diff --git a/src/diagnose.F90 b/src/diagnose.F90
index 958c08597497a341cb9a49ab7f2e659b60713b92..c3be68638cef60832c2f3790c9d5c0e162fb791c 100644
--- a/src/diagnose.F90
+++ b/src/diagnose.F90
@@ -95,20 +95,18 @@ SUBROUTINE diagnose_full(kstep)
USE grid, ONLY: &
local_nj,local_nky,local_nkx,local_nz,ngj,ngz,&
parray_full,pmax,jarray_full,jmax,&
- kyarray_full,kxarray_full,zarray_full, total_na
+ kyarray_full,kxarray_full,zarray_full
USE diagnostics_par
USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf, putarrnd
- USE species, ONLY: name
USE array
USE model, ONLY: EM
USE parallel, ONLY: my_id, comm0
USE collision, ONLY: coll_outputinputs
USE geometry, ONLY: gxx,gxy,gyy,gxz,gyz,gzz,hatR,hatZ,hatB,dBdx,dBdy,dBdz,Jacobian,gradz_coeff,Ckxky
IMPLICIT NONE
- CHARACTER :: letter_a
INTEGER, INTENT(in) :: kstep
INTEGER, parameter :: BUFSIZE = 2
- INTEGER :: rank = 0, ierr, ia
+ INTEGER :: rank = 0, ierr
INTEGER :: dims(1) = (/0/)
!____________________________________________________________________________
! 1. Initial diagnostics
@@ -256,15 +254,12 @@ END SUBROUTINE diagnose_full
!!-------------- Auxiliary routines -----------------!!
SUBROUTINE diagnose_0d
USE basic
- USE futils, ONLY: append, attach, getatt
+ USE futils, ONLY: append, attach, getatt, creatd
USE diagnostics_par
USE prec_const
USE processing
USE model, ONLY: Na
- USE species, ONLY: name
IMPLICIT NONE
- CHARACTER :: letter_a
- INTEGER :: ia
! Time measurement data
CALL append(fidres, "/profiler/Tc_rhs", REAL(chrono_mrhs%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_adv_field", REAL(chrono_advf%ttot,dp),ionode=0)
@@ -278,6 +273,10 @@ SUBROUTINE diagnose_0d
CALL append(fidres, "/profiler/Tc_grad", REAL(chrono_grad%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_nadiab", REAL(chrono_napj%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_step", REAL(chrono_step%ttot,dp),ionode=0)
+#ifdef TEST_SVD
+ CALL creatd(fidres, 0, (/0/), "/profiler/Tc_DLRA", "cumulative total DLRA computation time")
+ CALL append(fidres, "/profiler/Tc_DLRA", REAL(chrono_DLRA%ttot,dp),ionode=0)
+#endif
CALL append(fidres, "/profiler/time", REAL(time,dp),ionode=0)
! Processing data
CALL append(fidres, "/data/var0d/time", REAL(time,dp),ionode=0)
@@ -311,13 +310,9 @@ SUBROUTINE diagnose_3d
USE prec_const
USE processing, ONLY: compute_fluid_moments, compute_Napjz_spectrum
USE model, ONLY: EM
- USE species, ONLY: name
USE parallel, ONLY: manual_3D_bcast
IMPLICIT NONE
- CHARACTER :: letter_a
- INTEGER :: ia
COMPLEX(xp), DIMENSION(local_na,local_nky,local_nkx,local_nz) :: Na00_
- COMPLEX(xp), DIMENSION(local_na,local_np, local_nj, local_nz) :: Napjz_
! add current time, cstep and frame
CALL append(fidres, "/data/var3d/time", REAL(time,dp),ionode=0)
CALL append(fidres, "/data/var3d/cstep", real(cstep,dp),ionode=0)
@@ -337,8 +332,7 @@ SUBROUTINE diagnose_3d
ENDIF
CALL write_field3da_kykxz(Na00_, 'Na00')
! <<Napj>x>y spectrum
- Napjz_ = Napjz
- CALL write_field3da_pjz(Napjz_, 'Napjz')
+ CALL write_field3da_pjz(Napjz, 'Napjz')
ENDIF
!! Fuid moments
IF (write_dens .OR. write_fvel .OR. write_temp) &
@@ -351,15 +345,15 @@ SUBROUTINE diagnose_3d
CALL write_field3da_kykxz(uper, 'uper')
ENDIF
IF (write_temp) THEN
- CALL write_field3d_kykxz(Tpar, 'Tpar')
- CALL write_field3d_kykxz(Tper, 'Tper')
- CALL write_field3d_kykxz(temp, 'temp')
+ CALL write_field3da_kykxz(Tpar, 'Tpar')
+ CALL write_field3da_kykxz(Tper, 'Tper')
+ CALL write_field3da_kykxz(temp, 'temp')
ENDIF
CONTAINS
SUBROUTINE write_field3d_kykxz(field, text)
USE parallel, ONLY : gather_xyz, num_procs
IMPLICIT NONE
- COMPLEX(xp), DIMENSION(local_nky,total_nkx,local_nz), INTENT(IN) :: field
+ 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
@@ -376,16 +370,23 @@ SUBROUTINE diagnose_3d
SUBROUTINE write_field3da_kykxz(field, text)
USE parallel, ONLY : gather_xyz, num_procs
IMPLICIT NONE
- COMPLEX(xp), DIMENSION(local_na,local_nky,total_nkx,local_nz), INTENT(IN) :: field
+ 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/var3d", TRIM(text), iframe3d
IF (num_procs .EQ. 1) THEN ! no data distribution
CALL putarr(fidres, dset_name, field, ionode=0)
ELSE
- CALL gather_xyz(field,field_full,local_nky,total_nky,total_nkx,local_nz,total_nz)
+ 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, ionode=0)
ENDIF
END SUBROUTINE write_field3da_kykxz
@@ -393,7 +394,7 @@ SUBROUTINE diagnose_3d
SUBROUTINE write_field3da_pjz(field, text)
USE parallel, ONLY : gather_pjz, num_procs
IMPLICIT NONE
- COMPLEX(xp), DIMENSION(local_na,local_np,local_nj,local_nz), INTENT(IN) :: field
+ 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
@@ -402,7 +403,7 @@ SUBROUTINE diagnose_3d
IF (num_procs .EQ. 1) THEN ! no data distribution
CALL putarr(fidres, dset_name, field, ionode=0)
ELSE
- CALL gather_pjz(field,field_full,local_np,total_np,total_nj,local_nz,total_nz)
+ 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, ionode=0)
ENDIF
CALL attach(fidres, dset_name, "time", time)
@@ -418,7 +419,6 @@ SUBROUTINE diagnose_5d
USE grid, ONLY:total_np, total_nj, total_nky, total_nkx, total_nz, &
local_np, local_nj, local_nky, local_nkx, local_nz, &
ngp, ngj, ngz, total_na
- USE time_integration, ONLY: updatetlevel, ntimelevel
USE diagnostics_par
USE prec_const, ONLY: xp,dp
IMPLICIT NONE
@@ -436,18 +436,18 @@ SUBROUTINE diagnose_5d
CONTAINS
SUBROUTINE write_field5d(field, text)
- USE basic, ONLY: GATHERV_OUTPUT, jobnum, dt
- USE futils, ONLY: attach, putarr, putarrnd
- USE parallel, ONLY: gather_pjxyz, num_procs
- USE prec_const, ONLY: xp
+ USE basic, ONLY: GATHERV_OUTPUT, jobnum, dt
+ USE futils, ONLY: attach, putarr, putarrnd
+ USE parallel, ONLY: gather_pjxyz, num_procs
+ USE prec_const, ONLY: xp
IMPLICIT NONE
- COMPLEX(xp), DIMENSION(total_na,local_np+ngp,local_nj+ngj,local_nky,local_nkx,local_nz+ngz,ntimelevel), INTENT(IN) :: field
+ COMPLEX(xp), DIMENSION(:,:,:,:,:,:,:), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
COMPLEX(xp), DIMENSION(total_na,local_np,local_nj,local_nky,local_nkx,local_nz) :: field_sub
COMPLEX(xp), DIMENSION(total_na,total_np,total_nj,total_nky,total_nkx,total_nz) :: field_full
CHARACTER(LEN=50) :: dset_name
- field_sub = field(1:total_na,(1+ngp/2):(local_np+ngp/2),((1+ngj/2)):((local_nj+ngj/2)),&
- 1:local_nky,1:local_nkx, ((1+ngz/2)):((local_nz+ngz/2)),updatetlevel)
+ field_sub = field(1:total_na,(1+ngp/2):(local_np+ngp/2),(1+ngj/2):(local_nj+ngj/2),&
+ 1:local_nky,1:local_nkx,(1+ngz/2):(local_nz+ngz/2),1)
field_full = 0;
WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
IF (num_procs .EQ. 1) THEN
diff --git a/src/parallel_mod.F90 b/src/parallel_mod.F90
index e132fd04c4787c82b3fa9b6c64c88ebf10f0a08a..b4e398b6e7e13b67ae36524cd8b29279bd02166d 100644
--- a/src/parallel_mod.F90
+++ b/src/parallel_mod.F90
@@ -239,8 +239,8 @@ CONTAINS
SUBROUTINE gather_xyz(field_loc,field_tot,nky_loc,nky_tot,nkx_tot,nz_loc,nz_tot)
IMPLICIT NONE
INTEGER, INTENT(IN) :: nky_loc,nky_tot,nkx_tot,nz_loc,nz_tot
- COMPLEX(xp), DIMENSION(nky_loc,nkx_tot,nz_loc), INTENT(IN) :: field_loc
- COMPLEX(xp), DIMENSION(nky_tot,nkx_tot,nz_tot), INTENT(OUT) :: field_tot
+ COMPLEX(xp), DIMENSION(:,:,:), INTENT(IN) :: field_loc
+ COMPLEX(xp), DIMENSION(:,:,:), INTENT(OUT) :: field_tot
COMPLEX(xp), DIMENSION(nky_tot,nz_loc) :: buffer_yt_zl !full y, local z
COMPLEX(xp), DIMENSION(nky_tot,nz_tot) :: buffer_yt_zt !full y, full z
COMPLEX(xp), DIMENSION(nky_loc):: buffer_yl_zc !local y, constant z
@@ -272,42 +272,45 @@ CONTAINS
ENDDO
ENDIF
END SUBROUTINE gather_xyz
+
!!!!! Gather a field in kinetic + z coordinates on rank 0 !!!!!
- SUBROUTINE gather_pjz(field_loc,field_tot,np_loc,np_tot,nj_tot,nz_loc,nz_tot)
+ SUBROUTINE gather_pjz(field_loc,field_tot,na_tot,np_loc,np_tot,nj_tot,nz_loc,nz_tot)
IMPLICIT NONE
- INTEGER, INTENT(IN) :: np_loc,np_tot, nj_tot, nz_loc,nz_tot
- COMPLEX(xp), DIMENSION(np_loc,nj_tot,nz_loc), INTENT(IN) :: field_loc
- COMPLEX(xp), DIMENSION(np_tot,nj_tot,nz_tot), INTENT(OUT) :: field_tot
+ INTEGER, INTENT(IN) :: na_tot,np_loc,np_tot, nj_tot, nz_loc,nz_tot
+ COMPLEX(xp), DIMENSION(:,:,:,:), INTENT(IN) :: field_loc
+ COMPLEX(xp), DIMENSION(:,:,:,:), INTENT(OUT) :: field_tot
COMPLEX(xp), DIMENSION(np_tot,nz_loc) :: buffer_pt_zl !full p, local z
COMPLEX(xp), DIMENSION(np_tot,nz_tot) :: buffer_pt_zt !full p, full z
COMPLEX(xp), DIMENSION(np_loc) :: buffer_pl_zc !local p, constant z
COMPLEX(xp), DIMENSION(np_tot) :: buffer_pt_zc !full p, constant z
- INTEGER :: snd_p, snd_z, root_p, root_z, root_ky, ij, iz
+ INTEGER :: snd_p, snd_z, root_p, root_z, root_ky, ij, iz, ia
snd_p = np_loc ! Number of points to send along p (per z)
snd_z = np_tot*nz_loc ! Number of points to send along z (full p)
root_p = 0; root_z = 0; root_ky = 0
IF(rank_ky .EQ. root_ky) THEN
- DO ij = 1,nj_tot
- DO iz = 1,nz_loc
- ! fill a buffer to contain a slice of data at constant j and z
- buffer_pl_zc(1:np_loc) = field_loc(1:np_loc,ij,iz)
- CALL MPI_GATHERV(buffer_pl_zc, snd_p, mpi_xp_c, &
- buffer_pt_zc, rcv_p, dsp_p, mpi_xp_c, &
- root_p, comm_p, ierr)
- buffer_pt_zl(1:np_tot,iz) = buffer_pt_zc(1:np_tot)
+ DO ia= 1,na_tot
+ DO ij = 1,nj_tot
+ DO iz = 1,nz_loc
+ ! fill a buffer to contain a slice of data at constant j and z
+ buffer_pl_zc(1:np_loc) = field_loc(ia,1:np_loc,ij,iz)
+ CALL MPI_GATHERV(buffer_pl_zc, snd_p, mpi_xp_c, &
+ buffer_pt_zc, rcv_p, dsp_p, mpi_xp_c, &
+ root_p, comm_p, ierr)
+ buffer_pt_zl(1:np_tot,iz) = buffer_pt_zc(1:np_tot)
+ ENDDO
+ ! send the full line on y contained by root_p
+ IF(rank_p .EQ. root_p) THEN
+ CALL MPI_GATHERV(buffer_pt_zl, snd_z, mpi_xp_c, &
+ buffer_pt_zt, rcv_zp, dsp_zp, mpi_xp_c, &
+ root_z, comm_z, ierr)
+ ENDIF
+ ! ID 0 (the one who output) rebuild the whole array
+ IF(my_id .EQ. 0) &
+ field_tot(ia,1:np_tot,ij,1:nz_tot) = buffer_pt_zt(1:np_tot,1:nz_tot)
ENDDO
- ! send the full line on y contained by root_p
- IF(rank_p .EQ. root_p) THEN
- CALL MPI_GATHERV(buffer_pt_zl, snd_z, mpi_xp_c, &
- buffer_pt_zt, rcv_zp, dsp_zp, mpi_xp_c, &
- root_z, comm_z, ierr)
- ENDIF
- ! ID 0 (the one who output) rebuild the whole array
- IF(my_id .EQ. 0) &
- field_tot(1:np_tot,ij,1:nz_tot) = buffer_pt_zt(1:np_tot,1:nz_tot)
ENDDO
ENDIF
END SUBROUTINE gather_pjz
@@ -317,8 +320,8 @@ CONTAINS
SUBROUTINE gather_pjxyz(field_loc,field_tot,na_tot,np_loc,np_tot,nj_tot,nky_loc,nky_tot,nkx_tot,nz_loc,nz_tot)
IMPLICIT NONE
INTEGER, INTENT(IN) :: na_tot,np_loc,np_tot,nj_tot,nky_loc,nky_tot,nkx_tot,nz_loc,nz_tot
- COMPLEX(xp), DIMENSION(np_loc,nj_tot,nky_loc,nkx_tot,nz_loc), INTENT(IN) :: field_loc
- COMPLEX(xp), DIMENSION(na_tot,np_tot,nj_tot,nky_tot,nkx_tot,nz_tot), INTENT(OUT) :: field_tot
+ COMPLEX(xp), DIMENSION(:,:,:,:,:,:), INTENT(IN) :: field_loc
+ COMPLEX(xp), DIMENSION(:,:,:,:,:,:), INTENT(OUT) :: field_tot
COMPLEX(xp), DIMENSION(np_tot,nky_tot,nz_loc) :: buffer_pt_yt_zl ! full p, full y, local z
COMPLEX(xp), DIMENSION(np_tot,nky_tot,nz_tot) :: buffer_pt_yt_zt ! full p, full y, full z
COMPLEX(xp), DIMENSION(np_tot,nky_loc) :: buffer_pt_yl_zc ! full p, local y, constant z
@@ -336,7 +339,7 @@ CONTAINS
z: DO iz = 1,nz_loc
y: DO iy = 1,nky_loc
! fill a buffer to contain a slice of p data at constant j, ky, kx and z
- buffer_pl_cy_zc(1:np_loc) = field_loc(1:np_loc,ij,iy,ix,iz)
+ buffer_pl_cy_zc(1:np_loc) = field_loc(ia,1:np_loc,ij,iy,ix,iz)
CALL MPI_GATHERV(buffer_pl_cy_zc, snd_p, mpi_xp_c, &
buffer_pt_cy_zc, rcv_p, dsp_p, mpi_xp_c, &
root_p, comm_p, ierr)
@@ -368,7 +371,7 @@ CONTAINS
SUBROUTINE manual_3D_bcast(field_,n1,n2,n3)
IMPLICIT NONE
INTEGER, INTENT(IN) :: n1,n2,n3
- COMPLEX(xp), DIMENSION(n1,n2,n3), INTENT(INOUT) :: field_
+ COMPLEX(xp), DIMENSION(:,:,:), INTENT(INOUT) :: field_
COMPLEX(xp) :: buffer(n1,n2,n3)
INTEGER :: i_, root, world_rank, world_size, count, i1,i2,i3
root = 0;
@@ -441,7 +444,7 @@ CONTAINS
SUBROUTINE exchange_ghosts_1D(f,nbr_L,nbr_R,np,ng)
IMPLICIT NONE
INTEGER, INTENT(IN) :: np,ng, nbr_L, nbr_R
- COMPLEX(xp), DIMENSION(np+ng), INTENT(INOUT) :: f
+ COMPLEX(xp), DIMENSION(:), INTENT(INOUT) :: f
INTEGER :: ierr, first, last, ig
first = 1 + ng/2
last = np + ng/2