From e430a1a56d4c581a6b1d256a3a31591389cada48 Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Thu, 7 Dec 2023 17:56:07 +0100
Subject: [PATCH] add out board midplane diagnostics
---
src/diagnostics_mod.F90 | 109 ++++++++++++++++++++++++++++++++++++++--
src/grid_mod.F90 | 9 +++-
2 files changed, 112 insertions(+), 6 deletions(-)
diff --git a/src/diagnostics_mod.F90 b/src/diagnostics_mod.F90
index c2afdb02..e7b10a35 100644
--- a/src/diagnostics_mod.F90
+++ b/src/diagnostics_mod.F90
@@ -157,7 +157,7 @@ CONTAINS
SUBROUTINE diagnose_full(kstep)
USE basic, ONLY: speak,chrono_runt,&
- cstep,iframe0d,iframe3d,iframe5d,crashed
+ cstep,iframe0d,iframe2d,iframe3d,iframe5d,crashed
USE grid, ONLY: &
parray_full,jarray_full, kparray, &
kyarray_full,kxarray_full,zarray_full, ngz, total_nz, local_nz, ieven,&
@@ -256,13 +256,21 @@ CONTAINS
CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
END IF
! var2d group (gyro transport)
- IF (nsave_0d .GT. 0) THEN
+ 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 (write_phi) CALL creatg(fidres, "/data/var2d/phi_obmp", "phi out board midplane")
+ IF (write_phi.AND.EM) CALL creatg(fidres, "/data/var2d/psi_obmp", "psi out board midplane")
+ IF (write_Na00) CALL creatg(fidres, "/data/var2d/Na00_obmp", "gyrocenter density out board midplane")
+ IF (write_Na00) CALL creatg(fidres, "/data/var2d/Napj_obmp", "p,j moment spectrum out board midplane")
+ IF (write_dens) CALL creatg(fidres, "/data/var2d/dens_obmp", "density out board midplane")
+ IF (write_fvel) CALL creatg(fidres, "/data/var2d/upar_obmp", "parallel velocity out board midplane")
+ IF (write_temp) CALL creatg(fidres, "/data/var2d/temp_obmp", "temperature out board midplane")
#ifdef TEST_SVD
CALL creatg(fidres, "/data/var2d/sv_ky_pj", "singular values of the moment ky/pj cut")
#endif
+ CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
ENDIF
! var3d group (phi,psi, fluid moments, Ni00, Napjz)
IF (nsave_3d .GT. 0) THEN
@@ -430,19 +438,112 @@ CONTAINS
SUBROUTINE diagnose_2d
USE prec_const
USE basic
- USE futils, ONLY: putarr, append
+ USE fields, ONLY: phi, psi, moments
+ USE array, ONLY: Napjz,dens,upar,temp
+ USE futils, ONLY: append, getatt, attach, putarr
+ USE grid, ONLY: CONTAINSp0, ip0,ij0, local_na, total_na,&
+ total_np, total_nj, total_nky, total_nkx, total_nz, &
+ local_np, local_nky, local_nkx, local_nz, &
+ ngz, iz_obmp
+ USE time_integration, ONLY: updatetlevel
+ USE prec_const
+ USE processing, ONLY: compute_fluid_moments, compute_Napjz_spectrum
+ USE model, ONLY: EM
+ USE parallel, ONLY: manual_3D_bcast
#ifdef TEST_SVD
USE CLA, ONLY: Sf
#endif
IMPLICIT NONE
+ COMPLEX(xp), DIMENSION(local_na,local_nky,local_nkx,local_nz) :: Na00_
iframe2d=iframe2d+1
+ CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
CALL append(fidres,"/data/var2d/time", REAL(time,dp), ionode=0)
CALL append(fidres,"/data/var2d/cstep",REAL(cstep,dp),ionode=0)
#ifdef TEST_SVD
WRITE(dset_name, "(A, '/', i6.6)") "/data/var2d/sv_ky_pj/", iframe2d
CALL putarr(fidres, dset_name, Sf, ionode=0)
#endif
- END SUBROUTINE
+ ! Write current EM fields
+ IF (write_phi) CALL write_field2d_kykx_obmp(phi (:,:,(1+ngz/2):(local_nz+ngz/2)), 'phi_obmp')
+ IF (write_phi.AND.EM) CALL write_field2d_kykx_obmp(psi (:,:,(1+ngz/2):(local_nz+ngz/2)), 'psi_obmp')
+ IF (write_Na00) THEN
+ CALL compute_Napjz_spectrum
+ IF (CONTAINSp0) THEN
+ ! gyrocenter density
+ Na00_ = moments(:,ip0,ij0,:,:,(1+ngz/2):(local_nz+ngz/2),updatetlevel)
+ ELSE
+ Na00_ = 0._xp
+ ENDIF
+ CALL write_field2da_kykx_obmp(Na00_, 'Na00_obmp')
+ ! <<Napj>x>y spectrum
+ CALL write_field2da_pj_obmp(Napjz, 'Napj_obmp')
+ ENDIF
+ !! Fuid moments
+ IF (write_dens .OR. write_fvel .OR. write_temp) &
+ CALL compute_fluid_moments
+ IF (write_dens) CALL write_field2da_kykx_obmp(dens, 'dens_obmp')
+ IF (write_fvel) CALL write_field2da_kykx_obmp(upar, 'upar_obmp')
+ IF (write_temp) CALL write_field2da_kykx_obmp(temp, 'temp_obmp')
+ CONTAINS
+ SUBROUTINE write_field2d_kykx_obmp(field, text)
+ USE parallel, ONLY : gather_xyz, num_procs
+ IMPLICIT NONE
+ COMPLEX(xp), DIMENSION(:,:,:), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ COMPLEX(xp), DIMENSION(total_nky,total_nkx,total_nz) :: field_full
+ CHARACTER(50) :: dset_name
+ field_full = 0;
+ 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(:,:,iz_obmp), ionode=0)
+ ELSE
+ CALL gather_xyz(field,field_full,local_nky,total_nky,total_nkx,local_nz,total_nz)
+ CALL putarr(fidres, dset_name, field_full(:,:,iz_obmp), ionode=0)
+ ENDIF
+ END SUBROUTINE write_field2d_kykx_obmp
+
+ SUBROUTINE write_field2da_kykx_obmp(field, text)
+ USE parallel, ONLY : gather_xyz, num_procs
+ IMPLICIT NONE
+ COMPLEX(xp), DIMENSION(:,:,:,:), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ COMPLEX(xp), DIMENSION(total_na,total_nky,total_nkx,total_nz) :: field_full
+ COMPLEX(xp), DIMENSION(local_nky,total_nkx,local_nz) :: buff_local
+ COMPLEX(xp), DIMENSION(total_nky,total_nkx,total_nz) :: buff_full
+ CHARACTER(50) :: dset_name
+ INTEGER :: ia
+ field_full = 0;
+ 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(:,:,:,iz_obmp), ionode=0)
+ ELSE
+ DO ia = 1,total_Na
+ buff_local = field(ia,:,:,:)
+ CALL gather_xyz(buff_local,buff_full,local_nky,total_nky,total_nkx,local_nz,total_nz)
+ field_full(ia,:,:,:) = buff_full
+ ENDDO
+ CALL putarr(fidres, dset_name, field_full(:,:,:,iz_obmp), ionode=0)
+ ENDIF
+ END SUBROUTINE write_field2da_kykx_obmp
+
+ SUBROUTINE write_field2da_pj_obmp(field, text)
+ USE parallel, ONLY : gather_pjz, num_procs
+ IMPLICIT NONE
+ COMPLEX(xp), DIMENSION(:,:,:,:), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ COMPLEX(xp), DIMENSION(total_na,total_np,total_nj,total_nz) :: field_full
+ CHARACTER(LEN=50) :: dset_name
+ field_full = 0;
+ 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(:,:,:,iz_obmp), ionode=0)
+ ELSE
+ CALL gather_pjz(field,field_full,total_na,local_np,total_np,total_nj,local_nz,total_nz)
+ CALL putarr(fidres, dset_name, field_full(:,:,:,iz_obmp), ionode=0)
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field2da_pj_obmp
+ END SUBROUTINE diagnose_2d
SUBROUTINE diagnose_3d
USE basic
diff --git a/src/grid_mod.F90 b/src/grid_mod.F90
index b85b9b9b..3a070e77 100644
--- a/src/grid_mod.F90
+++ b/src/grid_mod.F90
@@ -45,8 +45,11 @@ MODULE grid
INTEGER, PUBLIC, PROTECTED :: ikxs,ikxe ! Fourier x mode
INTEGER, PUBLIC, PROTECTED :: izs ,ize ! z-grid
INTEGER, PUBLIC, PROTECTED :: ieven, iodd ! indices for the staggered grids
- INTEGER, PUBLIC, PROTECTED :: ip0, ip1, ip2, ip3, ij0, ij1, pp2
+ INTEGER, PUBLIC, PROTECTED :: ip0, ip1, ip2, ip3 ! p=0,1,2,3 indices
+ INTEGER, PUBLIC, PROTECTED :: ij0, ij1 ! j=0,1 indices
+ INTEGER, PUBLIC, PROTECTED :: pp2 ! p+2 index jump
INTEGER, PUBLIC, PROTECTED :: ikx0, iky0, ikx_max, iky_max ! Indices of k-grid origin and max
+ INTEGER, PUBLIC, PROTECTED :: iz_obmp ! outboard midplane index
! Total numbers of points for Hermite and Laguerre
INTEGER, PUBLIC, PROTECTED :: total_na
INTEGER, PUBLIC, PROTECTED :: total_np
@@ -592,6 +595,8 @@ CONTAINS
! Z stepping (#interval = #points since periodic)
deltaz = Lz/REAL(Nz,xp)
inv_deltaz = 1._xp/deltaz
+ ! Index of the outboard midplane
+ iz_obmp = Nz/2+1 ! we use the fact that 1/2 in integer gives 0
! Parallel hyperdiffusion coefficient
diff_dz_coeff = (deltaz/2._xp)**4 ! adaptive fourth derivative (~GENE)
IF (SG) THEN
@@ -601,7 +606,7 @@ CONTAINS
ENDIF
! Build the full grids on process 0 to diagnose it without comm
IF (Nz .EQ. 1) &
- Npol = 0._xp
+ Npol = 0._xp
zmax = 0; zmin = 0;
DO iz = 1,total_nz ! z in [-pi pi-dz] x Npol
zarray_full(iz) = REAL(iz-1,xp)*deltaz - Lz/2._xp
--
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