);
+ suptitle(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+ ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+ ' $\mu_{hd}=$',num2str(MU)]);
+ subplot(421);
+ for ip = 1:Pe_max
+ for ij = 1:Je_max
+ plt = @(x) squeeze(x(ip,ij,:));
+ plotname = ['$N_e^{',num2str(ip-1),num2str(ij-1),'}$'];
+ clr = line_colors(min(ip,numel(line_colors(:,1))),:);
+ lstyle = line_styles(min(ij,numel(line_styles)));
+ semilogy(Ts5D,plt(Ne_norm),'DisplayName',plotname,...
+ 'Color',clr,'LineStyle',lstyle{1}); hold on;
+ end
+ end
+ grid on; ylabel('$\sum_{k_r,k_z}|N_e^{pj}|$');
+ subplot(423)
+ for ip = 1:Pi_max
+ for ij = 1:Ji_max
+ plt = @(x) squeeze(x(ip,ij,:));
+ plotname = ['$N_i^{',num2str(ip-1),num2str(ij-1),'}$'];
+ clr = line_colors(min(ip,numel(line_colors(:,1))),:);
+ lstyle = line_styles(min(ij,numel(line_styles)));
+ semilogy(Ts5D,plt(Ni_norm),'DisplayName',plotname,...
+ 'Color',clr,'LineStyle',lstyle{1}); hold on;
+ end
+ end
+ grid on; ylabel('$\sum_{k_r,k_z}|N_i^{pj}|$'); xlabel('$t c_s/R$')
+ subplot(222)
+ plot(Ts0D,GGAMMA_RI*(2*pi/Nx/Ny)^2); hold on;
+ plot(Ts0D,PGAMMA_RI*(2*pi/Nx/Ny)^2);
+ legend(['Gyro. flux';'Part. flux']);
+ grid on; xlabel('$t c_s/R$'); ylabel('$\Gamma_{r,i}$')
+ if(~isnan(max(max(g_I(1,:,:)))))
+ subplot(223)
+ plot(ky,max(g_I(1,:,:),[],3),'-','DisplayName','Primar. instability'); hold on;
+ plot(kx,max(g_II(:,1,:),[],3),'x-','DisplayName','Second. instability'); hold on;
+ plot([max(ky)*2/3,max(ky)*2/3],[0,10],'--k', 'DisplayName','2/3 Orszag AA');
+ grid on; xlabel('$k\rho_s$'); ylabel('$\gamma R/c_s$'); legend('show');
+ ylim([0,max(max(g_I(1,:,:)))]); xlim([0,max(ky)]);
+ shearplot = 426; phiplot = 428;
+ else
+ shearplot = 223; phiplot = 224;
+ end
+ subplot(shearplot)
+ plt = @(x) mean(x,1);
+ clr = line_colors(min(ip,numel(line_colors(:,1))),:);
+ lstyle = line_styles(min(ij,numel(line_styles)));
+ plot(Ts3D,plt(shear_maxx_maxy),'DisplayName','$\max_{r,z}(s)$'); hold on;
+ plot(Ts3D,plt(shear_maxx_avgy),'DisplayName','$\max_{r}\langle s \rangle_z$'); hold on;
+ plot(Ts3D,plt(shear_avgx_maxy),'DisplayName','$\max_{z}\langle s \rangle_r$'); hold on;
+ plot(Ts3D,plt(shear_avgx_avgy),'DisplayName','$\langle s \rangle_{r,z}$'); hold on;
+ grid on; xlabel('$t c_s/R$'); ylabel('$shear$');
+ subplot(phiplot)
+ clr = line_colors(min(ip,numel(line_colors(:,1))),:);
+ lstyle = line_styles(min(ij,numel(line_styles)));
+ plot(Ts3D,plt(phi_maxx_maxy),'DisplayName','$\max_{r,z}(\phi)$'); hold on;
+ plot(Ts3D,plt(phi_maxx_avg),'DisplayName','$\max_{r}\langle\phi\rangle_z$'); hold on;
+ plot(Ts3D,plt(phi_avgx_maxy),'DisplayName','$\max_{z}\langle\phi\rangle_r$'); hold on;
+ plot(Ts3D,plt(phi_avgx_avgy),'DisplayName','$\langle\phi\rangle_{r,z}$'); hold on;
+ grid on; xlabel('$t c_s/R$'); ylabel('$E.S. pot$');
+save_figure
+end
+
+if 1
+%% Space time diagramm (fig 11 Ivanov 2020)
+TAVG = 5000; % Averaging time duration
+%Compute steady radial transport
+tend = Ts0D(end); tstart = tend - TAVG;
+[~,its0D] = min(abs(Ts0D-tstart));
+[~,ite0D] = min(abs(Ts0D-tend));
+SCALE = (2*pi/Nx/Ny)^2;
+gamma_infty_avg = mean(PGAMMA_RI(its0D:ite0D))*SCALE;
+gamma_infty_std = std (PGAMMA_RI(its0D:ite0D))*SCALE;
+% Compute steady shearing rate
+tend = Ts3D(end); tstart = tend - TAVG;
+[~,its2D] = min(abs(Ts3D-tstart));
+[~,ite2D] = min(abs(Ts3D-tend));
+shear_infty_avg = mean(mean(shear_maxx_avgy(:,its2D:ite2D),1));
+shear_infty_std = std (mean(shear_maxx_avgy(:,its2D:ite2D),1));
+% plots
+fig = figure; FIGNAME = ['ZF_transport_drphi','_',PARAMS];set(gcf, 'Position', [100, 100, 1200, 600])
+ subplot(311)
+% yyaxis left
+ plot(Ts0D,PGAMMA_RI*SCALE,'DisplayName','$\langle n_i d\phi/dz \rangle_z$'); hold on;
+ plot(Ts0D(its0D:ite0D),ones(ite0D-its0D+1,1)*gamma_infty_avg, '-k',...
+ 'DisplayName',['$\Gamma^{\infty} = $',num2str(gamma_infty_avg),'$\pm$',num2str(gamma_infty_std)]);
+ grid on; set(gca,'xticklabel',[]); ylabel('$\Gamma_r$')
+ ylim([0,5*abs(gamma_infty_avg)]); xlim([Ts0D(1),Ts0D(end)]);
+ title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+ ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+ ' $\mu_{hd}=$',num2str(MU)]);
+ %
+ subplot(312)
+ clr = line_colors(1,:);
+ lstyle = line_styles(1);
+% plt = @(x_) mean(x_,1);
+ plt = @(x_) x_(1,:);
+ plot(Ts3D,plt(shear_maxx_maxy),'DisplayName','$\max_{r,z}(s_\phi)$'); hold on;
+ plot(Ts3D,plt(shear_maxx_avgy),'DisplayName','$\max_{r}\langle s_\phi\rangle_z$'); hold on;
+ plot(Ts3D,plt(shear_avgx_maxy),'DisplayName','$\max_{z}\langle s_\phi\rangle_r$'); hold on;
+ plot(Ts3D,plt(shear_avgx_avgy),'DisplayName','$\langle s_\phi\rangle_{r,z}$'); hold on;
+ plot(Ts3D(its2D:ite2D),ones(ite2D-its2D+1,1)*shear_infty_avg, '-k',...
+ 'DisplayName',['$s^{\infty} = $',num2str(shear_infty_avg),'$\pm$',num2str(shear_infty_std)]);
+ ylim([0,shear_infty_avg*5.0]); xlim([Ts0D(1),Ts0D(end)]);
+ grid on; ylabel('Shear amp.');set(gca,'xticklabel',[]);% legend('show');
+ subplot(313)
+ [TY,TX] = meshgrid(x,Ts3D);
+ pclr = pcolor(TX,TY,squeeze((mean(dr2phi(:,:,1,:),2)))'); set(pclr, 'edgecolor','none'); legend('Shear ($\langle \partial_r^2\phi\rangle_z$)') %colorbar;
+ caxis(1*shear_infty_avg*[-1 1]); xlabel('$t c_s/R$'), ylabel('$x/\rho_s$'); colormap(bluewhitered(256))
+save_figure
+end
+
+if 0
+%% Space time diagramms
+tstart = 0; tend = Ts3D(end);
+[~,itstart] = min(abs(Ts3D-tstart));
+[~,itend] = min(abs(Ts3D-tend));
+trange = itstart:itend;
+[TY,TX] = meshgrid(x,Ts3D(trange));
+fig = figure; FIGNAME = ['space_time','_',PARAMS];set(gcf, 'Position', [100, 100, 1200, 600])
+ subplot(211)
+% pclr = pcolor(TX,TY,squeeze(mean(dens_i(:,:,trange).*dzphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
+ pclr = pcolor(TX,TY,squeeze(mean(ni00(:,:,trange).*dzphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
+ shading interp
+ colormap hot;
+ caxis([0.0,0.05*max(max(mean(ni00(:,:,its2D:ite2D).*dzphi(:,:,its2D:ite2D),2)))]);
+ caxis([0.0,0.01]); c = colorbar; c.Label.String ='\langle n_i\partial_z\phi\rangle_z';
+ xticks([]); ylabel('$x/\rho_s$')
+% legend('Radial part. transport $\langle n_i\partial_z\phi\rangle_z$')
+ title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+ ', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+ ' $\mu_{hd}=$',num2str(MU)]);
+ subplot(212)
+ pclr = pcolor(TX,TY,squeeze(mean(drphi(:,:,1,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
+ fieldmax = max(max(mean(abs(drphi(:,:,1,its2D:ite2D)),2)));
+ caxis([-fieldmax,fieldmax]); c = colorbar; c.Label.String ='\langle \partial_r\phi\rangle_z';
+ xlabel('$t c_s/R$'), ylabel('$x/\rho_s$')
+% legend('Zonal flow $\langle \partial_r\phi\rangle_z$')
+save_figure
+end
+
+if 0
+%% Averaged shear and Reynold stress profiles
+trange = its2D:ite2D;
+% trange = 100:200;
+figure;
+plt = @(x) squeeze(mean(mean(real(x(:,:,trange)),2),3))/max(abs(squeeze(mean(mean(real(x(:,:,trange)),2),3))));
+plot(r,plt(-dr2phi),'-k','DisplayName','Zonal shear'); hold on;
+plot(r,plt(-drphi.*dzphi),'-','DisplayName','$\Pi_\phi$'); hold on;
+% plot(r,plt(-drphi.*dzTe),'-','DisplayName','$\Pi_{Te}$'); hold on;
+plot(r,plt(-drphi.*dzTi),'-','DisplayName','$\Pi_{Ti}$'); hold on;
+plot(r,plt(-drphi.*dzphi-drphi.*dzTi),'-','DisplayName','$\Pi_\phi+\Pi_{Ti}$'); hold on;
+% plot(r,plt(-drphi.*dzphi-drphi.*dzTi-drphi.*dzTe),'-','DisplayName','$\Pi_\phi+\Pi_{Te}+\Pi_{Ti}$'); hold on;
+xlim([-L/2,L/2]); xlabel('$x/\rho_s$'); grid on; legend('show')
+end
+
+if 0
+%% |phi_k|^2 spectra (Kobayashi 2015 fig 3)
+tstart = 0.8*Ts3D(end); tend = Ts3D(end);
+[~,itstart] = min(abs(Ts3D-tstart));
+[~,itend] = min(abs(Ts3D-tend));
+trange = itstart:itend;
+%full kperp points
+phi_k_2 = reshape(mean(mean(abs(PHI(:,:,:,trange)),3),4).^2,[numel(KX),1]);
+kperp = reshape(sqrt(KX.^2+KY.^2),[numel(KX),1]);
+% interpolated kperps
+nk_noAA = floor(2/3*numel(kx));
+kp_ip = kx;
+[thg, rg] = meshgrid(linspace(0,pi,2*nk_noAA),kp_ip);
+[xn,yn] = pol2cart(thg,rg);
+[ky_s, sortIdx] = sort(ky);
+[xc,yc] = meshgrid(ky_s,kx);
+Z_rth = interp2(xc,yc,squeeze(mean((abs(PHI(:,sortIdx,trange))).^2,3)),xn,yn);
+phi_kp = mean(Z_rth,2);
+Z_rth = interp2(xc,yc,squeeze(mean((abs(Ni00(:,sortIdx,trange))).^2,3)),xn,yn);
+ni00_kp = mean(Z_rth,2);
+Z_rth = interp2(xc,yc,squeeze(mean((abs(Ne00(:,sortIdx,trange))).^2,3)),xn,yn);
+ne00_kp = mean(Z_rth,2);
+%for theorical trends
+a1 = phi_kp(2)*kp_ip(2).^(13/3);
+a2 = phi_kp(2)*kp_ip(2).^(3)./(1+kp_ip(2).^2).^(-2);
+fig = figure; FIGNAME = ['cascade','_',PARAMS];set(gcf, 'Position', [100, 100, 500, 500])
+% scatter(kperp,phi_k_2,'.k','MarkerEdgeAlpha',0.4,'DisplayName','$|\phi_k|^2$'); hold on; grid on;
+plot(kp_ip,phi_kp,'^','DisplayName','$\langle|\phi_k|^2\rangle_{k_\perp}$'); hold on;
+plot(kp_ip,ni00_kp, '^','DisplayName','$\langle|N_{i,k}^{00}|^2\rangle_{k_\perp}$'); hold on;
+plot(kp_ip,ne00_kp, '^','DisplayName','$\langle|N_{e,k}^{00}|^2\rangle_{k_\perp}$'); hold on;
+plot(kp_ip,a1*kp_ip.^(-13/3),'-','DisplayName','$k^{-13/3}$');
+plot(kp_ip,a2/100*kp_ip.^(-3)./(1+kp_ip.^2).^2,'-','DisplayName','$k^{-3}/(1+k^2)^2$');
+set(gca, 'XScale', 'log');set(gca, 'YScale', 'log'); grid on
+xlabel('$k_\perp \rho_s$'); legend('show','Location','southwest')
+title({['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
+', $L=',num2str(L),'$, $N=',num2str(Nx),'$'];[' $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
+' $\mu_{hd}=$',num2str(MU)]});
+xlim([0.1,10]);
+save_figure
+clear Z_rth phi_kp ni_kp Ti_kp
+end
+
+if 0
+%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Options
+t0 =00; iz = 1; ix = 1; iy = 1;
+skip_ = 1; DELAY = 1e-2*skip_;
+[~, it03D] = min(abs(Ts3D-t0)); FRAMES_3D = it03D:skip_:numel(Ts3D);
+[~, it05D] = min(abs(Ts5D-t0)); FRAMES_5D = it05D:skip_:numel(Ts5D);
+INTERP = 0; T = Ts3D; FRAMES = FRAMES_3D;
+% Field to plot
+FIELD = dens_e; NAME = 'ne'; FIELDNAME = 'n_e';
+% FIELD = dens_i; NAME = 'ni'; FIELDNAME = 'n_i';
+% FIELD = temp_e; NAME = 'Te'; FIELDNAME = 'n_i';
+% FIELD = temp_i; NAME = 'Ti'; FIELDNAME = 'n_i';
+% FIELD = ne00; NAME = 'ne00'; FIELDNAME = 'n_e^{00}';
+% FIELD = ni00; NAME = 'ni00'; FIELDNAME = 'n_i^{00}';
+% Slice
+% plt = @(x) real(x(ix, :, :,:)); X = Y_YZ; Y = Z_YZ; XNAME = 'y'; YNAME = 'z';
+% plt = @(x) real(x( :,iy, :,:)); X = X_XZ; Y = Z_XZ; XNAME = 'x'; YNAME = 'z';
+plt = @(x) real(x( :, :,iz,:)); X = X_XY; Y = Y_XY; XNAME = 'x'; YNAME = 'y';
+
+% Averaged
+% plt = @(x) mean(x,1); X = Y_YZ; Y = Z_YZ; XNAME = 'y'; YNAME = 'z';
+% plt = @(x) mean(x,2); X = X_XZ; Y = Z_XZ; XNAME = 'x'; YNAME = 'z';
+% plt = @(x) mean(x,3); X = X_XY; Y = Y_XY; XNAME = 'x'; YNAME = 'y';
+
+FIELD = squeeze(plt(FIELD));
+
+% Naming
+GIFNAME = [NAME,sprintf('_%.2d',JOBNUM),'_',PARAMS];
+
+% Create movie (gif or mp4)
+create_gif
+% create_mov
+end
+
+if 0
+%% Photomaton : real space
+
+% Chose the field to plot
+% FIELD = ni00; FNAME = 'ni00'; FIELDLTX = 'n_i^{00}';
+% FIELD = ne00; FNAME = 'ne00'; FIELDLTX = 'n_e^{00}'
+% FIELD = dens_i; FNAME = 'ni'; FIELDLTX = 'n_i';
+% FIELD = dens_e; FNAME = 'ne'; FIELDLTX = 'n_e';
+% FIELD = temp_i; FNAME = 'Ti'; FIELDLTX = 'T_i';
+% FIELD = temp_e; FNAME = 'Te'; FIELDLTX = 'T_e';
+FIELD = phi; FNAME = 'phi'; FIELDLTX = '\phi';
+
+% Chose when to plot it
+tf = [0 1 2 3];
+
+% Slice
+ix = 1; iy = 1; iz = 1;
+% plt = @(x,it) real(x(ix, :, :,it)); X = Y_YZ; Y = Z_YZ; XNAME = 'y'; YNAME = 'z'; FIELDLTX = [FIELDLTX,'(x=',num2str(round(x(ix))),')']
+% plt = @(x,it) real(x( :,iy, :,it)); X = X_XZ; Y = Z_XZ; XNAME = 'x'; YNAME = 'z'; FIELDLTX = [FIELDLTX,'(y=',num2str(round(y(iy))),')']
+% plt = @(x,it) real(x( :, :,iz,it)); X = X_XY; Y = Y_XY; XNAME = 'x'; YNAME = 'y'; FIELDLTX = [FIELDLTX,'(x=',num2str(round(z(iz))),')']
+
+% Averaged
+% plt = @(x,it) mean(x(:,:,:,it),1); X = Y_YZ; Y = Z_YZ; XNAME = 'y'; YNAME = 'z'; FIELDLTX = ['\langle',FIELDLTX,'\rangle_x']
+% plt = @(x,it) mean(x(:,:,:,it),2); X = X_XZ; Y = Z_XZ; XNAME = 'x'; YNAME = 'z'; FIELDLTX = ['\langle',FIELDLTX,'\rangle_y']
+plt = @(x,it) mean(x(:,:,:,it),3); X = X_XY; Y = Y_XY; XNAME = 'x'; YNAME = 'y'; FIELDLTX = ['\langle',FIELDLTX,'\rangle_z']
+
+
+%
+TNAME = [];
+fig = figure; FIGNAME = [FNAME,TNAME,'_snaps','_',PARAMS]; set(gcf, 'Position', [100, 100, 1500, 350])
+plt_2 = @(x) x./max(max(x));
+ for i_ = 1:numel(tf)
+ [~,it] = min(abs(Ts3D-tf(i_))); TNAME = [TNAME,'_',num2str(Ts3D(it))];
+ subplot(1,numel(tf),i_)
+ DATA = plt_2(squeeze(plt(FIELD,it)));
+ pclr = pcolor((X),(Y),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
+ colormap(bluewhitered); caxis([-1,1]);
+ xlabel(latexize(XNAME)); ylabel(latexize(YNAME));set(gca,'ytick',[]);
+ title(sprintf('$t c_s/R=%.0f$',Ts3D(it)));
+ end
+ legend(latexize(FIELDLTX));
+save_figure
+end
+
+%%
+% ZF_fourier_analysis
+end
\ No newline at end of file
diff --git a/wk/compile_cosolver_mat.m b/wk/compile_cosolver_mat.m
index 983d6618..7b2310dd 100644
--- a/wk/compile_cosolver_mat.m
+++ b/wk/compile_cosolver_mat.m
@@ -1,14 +1,14 @@
addpath(genpath('../matlab')) % ... add
%% Grid configuration
-N = 200; % Frequency gridpoints (Nkr = N/2)
+N = 200; % Frequency gridpoints (Nkx = N/2)
L = 120; % Size of the squared frequency domain
dk = 2.*pi/L;
kmax = N/2*dk;
-kr = dk*(0:N/2);
-kz = dk*(0:N/2);
-[KZ, KR]= meshgrid(kz,kr);
-KPERP = sqrt(KR.^2 + KZ.^2);
-kperp = reshape(KPERP,[1,numel(kr)^2]);
+kx = dk*(0:N/2);
+ky = dk*(0:N/2);
+[ky, kx]= meshgrid(ky,kx);
+KPERP = sqrt(kx.^2 + ky.^2);
+kperp = reshape(KPERP,[1,numel(kx)^2]);
kperp = uniquetol(kperp,1e-14);
Nperp = numel(kperp);
%% Model
diff --git a/wk/compute_collision_mat.m b/wk/compute_collision_mat.m
index a429236e..ac5214c1 100644
--- a/wk/compute_collision_mat.m
+++ b/wk/compute_collision_mat.m
@@ -1,14 +1,14 @@
addpath(genpath('../matlab')) % ... add
%% Grid configuration
-N = 200; % Frequency gridpoints (Nkr = N/2)
+N = 200; % Frequency gridpoints (Nkx = N/2)
L = 120; % Size of the squared frequency domain
dk = 2.*pi/L;
kmax = N/2*dk;
-kr = dk*(0:N/2);
-kz = dk*(0:N/2);
-[KZ, KR]= meshgrid(kz,kr);
-KPERP = sqrt(KR.^2 + KZ.^2);
-kperp = reshape(KPERP,[1,numel(kr)^2]);
+kx = dk*(0:N/2);
+ky = dk*(0:N/2);
+[ky, kx]= meshgrid(ky,kx);
+KPERP = sqrt(kx.^2 + ky.^2);
+kperp = reshape(KPERP,[1,numel(kx)^2]);
kperp = uniquetol(kperp,1e-14);
Nperp = numel(kperp);
%% Model
diff --git a/wk/continue_multiple_runs_marconi.m b/wk/continue_multiple_runs_marconi.m
index 0e701e36..47f91c36 100644
--- a/wk/continue_multiple_runs_marconi.m
+++ b/wk/continue_multiple_runs_marconi.m
@@ -1,5 +1,5 @@
%% Paste the list of continue_run calls
-continue_run('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/300x150_L_100_P_10_J_5_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00/out.txt')
+continue_run('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-02_SGGK_CLOS_0_mu_1e-02/out.txt')
%% Functions to modify preexisting fort.90 input file and launch on marconi
function [] = continue_run(outfilename)
@@ -10,8 +10,8 @@ function [] = continue_run(outfilename)
if(strcmp(CLUSTER.PART,'dbg')); CLUSTER.TIME = '00:30:00'; end;
CLUSTER.MEM = '64GB'; % Memory
CLUSTER.JNAME = 'HeLaZ';% Job name
- NP_P = 3; % MPI processes along p
- NP_KX = 32; % MPI processes along kx
+ NP_P = 2; % MPI processes along p
+ NP_KX = 24; % MPI processes along kx
% Compute processes distribution
Ntot = NP_P * NP_KX;
Nnodes = ceil(Ntot/48);
@@ -44,36 +44,33 @@ function [] = continue_run(outfilename)
line = A{35};
line = line(end-2:end);
if(line(1) == '='); line = line(end); end;
- J2L = str2num(line)+1;
+ J2L = str2num(line) + 1;
end
% Change job 2 load in fort.90
A{35} = [' job2load = ',num2str(J2L)];
disp(A{35})
% Change time step
- line_= A{3}; dt_old = str2num(line_(12:end));
- A{3} = [' dt = ',num2str(1.5*dt_old)];
+ A{3} = [' dt = 0.005'];
% Increase endtime
- A{4} = [' tmax = 20000'];
+ A{4} = [' tmax = 10000'];
% Put non linear term back
- line_= A{41}; NL_old = str2num(line_(13:end));
- A{41} = [' NL_CLOS = ',num2str(NL_old)];
-% A{41} = [' NL_CLOS = -1'];
+ A{41} = [' NL_CLOS = -1'];
% change HD
- line_= A{43}; mu_old = str2num(line_(13:end));
- A{43} = [' mu = ',num2str(0*mu_old)];
- % change N
- line_= A{13}; N_old = str2num(line_(8:end));
- A{13} = [' Nr = ',num2str(N_old)];
- A{15} = [' Nz = ',num2str(N_old)];
+ line_= A{43};
+ mu_old = str2num(line_(13:end));
+ A{43} = [' mu = ',num2str(mu_old*2)];
% change L
- line_= A{14}; L_old = str2num(line_(8:end));
- A{14} = [' Lr = ',num2str(L_old)];
- A{16} = [' Lz = ',num2str(L_old)];
+ line_= A{14};
+ L_old = str2num(line_(8:end));
+ A{14} = [' Lx = ',num2str(L_old)];
+ A{16} = [' Ly = ',num2str(L_old)];
% change eta N
- line_= A{53}; etan_old = str2num(line_(13:end));
+ line_= A{53};
+ etan_old = str2num(line_(13:end));
A{53} = [' eta_n = ',num2str(etan_old)];
% change eta B
- line_= A{55}; etab_old = str2num(line_(13:end));
+ line_= A{55};
+ etab_old = str2num(line_(13:end));
A{55} = [' eta_B = ',num2str(etab_old)];
% Rewrite fort.90
fid = fopen('fort.90', 'w');
diff --git a/wk/daint_run.m b/wk/daint_run.m
index e7f53ac3..95806c96 100644
--- a/wk/daint_run.m
+++ b/wk/daint_run.m
@@ -6,7 +6,7 @@ addpath(genpath('../matlab')) % ... add
%% CLUSTER PARAMETERS
CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
NP_P = 2; % MPI processes along p
-NP_KR = 18; % MPI processes along kr
+NP_KX = 18; % MPI processes along kx
CLUSTER.PART = 'normal'; % debug or normal
if(strcmp(CLUSTER.PART,'debug')); CLUSTER.TIME = '00:30:00'; end;
CLUSTER.MEM = '12GB'; % Memory
@@ -18,7 +18,7 @@ NU = 0.1; % Collision frequency
ETAB = 0.6; % Magnetic gradient
NU_HYP = 1.0; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-N = 200; % Frequency gridpoints (Nkr = N/2)
+N = 200; % Frequency gridpoints (Nkx = N/2)
L = 120; % Size of the squared frequency domain
P = 12; % Electron and Ion highest Hermite polynomial degree
J = 06; % Electron and Ion highest Laguerre polynomial degree
@@ -38,7 +38,7 @@ SIMID = ['HeLaZ_v2.5_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulati
% SIMID = 'test_marconi_sugama'; % Name of the simulation
SIMID = sprintf(SIMID,NU);
PREFIX =[];
-% PREFIX = sprintf('%d_%d_',NP_P, NP_KR);
+% PREFIX = sprintf('%d_%d_',NP_P, NP_KX);
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Full Couloumb ; +/- for GK/DK)
CO = 1;
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
@@ -55,11 +55,11 @@ W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% fixed parameters (for current study)
-KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
-KREQ0 = 0; % put kr = 0
+KX0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
+KXEQ0 = 0; % put kx = 0
KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
-NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
+NON_LIN = 1 *(1-KXEQ0); % activate non-linearity (is cancelled if KXEQ0 = 1)
PMAXE = P; % Highest electron Hermite polynomial degree
JMAXE = J; % Highest '' Laguerre ''
PMAXI = P; % Highest ion Hermite polynomial degree
@@ -72,11 +72,11 @@ ETAT = 0.0; % Temperature gradient
ETAN = 1.0; % Density gradient
TAU = 1.0; % e/i temperature ratio
% Compute processes distribution
-Ntot = NP_P * NP_KR;
+Ntot = NP_P * NP_KX;
Nnodes = ceil(Ntot/36);
Nppn = Ntot/Nnodes;
CLUSTER.NODES = num2str(Nnodes); % MPI process along p
-CLUSTER.NTPN = num2str(Nppn); % MPI process along kr
+CLUSTER.NTPN = num2str(Nppn); % MPI process along kx
CLUSTER.CPUPT = '1'; % CPU per task
CLUSTER.NTPC = '1'; % N tasks per core (openmp threads)
%% Run file management scripts
@@ -84,6 +84,6 @@ setup
write_sbash_daint
system('rm fort.90 setup_and_run.sh batch_script.sh');
disp('done');
-if(mod(NP_P*NP_KR,36)~= 0)
+if(mod(NP_P*NP_KX,36)~= 0)
disp('WARNING : unused cores (ntot cores must be a 36 multiple)');
end
\ No newline at end of file
diff --git a/wk/fig_post_processing.m b/wk/fig_post_processing.m
index 1479162b..e51be527 100644
--- a/wk/fig_post_processing.m
+++ b/wk/fig_post_processing.m
@@ -37,7 +37,7 @@ Results_150x75.P = [2, 4, 6, 2, 4, 6
Results_150x75.J = [1, 2, 3 1 2 3 4 1, 2, 3 1, 2, 3 4 1, 2 5];
Results_150x75.etaB = [0.49, 0.49 0.49 0.59 0.59 0.59 0.59 0.50, 0.50 0.50 0.60, 0.60 0.60 0.60 0.51 0.51 0.51];
Results_150x75.nu = [1.0, 1.0 1.0 1.0 1.0 1.0 1.0 0.5, 0.5 0.5 0.5, 0.5 0.5 0.5 0.1 0.1 0.1];
-Results_150x75.mrkr = [ '*', '*', '*', '*', '*', '*', '*', 'o', 'o', 'o', 'o', 'o', 'o', 'o' 's' 's' 's'];
+Results_150x75.mrkx = [ '*', '*', '*', '*', '*', '*', '*', 'o', 'o', 'o', 'o', 'o', 'o', 'o' 's' 's' 's'];
Results_150x75.iclr = [ 1, 2, 3, 1 2 3 4 1, 2, 3 1, 2, 3 4 1 2 5];
% Ricci_Rogers.Gamma = [2 1e-1];
@@ -61,7 +61,7 @@ plot(10,10,'sk','MarkerSize',10, 'LineWidth',1.0);
res = Results_150x75;
for i = 1:numel(res.Gamma)
errorbar(res.etaB(i),res.Gamma(i)*SCALING,res.error(i)*SCALING,...
- res.mrkr(i),'DisplayName','256x128', 'color', line_colors(res.iclr(i),:),...
+ res.mrkx(i),'DisplayName','256x128', 'color', line_colors(res.iclr(i),:),...
'MarkerSize',12, 'LineWidth',2.0);
hold on;
end
diff --git a/wk/flux_results.m b/wk/flux_results.m
index 22f77dcb..594b3b62 100644
--- a/wk/flux_results.m
+++ b/wk/flux_results.m
@@ -17,7 +17,7 @@ Results_256x128.L = [ 66, 66, 66, 50, 66, 66, 66, 66, 66,
Results_256x128.P = [ 2, 3, 4, 5, 2, 3, 4, 2, 3, 4];
Results_256x128.J = [ 1, 2, 2, 3, 1, 2, 2, 1, 2, 2];
Results_256x128.etaB = [ 0.5, 0.5, 0.5, 0.5, 0.4, 0.4, 0.4, 0.6, 0.6, 0.6];
-Results_256x128.mrkr = [ 'v', '>', '^', 'o', 'v', '>', '^', 'v', '>', '^'];
+Results_256x128.mrkx = [ 'v', '>', '^', 'o', 'v', '>', '^', 'v', '>', '^'];
Results_256x128.clr = [ 'k', 'k', 'k', 'r', 'r', 'r', 'r', 'k', 'k', 'k'];
% Low definition results (128x64)
% Results_128x64.Gamma = [0.29, 0.05, 7e-4, 0.31, 3.7, 2e-3];
@@ -26,7 +26,7 @@ Results_256x128.clr = [ 'k', 'k', 'k', 'r', 'r', 'r', 'r', 'k', 'k',
% Results_128x64.J = [ 1, 1, 1, 1, 1, 1];
% Results_128x64.NU = [0.01, 0.1, 0.01, 0.01, 0.01, 0.01];
% Results_128x64.etaB = [ 0.5, 0.5, 0.67, 0.5 0.4, 0.6];
-% Results_128x64.mrkr = [ 's', 's', 's', 's', 's', 's'];
+% Results_128x64.mrkx = [ 's', 's', 's', 's', 's', 's'];
% Results_128x64.clr = [ 'b', 'b', 'b', 'r', 'r', 'r'];
% Ricci_Rogers.Gamma = [2.5 1 1e-2];
@@ -41,14 +41,14 @@ hold on;
res = Results_256x128;
for i = 1:numel(res.Gamma)
semilogy(res.etaB(i),res.Gamma(i)*SCALING,...
- res.mrkr(i),'DisplayName','256x128', 'color', res.clr(i));
+ res.mrkx(i),'DisplayName','256x128', 'color', res.clr(i));
hold on;
end
% res = Results_128x64;
% for i = 1:numel(res.Gamma)
% if res.NU(i) == 0.01
% semilogy(res.etaB(i),res.Gamma(i),...
-% res.mrkr(i),'DisplayName','128x64', 'color', res.clr(i));
+% res.mrkx(i),'DisplayName','128x64', 'color', res.clr(i));
% end
% hold on;
% end
@@ -67,7 +67,7 @@ Results_256x128.Gamma = [0.026,0.026, 1e-2, 1, 1, 1, 2e-2, 1, 0.15,
Results_256x128.P = [ 2, 3, 4, 2, 3, 4, 2, 3, 4, 4];
Results_256x128.J = [ 1, 2, 2, 1, 2, 2, 1, 2, 2, 2];
Results_256x128.etaB = [ 0.5, 0.5, 0.5, 0.4, 0.4, 0.4, 0.6, 0.6, 0.6, 0.7];
-Results_256x128.mrkr = [ 'v', '>', '^', 'v', '>', '^', 'v', '>', '^', '^'];
+Results_256x128.mrkx = [ 'v', '>', '^', 'v', '>', '^', 'v', '>', '^', '^'];
Results_256x128.clr = [ 'k', 'k', 'k', 'b', 'b', 'b', 'r', 'b', 'r', 'r'];
% Ricci_Rogers.Gamma = [2 1e-1];
@@ -84,7 +84,7 @@ hold on;
res = Results_256x128;
for i = 1:numel(res.Gamma)
semilogy(res.etaB(i),res.Gamma(i)*SCALING,...
- res.mrkr(i),'DisplayName','256x128', 'color', res.clr(i));
+ res.mrkx(i),'DisplayName','256x128', 'color', res.clr(i));
hold on;
end
@@ -104,7 +104,7 @@ Results_256x128.Gamma = [0.026,0.026, 1e-2, 1, 1, 1, 2e-2, 1, 0.15,
Results_256x128.P = [ 2, 3, 4, 2, 3, 4, 2, 3, 4, 4];
Results_256x128.J = [ 1, 2, 2, 1, 2, 2, 1, 2, 2, 2];
Results_256x128.etaB = [ 0.5, 0.5, 0.5, 0.4, 0.4, 0.4, 0.6, 0.6, 0.6, 0.7];
-Results_256x128.mrkr = [ 'v', '>', '^', 'v', '>', '^', 'v', '>', '^', '^'];
+Results_256x128.mrkx = [ 'v', '>', '^', 'v', '>', '^', 'v', '>', '^', '^'];
Results_256x128.clr = [ 'k', 'k', 'k', 'b', 'b', 'b', 'r', 'b', 'r', 'r'];
% Ricci_Rogers.Gamma = [2 1e-1];
@@ -121,7 +121,7 @@ hold on;
res = Results_256x128;
for i = 1:numel(res.Gamma)
semilogy(res.etaB(i),res.Gamma(i)*SCALING,...
- res.mrkr(i),'DisplayName','256x128', 'color', res.clr(i));
+ res.mrkx(i),'DisplayName','256x128', 'color', res.clr(i));
hold on;
end
@@ -140,7 +140,7 @@ Results_150x75.Gamma = [0.026,0.026, 1e-2, 1, 1, 1, 2e-2, 1, 0.15,
Results_150x75.P = [ 2, 3, 4, 2, 3, 4, 2, 3, 4, 4];
Results_150x75.J = [ 1, 2, 2, 1, 2, 2, 1, 2, 2, 2];
Results_150x75.etaB = [ 0.5, 0.5, 0.5, 0.4, 0.4, 0.4, 0.6, 0.6, 0.6, 0.7];
-Results_150x75.mrkr = [ 'v', '>', '^', 'v', '>', '^', 'v', '>', '^', '^'];
+Results_150x75.mrkx = [ 'v', '>', '^', 'v', '>', '^', 'v', '>', '^', '^'];
Results_150x75.clr = [ 'k', 'k', 'k', 'b', 'b', 'b', 'r', 'b', 'r', 'r'];
% Ricci_Rogers.Gamma = [2 1e-1];
@@ -157,7 +157,7 @@ hold on;
res = Results_150x75;
for i = 1:numel(res.Gamma)
semilogy(res.etaB(i),res.Gamma(i)*SCALING,...
- res.mrkr(i),'DisplayName','256x128', 'color', res.clr(i));
+ res.mrkx(i),'DisplayName','256x128', 'color', res.clr(i));
hold on;
end
diff --git a/wk/izar_run.m b/wk/izar_run.m
index 168f6911..035adff3 100644
--- a/wk/izar_run.m
+++ b/wk/izar_run.m
@@ -9,14 +9,14 @@ CLUSTER.PART = 'gpu'; % debug/gpu
CLUSTER.MEM = '4G'; % Memory
CLUSTER.JNAME = 'gamma_inf';% Job name
NP_P = 1; % MPI processes along p (nodes)
-NP_KR = 20; % MPI processes along kr (cpu)
+NP_KX = 20; % MPI processes along kx (cpu)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.1; % Collision frequency
ETAB = 0.6; % Magnetic gradient
NU_HYP = 1.0; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-N = 50; % Frequency gridpoints (Nkr = N/2)
+N = 50; % Frequency gridpoints (Nkx = N/2)
L = 10; % Size of the squared frequency domain
P = 04; % Electron and Ion highest Hermite polynomial degree
J = 04; % Electron and Ion highest Laguerre polynomial degree
@@ -36,7 +36,7 @@ JOB2LOAD= 0;
% SIMID = sprintf(SIMID,NU);
SIMID = 'izar_setup'; % Name of the simulation
PREFIX =[];
-% PREFIX = sprintf('%d_%d_',NP_P, NP_KR);
+% PREFIX = sprintf('%d_%d_',NP_P, NP_KX);
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Full Couloumb ; +/- for GK/DK)
CO = 1;
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
@@ -53,11 +53,11 @@ W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% fixed parameters (for current study)
-KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
-KREQ0 = 0; % put kr = 0
+KX0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
+KXEQ0 = 0; % put kx = 0
KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
-NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
+NON_LIN = 1 *(1-KXEQ0); % activate non-linearity (is cancelled if KXEQ0 = 1)
PMAXE = P; % Highest electron Hermite polynomial degree
JMAXE = J; % Highest '' Laguerre ''
PMAXI = P; % Highest ion Hermite polynomial degree
@@ -70,17 +70,17 @@ ETAT = 0.0; % Temperature gradient
ETAN = 1.0; % Density gradient
TAU = 1.0; % e/i temperature ratio
% Compute processes distribution
-Ntot = NP_P * NP_KR;
+Ntot = NP_P * NP_KX;
Nnodes = ceil(Ntot/48);
Nppn = Ntot/Nnodes;
CLUSTER.NODES = num2str(Nnodes); % MPI process along p
-CLUSTER.NTPN = num2str(Nppn); % MPI process along kr
+CLUSTER.NTPN = num2str(Nppn); % MPI process along kx
CLUSTER.CPUPT = '1'; % CPU per task
%% Run file management scripts
setup
write_sbash_izar
system('rm fort.90 setup_and_run.sh batch_script.sh');
disp('done');
-if(mod(NP_P*NP_KR,20)~= 0)
+if(mod(NP_P*NP_KX,20)~= 0)
disp('WARNING : unused cores (ntot cores must be a 20 multiple)');
end
\ No newline at end of file
diff --git a/wk/linear_study.m b/wk/linear_study.m
index 5838766d..223568a4 100644
--- a/wk/linear_study.m
+++ b/wk/linear_study.m
@@ -1,5 +1,5 @@
-for NU = [0.14]
-for ETAB = [1/1.4]
+for NU = [0.01]
+for ETAN = [2.0]
for CO = [3]
%clear all;
addpath(genpath('../matlab')) % ... add
@@ -11,24 +11,24 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%% PHYSICAL PARAMETERS
% NU = 1.0; % Collision frequency
TAU = 1.0; % e/i temperature ratio
-% ETAB = 0.5;
-ETAN = 1.0; % Density gradient
+ETAB = 1.0;
+% ETAN = ETAN; % Density gradient
ETAT = 0.0; % Temperature gradient
NU_HYP = 0.0; % Hyperdiffusivity coefficient
LAMBDAD = 0.0;
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 50; % Frequency gridpoints (Nkr = N/2)
+N = 50; % Frequency gridpoints (Nkx = N/2)
L = 100; % Size of the squared frequency domain
-KREQ0 = 1; % put kr = 0
+KXEQ0 = 1; % put kx = 0
MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARMETERS
-TMAX = 100; % Maximal time unit
+TMAX = 200; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 1; % Sampling per time unit for 2D arrays
-SPS5D = 1/200; % Sampling per time unit for 5D arrays
+SPS5D = 1/50; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 00;
@@ -36,7 +36,7 @@ JOB2LOAD= 00;
% SIMID = 'v2.7_lin_analysis'; % Name of the simulation
SIMID = 'kobayashi_2015_fig2'; % Name of the simulation
% SIMID = 'v2.6_lin_analysis'; % Name of the simulation
-NON_LIN = 0 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
+NON_LIN = 0 *(1-KXEQ0); % activate non-linearity (is cancelled if KXEQ0 = 1)
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Full Couloumb ; +/- for GK/DK)
% CO = 2;
@@ -68,11 +68,11 @@ MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
%% PARAMETER SCANS
if 1
%% Parameter scan over PJ
-PA = [2, 6, 10];
-JA = [1, 3, 5];
-% PA = [2 4];
-% JA = [1 2];
-DTA= DT./sqrt(JA)/4;
+% PA = [2 4 6 10];
+% JA = [1 2 3 5];
+PA = [2];
+JA = [1];
+DTA= DT*ones(size(JA));%./sqrt(JA);
% DTA= DT;
mup_ = MU_P;
muj_ = MU_J;
@@ -101,20 +101,20 @@ for i = 1:Nparam
tend = Ts2D(end); tstart = 0.4*tend;
[~,itstart] = min(abs(Ts2D-tstart));
[~,itend] = min(abs(Ts2D-tend));
- for ikr = 1:N/2+1
- gamma_Ni00(i,ikr) = (LinearFit_s(Ts2D(itstart:itend)',(squeeze(abs(Ni00(ikr,1,itstart:itend))))));
- Ni00_ST(i,ikr,1:numel(Ts2D)) = squeeze((Ni00(ikr,1,:)));
+ for ikx = 1:N/2+1
+ gamma_Ni00(i,ikx) = (LinearFit_s(Ts2D(itstart:itend)',(squeeze(abs(Ni00(ikx,1,itstart:itend))))));
+ Ni00_ST(i,ikx,1:numel(Ts2D)) = squeeze((Ni00(ikx,1,:)));
end
tend = Ts5D(end); tstart = 0.4*tend;
[~,itstart] = min(abs(Ts5D-tstart));
[~,itend] = min(abs(Ts5D-tend));
- for ikr = 1:N/2+1
- gamma_Nipj(i,ikr) = LinearFit_s(Ts5D(itstart:itend)',squeeze(max(max(abs(Nipj(:,:,ikr,1,itstart:itend)),[],1),[],2)));
+ for ikx = 1:N/2+1
+ gamma_Nipj(i,ikx) = LinearFit_s(Ts5D(itstart:itend)',squeeze(max(max(abs(Nipj(:,:,ikx,1,itstart:itend)),[],1),[],2)));
end
gamma_Ni00(i,:) = real(gamma_Ni00(i,:) .* (gamma_Ni00(i,:)>=0.0));
gamma_Nipj(i,:) = real(gamma_Nipj(i,:) .* (gamma_Nipj(i,:)>=0.0));
-% kzmax = abs(kr(ikzmax));
-% Bohm_transport(i) = ETAB/ETAN*gmax/kzmax^2;
+% kymax = abs(kx(ikymax));
+% Bohm_transport(i) = ETAB/ETAN*gmax/kymax^2;
% Clean output
system(['rm -r ',BASIC.RESDIR]);
end
@@ -128,14 +128,14 @@ plt = @(x) x;
for i = 1:Nparam
clr = line_colors(mod(i-1,numel(line_colors(:,1)))+1,:);
linestyle = line_styles(floor((i-1)/numel(line_colors(:,1)))+1);
- semilogx(plt(SCALE*kr(2:numel(kr))),plt(gamma_Ni00(i,2:end)),...
+ semilogx(plt(SCALE*kx(2:numel(kx))),plt(gamma_Ni00(i,2:end)),...
'Color',clr,...
'LineStyle',linestyle{1},'Marker','^',...
- 'DisplayName',['$\eta_B=',num2str(ETAB),'$, $\nu_{',CONAME,'}=',num2str(NU),'$, $P=',num2str(PA(i)),'$, $J=',num2str(JA(i)),'$']);
+ 'DisplayName',['$\eta=',num2str(ETAB/ETAN),'$, $\nu_{',CONAME,'}=',num2str(NU),'$, $P=',num2str(PA(i)),'$, $J=',num2str(JA(i)),'$']);
hold on;
end
- grid on; xlabel('$k_z\rho_s^{R}$'); ylabel('$\gamma(N_i^{00})L_\perp/c_s$'); xlim([0.0,max(kr)]);
- title(['$\eta_B=',num2str(ETAB),'$, $\nu_{',CONAME,'}=',num2str(NU),'$'])
+ grid on; xlabel('$k_z\rho_s^{R}$'); ylabel('$\gamma(N_i^{00})L_\perp/c_s$'); xlim([0.0,max(kx)]);
+ title(['$\eta=',num2str(ETAB/ETAN),'$, $\nu_{',CONAME,'}=',num2str(NU),'$'])
legend('show'); xlim([0.01,10])
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.png']);
@@ -168,14 +168,14 @@ for i = 1:Nparam
% Load and process results
load_results
tend = Ts2D(end); tstart = 0.4*tend;
- for ikr = 1:N/2+1
- gamma_Ni(i,ikr) = LinearFit_s(Ts2D,squeeze(abs(Ni00(ikr,1,:))),tstart,tend);
- Ni00_ST(i,ikr,1:numel(Ts2D)) = squeeze((Ni00(ikr,1,:)));
+ for ikx = 1:N/2+1
+ gamma_Ni(i,ikx) = LinearFit_s(Ts2D,squeeze(abs(Ni00(ikx,1,:))),tstart,tend);
+ Ni00_ST(i,ikx,1:numel(Ts2D)) = squeeze((Ni00(ikx,1,:)));
end
gamma_Ni(i,:) = real(gamma_Ni(i,:) .* (gamma_Ni(i,:)>=0.0));
- [gmax,ikzmax] = max(gamma_Ni(i,:));
- kzmax = abs(kr(ikzmax));
- Bohm_transport(i) = ETAB/ETAN*gmax/kzmax^2;
+ [gmax,ikymax] = max(gamma_Ni(i,:));
+ kymax = abs(kx(ikymax));
+ Bohm_transport(i) = ETAB/ETAN*gmax/kymax^2;
% Clean output
system(['rm -r ',BASIC.RESDIR])
end
@@ -187,13 +187,13 @@ plt = @(x) circshift(x,N/2-1);
for i = 1:Nparam
clr = line_colors(mod(i-1,numel(line_colors(:,1)))+1,:);
linestyle = line_styles(floor((i-1)/numel(line_colors(:,1)))+1);
- plot(plt(kz),plt(gamma_Ni(i,:)),...
+ plot(plt(ky),plt(gamma_Ni(i,:)),...
'Color',clr,...
'LineStyle',linestyle{1},...
'DisplayName',['$\eta_B=$',num2str(eta_B(i))]);
hold on;
end
-grid on; xlabel('$k_z\rho_s$'); ylabel('$\gamma(N_i^{00})\rho_2/c_s$'); xlim([0.0,max(kz)]);
+grid on; xlabel('$k_z\rho_s$'); ylabel('$\gamma(N_i^{00})\rho_2/c_s$'); xlim([0.0,max(ky)]);
title(['$P_e=',num2str(PMAXE),'$',', $J_e=',num2str(JMAXE),'$',...
', $P_i=',num2str(PMAXE),'$',', $J_i=',num2str(JMAXI),'$'])
legend('show')
diff --git a/wk/load_multiple_outputs_marconi.m b/wk/load_multiple_outputs_marconi.m
index f6471561..a1bb1957 100644
--- a/wk/load_multiple_outputs_marconi.m
+++ b/wk/load_multiple_outputs_marconi.m
@@ -1,5 +1,11 @@
addpath(genpath('../matlab')) % ... add
%% Paste the list of simulation results to load
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/100x50_L_50_P_6_J_3_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00/out.txt')
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/300x150_L_100_P_10_J_5_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.8_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-03_SGGK_CLOS_0_mu_2e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-02_DGGK_CLOS_0_mu_1e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/300x150_L_100_P_6_J_3_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/300x150_L_100_P_10_J_5_eta_0.71429_nu_1e-02_PAGK_CLOS_0_mu_0e+00/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_6_J_3/200x100_L_120_P_6_J_3_eta_0.6_nu_1e-02_DGGK_CLOS_0_mu_1e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_6_J_3/200x100_L_120_P_6_J_3_eta_0.6_nu_1e-02_SGGK_CLOS_0_mu_1e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_6_J_3/200x100_L_120_P_6_J_3_eta_0.6_nu_1e+00_SGGK_CLOS_0_mu_1e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-02_SGGK_CLOS_0_mu_1e-02/out.txt')
diff --git a/wk/local_run.m b/wk/local_run.m
index 77030a96..c3a7bb8e 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -5,21 +5,23 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.1; % Collision frequency
-ETAB = 1.0; % Magnetic gradient
-ETAN = 2.0; % Density gradient
+ETAN = 0/0.6; % Density gradient drive (R/Ln)
NU_HYP = 0.0;
%% GRID PARAMETERS
-N = 50; % Frequency gridpoints (Nkr = N/2)
-L = 50; % Size of the squared frequency domain
+N = 100; % Frequency gridpoints (Nkx = N/2)
+L = 60; % Size of the squared frequency domain
+Nz = 1; % number of perpendicular planes (parallel grid)
+q0 = 1.0; % q factor ()
P = 2;
J = 1;
MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
-TMAX = 100; % Maximal time unit
+TMAX = 10; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
+SPS3D = 2; % Sampling per time unit for 3D arrays
SPS5D = 1; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints/10
RESTART = 0; % To restart from last checkpoint
@@ -27,15 +29,17 @@ JOB2LOAD= 0;
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; +/- for GK/DK)
-CO = 0;
+CO = 1;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = -1; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
+% SIMID = 'test_3D'; % Name of the simulation
% SIMID = 'HD_study'; % Name of the simulation
-SIMID = 'test_3D'; % Name of the simulation
-% SIMID = 'kobayashi'; % Name of the simulation
-% SIMID = ['v2.7_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
-NON_LIN = 0; % activate non-linearity (is cancelled if KREQ0 = 1)
+SIMID = 'Blob_diffusion'; % Name of the simulation
+% SIMID = ['v3.0_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
+NON_LIN = 1; % activate non-linearity (is cancelled if KXEQ0 = 1)
+% INIT options
INIT_ZF = 0; ZF_AMP = 0.0;
+INIT_BLOB = 1; WIPE_TURB = 1;
%% OUTPUTS
W_DOUBLE = 0;
W_GAMMA = 1;
@@ -53,8 +57,8 @@ JMAXE = J; % Highest '' Laguerre ''
PMAXI = P; % Highest ion Hermite polynomial degree
JMAXI = J; % Highest '' Laguerre ''
KERN = 0; % Kernel model (0 : GK)
-KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
-KREQ0 = 0; % put kr = 0
+KX0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
+KXEQ0 = 0; % put kx = 0
KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
kmax = N*pi/L;% Highest fourier mode
@@ -64,9 +68,10 @@ MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
NOISE0 = 1.0e-5;
TAU = 1.0; % e/i temperature ratio
ETAT = 0.0; % Temperature gradient
+ETAB = 1.0; % Magnetic gradient (1.0 to set R=LB)
INIT_PHI= 1; % Start simulation with a noisy phi and moments
%% Setup and file management
setup
system('rm fort.90');
outfile = [BASIC.RESDIR,'out.txt'];
-disp(outfile);
\ No newline at end of file
+disp(outfile);
diff --git a/wk/marconi_scaling.m b/wk/marconi_scaling.m
index 8c5cd7ee..b33ec6ed 100644
--- a/wk/marconi_scaling.m
+++ b/wk/marconi_scaling.m
@@ -1,13 +1,13 @@
%% Load results np = 24
np_p_24 = [1 2 3 4];
-np_kr_24= [24 12 8 6];
+np_kx_24= [24 12 8 6];
el_ti_np_24= zeros(numel(np_p_24),1);
for i_ = 1:numel(np_p_24)
- npp_ = np_p_24(i_); npkr = np_kr_24(i_);
+ npp_ = np_p_24(i_); npkx = np_kx_24(i_);
%% Load from Marconi
outfile =['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_parallel_scaling_2D/',...
- sprintf('%d_%d',npp_,npkr),...
+ sprintf('%d_%d',npp_,npkx),...
'_200x100_L_120_P_12_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt'];
BASIC.RESDIR = load_marconi(outfile);
compile_results
@@ -16,14 +16,14 @@ for i_ = 1:numel(np_p_24)
end
%% Load results np = 48
np_p_48 = [1 2 3 4 6];
-np_kr_48= [48 24 16 12 8];
+np_kx_48= [48 24 16 12 8];
el_ti_np_48= zeros(numel(np_p_48),1);
for i_ = 1:numel(np_p_48)
- npp_ = np_p_48(i_); npkr = np_kr_48(i_);
+ npp_ = np_p_48(i_); npkx = np_kx_48(i_);
%% Load from Marconi
outfile =['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_parallel_scaling_2D/',...
- sprintf('%d_%d',npp_,npkr),...
+ sprintf('%d_%d',npp_,npkx),...
'_200x100_L_120_P_12_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt'];
BASIC.RESDIR = load_marconi(outfile);
compile_results
@@ -33,14 +33,14 @@ end
%% Load results np = 72
np_p_72 = [ 2 3];
-np_kr_72= [36 24];
+np_kx_72= [36 24];
el_ti_np_72= zeros(numel(np_p_72),1);
for i_ = 1:numel(np_p_72)
- npp_ = np_p_72(i_); npkr = np_kr_72(i_);
+ npp_ = np_p_72(i_); npkx = np_kx_72(i_);
%% Load from Marconi
outfile =['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_parallel_scaling_2D/',...
- sprintf('%d_%d',npp_,npkr),...
+ sprintf('%d_%d',npp_,npkx),...
'_200x100_L_120_P_12_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt'];
BASIC.RESDIR = load_marconi(outfile);
compile_results
diff --git a/wk/open_figure_script.m b/wk/open_figure_script.m
index b7ef07f7..cc22dcf6 100644
--- a/wk/open_figure_script.m
+++ b/wk/open_figure_script.m
@@ -3,7 +3,10 @@ fname_='';
%% Marconi output file
fname_='';
fname_='';
-fname_='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-02/out.txt';
+fname_='';
+fname_='';
+fname_='';
+fname_='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_6_J_3/200x100_L_60_P_6_J_3_eta_0.6_nu_1e-03_SGGK_CLOS_0_mu_1e-03/out.txt';
simname_ = fname_(54:end-8);
%%
@@ -12,8 +15,8 @@ simname_ = fname_(54:end-8);
% simname_ = '';
% simname_ = '';
% simname_ = '';
-% simname_ = 'v2.7_P_2_J_1/100x50_L_200_P_2_J_1_eta_0.6_nu_1e+00_SGGK_CLOS_0_mu_0e+00';
-simname_ = 'v2.7_P_2_J_1/100x50_L_100_P_2_J_1_eta_0.6_nu_1e+00_DGGK_CLOS_0_mu_0e+00';
+% simname_ = '';
+
diff --git a/wk/photomaton.m b/wk/photomaton.m
index 34474be9..39f6813d 100644
--- a/wk/photomaton.m
+++ b/wk/photomaton.m
@@ -1,48 +1,44 @@
if 0
%% Photomaton : real space
-% FIELD = ni00; FNAME = 'ni00'; FIELDLTX = '$n_i^{00}$'; XX = RR; YY = ZZ;
-FIELD = ne00; FNAME = 'ne00'; FIELDLTX = '$n_e^{00}$'; XX = RR; YY = ZZ;
-% FIELD = dens_i; FNAME = 'ni'; FIELDLTX = '$n_i$'; XX = RR; YY = ZZ;
-% FIELD = dens_e; FNAME = 'ne'; FIELDLTX = '$n_e$'; XX = RR; YY = ZZ;
-% FIELD = temp_i; FNAME = 'Ti'; FIELDLTX = '$T_i$'; XX = RR; YY = ZZ;
-% FIELD = temp_e; FNAME = 'Te'; FIELDLTX = '$T_e$'; XX = RR; YY = ZZ;
-% FIELD = phi; FNAME = 'phi'; FIELDLTX = '$\phi$'; XX = RR; YY = ZZ;
-% FIELD = drphi; FNAME = 'ZF'; FIELDLTX = '$u^{ZF}_z$'; XX = RR; YY = ZZ;
-% FIELD = -dr2phi; FNAME = 'shear'; FIELDLTX = '$s$'; XX = RR; YY = ZZ;
- plt = @(x) x./max(max(x));
+
+% Chose the field to plot
+% FIELD = ni00; FNAME = 'ni00'; FIELDLTX = 'n_i^{00}';
+% FIELD = ne00; FNAME = 'ne00'; FIELDLTX = 'n_e^{00}'
+% FIELD = dens_i; FNAME = 'ni'; FIELDLTX = 'n_i';
+% FIELD = dens_e; FNAME = 'ne'; FIELDLTX = 'n_e';
+% FIELD = temp_i; FNAME = 'Ti'; FIELDLTX = 'T_i';
+% FIELD = temp_e; FNAME = 'Te'; FIELDLTX = 'T_e';
+FIELD = phi; FNAME = 'phi'; FIELDLTX = '\phi';
+
+% Chose when to plot it
+tf = [0 10 50 100];
+
+% Slice
+ix = 1; iy = 1; iz = 1;
+% plt = @(x,it) real(x(ix, :, :,it)); X = Y_YZ; Y = Z_YZ; XNAME = 'y'; YNAME = 'z'; FIELDLTX = [FIELDLTX,'(x=',num2str(round(x(ix))),')']
+% plt = @(x,it) real(x( :,iy, :,it)); X = X_XZ; Y = Z_XZ; XNAME = 'x'; YNAME = 'z'; FIELDLTX = [FIELDLTX,'(y=',num2str(round(y(iy))),')']
+% plt = @(x,it) real(x( :, :,iz,it)); X = X_XY; Y = Y_XY; XNAME = 'x'; YNAME = 'y'; FIELDLTX = [FIELDLTX,'(x=',num2str(round(z(iz))),')']
+
+% Averaged
+% plt = @(x,it) mean(x(:,:,:,it),1); X = Y_YZ; Y = Z_YZ; XNAME = 'y'; YNAME = 'z'; FIELDLTX = ['\langle',FIELDLTX,'\rangle_x']
+% plt = @(x,it) mean(x(:,:,:,it),2); X = X_XZ; Y = Z_XZ; XNAME = 'x'; YNAME = 'z'; FIELDLTX = ['\langle',FIELDLTX,'\rangle_y']
+plt = @(x,it) mean(x(:,:,:,it),3); X = X_XY; Y = Y_XY; XNAME = 'x'; YNAME = 'y'; FIELDLTX = ['\langle',FIELDLTX,'\rangle_z']
+
+
+%
TNAME = [];
-tf = 500; [~,it1] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-tf = 1000; [~,it2] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-tf = 1250; [~,it3] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-tf = 1750; [~,it4] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
fig = figure; FIGNAME = [FNAME,TNAME,'_snaps','_',PARAMS]; set(gcf, 'Position', [100, 100, 1500, 350])
- subplot(141)
- DATA = plt(FIELD(:,:,it1));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap(bluewhitered); caxis([-1,1]);
- xlabel('$r/\rho_s$'); ylabel('$z/\rho_s$');set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it1)));
- subplot(142)
- DATA = plt(FIELD(:,:,it2));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap(bluewhitered); caxis([-1,1]);
- xlabel('$r/\rho_s$');ylabel('$z/\rho_s$'); set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it2)));
- subplot(143)
- DATA = plt(FIELD(:,:,it3));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap(bluewhitered); caxis([-1,1]);
- xlabel('$r/\rho_s$');ylabel('$z/\rho_s$');set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it3)));
- subplot(144)
- DATA = plt(FIELD(:,:,it4));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
+plt_2 = @(x) x./max(max(x));
+ for i_ = 1:numel(tf)
+ [~,it] = min(abs(Ts3D-tf(i_))); TNAME = [TNAME,'_',num2str(Ts3D(it))];
+ subplot(1,numel(tf),i_)
+ DATA = plt_2(squeeze(plt(FIELD,it)));
+ pclr = pcolor((X),(Y),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
colormap(bluewhitered); caxis([-1,1]);
- xlabel('$r/\rho_s$');ylabel('$z/\rho_s$'); set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it4)));
- suptitle([FIELDLTX,', $\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
- ', $L=',num2str(L),'$, $N=',num2str(Nr),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
- ' $\mu_{hd}=$',num2str(MU)]);
+ xlabel(latexize(XNAME)); ylabel(latexize(YNAME));set(gca,'ytick',[]);
+ title(sprintf('$t c_s/R=%.0f$',Ts3D(it)));
+ end
+ legend(latexize(FIELDLTX));
save_figure
end
@@ -51,58 +47,13 @@ if 0
figure
skip = 2;
plt = @(x) x./max(max(x));
-FNAME = 'ZF'; FIELDLTX = '$\bm{u}^{ZF}$'; XX = RR; YY = ZZ;
+FNAME = 'ZF'; FIELDLTX = '$\bm{u}^{ZF}$'; X_XY = RR; Y_XY = ZZ;
tf = 1200; [~,it1] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
UY = plt(drphi(1:skip:end,1:skip:end,it1)); UX = plt(-dzphi(1:skip:end,1:skip:end,it1));
-pclr = pcolor(XX,YY,plt(ni00(:,:,it1))); set(pclr, 'edgecolor','none');
+pclr = pcolor(X_XY,Y_XY,plt(ni00(:,:,it1))); set(pclr, 'edgecolor','none');
hold on
-quiver((XX(1:skip:end,1:skip:end)),(YY(1:skip:end,1:skip:end)),UX,UY,'r'); xlim(L/2*[-1 1]); ylim(L/2*[-1 1]);
+quiver((X_XY(1:skip:end,1:skip:end)),(Y_XY(1:skip:end,1:skip:end)),UX,UY,'r'); xlim(L/2*[-1 1]); ylim(L/2*[-1 1]);
pbaspect([1 1 1])
xlabel('$r/\rho_s$');ylabel('$z/\rho_s$');set(gca,'ytick',[]);
title(sprintf('$t c_s/R=%.0f$',Ts2D(it1)));
-end
-
-
-%%
-if 0
-%% Photomaton : k space
-% FIELD = Ni00; FNAME = 'Ni00'; FIELDLTX = '$N_i^{00}$'; XX = KR; YY = KZ;
-FIELD = Ne00; FNAME = 'Ne00'; FIELDLTX = '$N_e^{00}$'; XX = KR; YY = KZ;
-FIELD = PHI; FNAME = 'PHI'; FIELDLTX = '$\tilde\phi$'; XX = KR; YY = KZ;
-FIELD = ifftshift((abs(FIELD)),2); XX = fftshift(XX,2); YY = fftshift(YY,2);
-plt = @(x) x./max(max(x));
-TNAME = [];
-tf = 500; [~,it1] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-tf = 1000; [~,it2] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-tf = 1250; [~,it3] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-tf = 1750; [~,it4] = min(abs(Ts2D-tf)); TNAME = [TNAME,'_',num2str(tf)];
-fig = figure; FIGNAME = [FNAME,TNAME,'_snaps','_',PARAMS]; set(gcf, 'Position', [100, 100, 1500, 350])
- subplot(141)
- DATA = plt(FIELD(:,:,it1));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap gray;
- xlabel('$r/\rho_s$'); ylabel('$z/\rho_s$');set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it1)));
- subplot(142)
- DATA = plt(FIELD(:,:,it2));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap(bluewhitered);
- xlabel('$r/\rho_s$');ylabel('$z/\rho_s$'); set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it2)));
- subplot(143)
- DATA = plt(FIELD(:,:,it3));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap(bluewhitered);
- xlabel('$r/\rho_s$');ylabel('$z/\rho_s$');set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it3)));
- subplot(144)
- DATA = plt(FIELD(:,:,it4));
- pclr = pcolor((XX),(YY),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
- colormap(bluewhitered);
- xlabel('$r/\rho_s$');ylabel('$z/\rho_s$'); set(gca,'ytick',[]);
- title(sprintf('$t c_s/R=%.0f$',Ts2D(it4)));
- suptitle([FIELDLTX,', $\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
- ', $L=',num2str(L),'$, $N=',num2str(Nr),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
- ' $\mu_{hd}=$',num2str(MU)]);
-save_figure
end
\ No newline at end of file
diff --git a/wk/plot_cosol_mat.m b/wk/plot_cosol_mat.m
new file mode 100644
index 00000000..876a233a
--- /dev/null
+++ b/wk/plot_cosol_mat.m
@@ -0,0 +1,63 @@
+MAT = results.iCa;
+figure
+suptitle('DGGK,P=6,J=3');
+subplot(221)
+ imagesc(log(abs(MAT)));
+ title('log abs')
+subplot(222)
+ imagesc(imag(MAT)); colormap(bluewhitered)
+ title('imag'); colorbar
+subplot(223)
+ imagesc(imag(MAT)>0);
+ title('imag$>$0');
+subplot(224)
+ imagesc(imag(MAT)<0);
+ title('imag$<$0');
+
+
+ %% SGGK
+P_ = 20; J_ = 10;
+mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5';
+SGGK_self = h5read(mat_file_name,'/00149/Caapj/Ciipj');
+SGGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
+SGGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
+
+figure
+MAT = 1i*SGGK_self; suptitle('SGGK ii,P=20,J=10, k=8');
+% MAT = 1i*SGGK_ei; suptitle('SGGK ei,P=20,J=10');
+% MAT = 1i*SGGK_ie; suptitle('SGGK ie,P=20,J=10');
+subplot(221)
+ imagesc(abs(MAT));
+ title('log abs')
+subplot(222)
+ imagesc(imag(MAT)); colormap(bluewhitered)
+ title('imag'); colorbar
+subplot(223)
+ imagesc(imag(MAT)>0);
+ title('imag$>$0');
+subplot(224)
+ imagesc(imag(MAT)<0);
+ title('imag$<$0');
+
+ %% PAGK
+P_ = 20; J_ = 10;
+mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5';
+PAGK_self = h5read(mat_file_name,'/00149/Caapj/Ceepj');
+% PAGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
+% PAGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
+
+figure
+MAT = 1i*PAGK_self; suptitle('PAGK ii,P=20,J=10, k=8');
+
+subplot(221)
+ imagesc(abs(MAT));
+ title('log abs')
+subplot(222)
+ imagesc(imag(MAT)); colormap(bluewhitered)
+ title('imag'); colorbar
+subplot(223)
+ imagesc(imag(MAT)>0);
+ title('imag$>$0');
+subplot(224)
+ imagesc(imag(MAT)<0);
+ title('imag$<$0');
diff --git a/wk/ppb110_run.m b/wk/ppb110_run.m
index a241120d..2eddbcd1 100644
--- a/wk/ppb110_run.m
+++ b/wk/ppb110_run.m
@@ -17,7 +17,7 @@ NU = 1.0; % Collision frequency
ETAB = 0.5; % Magnetic gradient
NU_HYP = 0.1; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-N = 150; % Frequency gridpoints (Nkr = N/2)
+N = 150; % Frequency gridpoints (Nkx = N/2)
L = 70; % Size of the squared frequency domain
P = 2; % Electron and Ion highest Hermite polynomial degree
J = 1; % Electron and Ion highest Laguerre polynomial degree
@@ -41,11 +41,11 @@ KERN = 0; % Kernel model (0 : GK)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% fixed parameters (for current study)
-KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst. (not implemented)
-KREQ0 = 0; % put kr = 0
+KX0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst. (not implemented)
+KXEQ0 = 0; % put kx = 0
KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
-NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
+NON_LIN = 1 *(1-KXEQ0); % activate non-linearity (is cancelled if KXEQ0 = 1)
PMAXE = P; % Highest electron Hermite polynomial degree
JMAXE = J; % Highest '' Laguerre ''
PMAXI = P; % Highest ion Hermite polynomial degree
diff --git a/wk/spectral_analysis.m b/wk/spectral_analysis.m
index afb9f717..8830f118 100644
--- a/wk/spectral_analysis.m
+++ b/wk/spectral_analysis.m
@@ -19,7 +19,7 @@ for ij = 1:Nji
end
grid on; ylim([1e0,1e10]);
xlabel('$p$');
- TITLE = ['$\sum_{kr,kz} |N_i^{p',num2str(Ji(ij)),'}|^2$']; title(TITLE);
+ TITLE = ['$\sum_{kx,ky} |N_i^{p',num2str(Ji(ij)),'}|^2$']; title(TITLE);
end
save_figure
end
@@ -42,26 +42,26 @@ for ip = 1:2:Npi
'DisplayName',['t=',num2str(Ts5D(it5))]); hold on;
grid on;
xlabel('$j$'); ylim([1e-20,1e10]);
- TITLE = ['$\sum_{kr,kz} |N_i^{',num2str(Pi(ip)),'j}|^2$']; title(TITLE);
+ TITLE = ['$\sum_{kx,ky} |N_i^{',num2str(Pi(ip)),'j}|^2$']; title(TITLE);
end
end
save_figure
end
%%
-no_AA = (2:floor(2*Nkr/3));
+no_AA = (2:floor(2*Nkx/3));
tKHI = 100;
[~,itKHI] = min(abs(Ts2D-tKHI));
after_KHI = (itKHI:Ns2D);
if 0
-%% Phi frequency space time diagram at kz=kz(ikz)
-kz_ = 0.0;
-[~,ikz] = min(abs(kz-kz_));
+%% Phi frequency space time diagram at ky=ky(iky)
+ky_ = 0.0;
+[~,iky] = min(abs(ky-ky_));
fig = figure; FIGNAME = ['phi_freq_diag_',PARAMS];set(gcf, 'Position', [100, 100, 500, 400]);
- [TY,TX] = meshgrid(Ts2D(after_KHI),kr(no_AA));
- pclr = pcolor(TX,TY,(squeeze(abs(PHI(no_AA,ikz,(after_KHI)))))); set(pclr, 'edgecolor','none'); colorbar;
+ [TY,TX] = meshgrid(Ts2D(after_KHI),kx(no_AA));
+ pclr = pcolor(TX,TY,(squeeze(abs(PHI(no_AA,iky,(after_KHI)))))); set(pclr, 'edgecolor','none'); colorbar;
caxis([0,10000]); colormap hot
ylabel('$t c_s/R$'), xlabel('$0<k_r<2/3 k_r^{\max}$')
- legend(['$|\tilde\phi(k_z=',num2str(kz_),')|$'])
+ legend(['$|\tilde\phi(k_z=',num2str(ky_),')|$'])
title('Spectrogram of $\phi$')
end
\ No newline at end of file
--
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