diff --git a/src/array_mod.F90 b/src/array_mod.F90
index b423cc2a6838d5c50ea385767d674b191bb58f9f..ef3d3a4075c0998fed3dac64e6b9b92270be8061 100644
--- a/src/array_mod.F90
+++ b/src/array_mod.F90
@@ -67,13 +67,14 @@ MODULE array
! moments
COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_e_full
COMPLEX(dp), DIMENSION(:,:,:,:,:), ALLOCATABLE :: moments_i_full
-
+
! ES potential
COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: phi_full
! Gyrocenter density for electron and ions (ikx,iky,iz)
COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: Ne00
COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: Ni00
+ COMPLEX(dp), DIMENSION(:,:,:), ALLOCATABLE :: Ni00_full
! Kinetic spectrum sum_kx,ky(|Napj(z)|^2), (ip,ij,iz)
REAL(dp), DIMENSION(:,:,:), ALLOCATABLE :: Nepjz
diff --git a/src/collision_mod.F90 b/src/collision_mod.F90
index ea43b1d3fc804b528b8e74fe5b54cd657ca7bfc3..f2ca2956cfe02df87cf24e46ee46bcbda6f953ac 100644
--- a/src/collision_mod.F90
+++ b/src/collision_mod.F90
@@ -499,7 +499,7 @@ CONTAINS
! Sum up all the sub collision terms on root 0
CALL MPI_REDUCE(local_sum_e, buffer_e, total_np_e, 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,&
+ CALL MPI_SCATTERV(buffer_e, rcv_p_e, dsp_p_e, MPI_DOUBLE_COMPLEX,&
TColl_distr_e, local_np_e, MPI_DOUBLE_COMPLEX,&
0, comm_p, ierr)
ELSE
@@ -522,7 +522,7 @@ CONTAINS
CALL MPI_REDUCE(local_sum_i, buffer_i, total_np_i, 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,&
+ CALL MPI_SCATTERV(buffer_i, rcv_p_i, dsp_p_i, MPI_DOUBLE_COMPLEX,&
TColl_distr_i, local_np_i, MPI_DOUBLE_COMPLEX, &
0, comm_p, ierr)
ELSE
diff --git a/src/diag_headers/diagnose_full.h b/src/diag_headers/diagnose_full.h
index 93b45ca0f9213122500a387996d31a67823f94a7..091ff4b0ee6ef82cdf7280bda9d72dbb1e68903e 100644
--- a/src/diag_headers/diagnose_full.h
+++ b/src/diag_headers/diagnose_full.h
@@ -115,9 +115,11 @@ IF ((kstep .EQ. 0)) THEN
IF(KIN_E)&
CALL creatg(fidres, "/data/var3d/Ne00", "Ne00")
CALL creatg(fidres, "/data/var3d/Ni00", "Ni00")
+ CALL creatg(fidres, "/data/var3d/Ni00_gatherv", "Ni00_gatherv")
IF(KIN_E)&
CALL creatg(fidres, "/data/var3d/Nepjz", "Nepjz")
CALL creatg(fidres, "/data/var3d/Nipjz", "Nipjz")
+ CALL creatg(fidres, "/data/var3d/Nipjz_full", "Nipjz")
ENDIF
IF (write_dens) THEN
@@ -317,6 +319,11 @@ SUBROUTINE diagnose_3d
ENDIF
CALL write_field3d_kykxz(Ni00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ni00')
+ WRITE(dset_name, "(A, '/', i6.6)") "/data/var3d/Ni00_gatherv", iframe3d
+ CALL gather_xyz(Ni00(ikys:ikye,1:Nkx,izs:ize),Ni00_full(1:Nky,1:Nkx,1:Nz))
+ CALL putarr(fidres, dset_name, Ni00_full(1:Nky,1:Nkx,1:Nz), ionode=0)
+ CALL attach(fidres, dset_name, "time", time)
+
CALL compute_Napjz_spectrum
IF(KIN_E) &
CALL write_field3d_pjz_e(Nepjz(ips_e:ipe_e,ijs_e:ije_e,izs:ize), 'Nepjz')
diff --git a/src/diagnose.F90 b/src/diagnose.F90
index 4296d0eb0507153b9c5a98534ccf394628c6f70b..729b0e50ad26f204531a6643b4870a045f1dbd66 100644
--- a/src/diagnose.F90
+++ b/src/diagnose.F90
@@ -26,12 +26,6 @@ SUBROUTINE diagnose(kstep)
END IF
!! Specific diagnostic calls
CALL diagnose_full(kstep)
- ! IF(nsave_5d .GT. 0) CALL diagnose_moments(kstep)
- ! IF(nsave_3d .GT. 0) CALL diagnose_momspectrum(kstep)
- ! IF(nsave_3d .GT. 0) CALL diagnose_fields(kstep)
- ! IF(nsave_0d .GT. 0) CALL diagnose_profiler(kstep)
- ! IF(nsave_0d .GT. 0) CALL diagnose_gridgeom(kstep)
- ! IF(nsave_0d .GT. 0) CALL diagnose_timetraces(kstep)
CALL cpu_time(t1_diag); tc_diag = tc_diag + (t1_diag - t0_diag)
@@ -106,5 +100,498 @@ SUBROUTINE init_outfile(comm,file0,file,fid)
CALL putfile(fid, TRIM(str), TRIM(input_fname),ionode=0)
END SUBROUTINE init_outfile
-!! Auxiliary routines hidden in headers
-INCLUDE 'diag_headers/diagnose_full.h'
+SUBROUTINE diagnose_full(kstep)
+USE basic
+USE grid
+USE diagnostics_par
+USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf, putarrnd
+USE array
+USE model
+USE initial_par
+USE fields
+USE time_integration
+USE parallel
+USE prec_const
+USE collision, ONLY: coll_outputinputs
+USE geometry
+IMPLICIT NONE
+
+INTEGER, INTENT(in) :: kstep
+INTEGER, parameter :: BUFSIZE = 2
+INTEGER :: rank = 0
+INTEGER :: dims(1) = (/0/)
+INTEGER :: cp_counter = 0
+CHARACTER(len=256) :: str,test_
+!____________________________________________________________________________
+! 1. Initial diagnostics
+
+IF ((kstep .EQ. 0)) THEN
+ CALL init_outfile(comm0, resfile0,resfile,fidres)
+
+ ! Profiler time measurement
+ CALL creatg(fidres, "/profiler", "performance analysis")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_rhs", "cumulative rhs computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_adv_field", "cumulative adv. fields computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_clos", "cumulative closure computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_ghost", "cumulative communication time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_coll", "cumulative collision computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_poisson", "cumulative poisson computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_Sapj", "cumulative Sapj computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_checkfield", "cumulative checkfield computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_diag", "cumulative sym computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_process", "cumulative process computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_step", "cumulative total step computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/time", "current simulation time")
+
+ ! Grid info
+ CALL creatg(fidres, "/data/grid", "Grid data")
+ CALL putarr(fidres, "/data/grid/coordkx", kxarray_full, "kx*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordky", kyarray_full, "ky*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordz", zarray_full, "z/R", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordp_e" , parray_e_full, "p_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordj_e" , jarray_e_full, "j_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordp_i" , parray_i_full, "p_i", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordj_i" , jarray_i_full, "j_i", ionode=0)
+
+ ! Metric info
+ CALL creatg(fidres, "/data/metric", "Metric data")
+ CALL putarrnd(fidres, "/data/metric/gxx", gxx(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gxy", gxy(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gyy", gyy(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gyz", gyz(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gzz", gzz(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/hatR", hatR(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/hatZ", hatZ(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/hatB", hatB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradxB", gradxB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradyB", gradyB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradzB", gradzB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/Jacobian", Jacobian(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradz_coeff", gradz_coeff(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/Ckxky", Ckxky(ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/1, 1, 3/))
+ CALL putarrnd(fidres, "/data/metric/kernel_i", kernel_i(ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/ 1, 2, 4/))
+
+ ! var0d group (gyro transport)
+ IF (nsave_0d .GT. 0) THEN
+ CALL creatg(fidres, "/data/var0d", "0d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var0d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var0d/cstep", "iteration number")
+
+ IF (write_gamma) THEN
+ CALL creatd(fidres, rank, dims, "/data/var0d/gflux_ri", "Radial gyro ion transport")
+ CALL creatd(fidres, rank, dims, "/data/var0d/pflux_ri", "Radial part ion transport")
+ ENDIF
+ IF (write_hf) THEN
+ CALL creatd(fidres, rank, dims, "/data/var0d/hflux_x", "Radial part ion heat flux")
+ ENDIF
+ IF (cstep==0) THEN
+ iframe0d=0
+ ENDIF
+ CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
+ END IF
+
+
+ ! 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
+
+ ! 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_phi) THEN
+ CALL creatg(fidres, "/data/var3d/phi_gatherv", "phi_gatherv")
+ ENDIF
+
+ IF (write_Na00) THEN
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var3d/Ne00", "Ne00")
+ CALL creatg(fidres, "/data/var3d/Ni00", "Ni00")
+ CALL creatg(fidres, "/data/var3d/Ni00_gatherv", "Ni00_gatherv")
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var3d/Nepjz", "Nepjz")
+ CALL creatg(fidres, "/data/var3d/Nipjz", "Nipjz")
+ CALL creatg(fidres, "/data/var3d/Nipjz_gatherv", "Nipjz_gatherv")
+ ENDIF
+
+ IF (write_dens) THEN
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var3d/dens_e", "dens_e")
+ CALL creatg(fidres, "/data/var3d/dens_i", "dens_i")
+ ENDIF
+
+ IF (write_fvel) THEN
+ IF(KIN_E) THEN
+ CALL creatg(fidres, "/data/var3d/upar_e", "upar_e")
+ CALL creatg(fidres, "/data/var3d/uper_e", "uper_e")
+ ENDIF
+ CALL creatg(fidres, "/data/var3d/upar_i", "upar_i")
+ CALL creatg(fidres, "/data/var3d/uper_i", "uper_i")
+ ENDIF
+
+ IF (write_temp) THEN
+ IF(KIN_E) THEN
+ CALL creatg(fidres, "/data/var3d/Tper_e", "Tper_e")
+ CALL creatg(fidres, "/data/var3d/Tpar_e", "Tpar_e")
+ CALL creatg(fidres, "/data/var3d/temp_e", "temp_e")
+ ENDIF
+ CALL creatg(fidres, "/data/var3d/Tper_i", "Tper_i")
+ CALL creatg(fidres, "/data/var3d/Tpar_i", "Tpar_i")
+ CALL creatg(fidres, "/data/var3d/temp_i", "temp_i")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe3d=0
+ ENDIF
+ CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
+ END IF
+
+ ! var5d group (moments)
+ IF (nsave_5d .GT. 0) THEN
+ CALL creatg(fidres, "/data/var5d", "5d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var5d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var5d/cstep", "iteration number")
+
+ IF (write_Napj) THEN
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
+ CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
+ ENDIF
+
+ IF (write_Sapj) THEN
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var5d/Sepj", "Sepj")
+ CALL creatg(fidres, "/data/var5d/Sipj", "Sipj")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe5d=0
+ END IF
+ CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
+ END IF
+ENDIF
+
+!_____________________________________________________________________________
+! 2. Periodic diagnostics
+!
+IF (kstep .GE. 0) THEN
+
+ ! 2.1 0d history arrays
+ IF (nsave_0d .GT. 0) THEN
+ IF ( MOD(cstep, nsave_0d) == 0 ) THEN
+ CALL diagnose_0d
+ END IF
+ END IF
+
+ ! 2.2 1d profiles
+ ! empty in our case
+
+ ! 2.3 2d profiles
+ ! 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
+
+ ! 2.4 3d profiles
+ IF (nsave_5d .GT. 0 .AND. cstep .GT. 0) THEN
+ IF (MOD(cstep, nsave_5d) == 0) THEN
+ CALL diagnose_5d
+ END IF
+ END IF
+
+!_____________________________________________________________________________
+! 3. Final diagnostics
+
+ELSEIF (kstep .EQ. -1) THEN
+ CALL attach(fidres, "/data/input","cpu_time",finish-start)
+
+ ! make a checkpoint at last timestep if not crashed
+ IF(.NOT. crashed) THEN
+ IF(my_id .EQ. 0) write(*,*) 'Saving last state'
+ IF (nsave_5d .GT. 0) &
+ CALL diagnose_5d
+ ENDIF
+
+ ! Close all diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidres)
+
+END IF
+
+END SUBROUTINE diagnose_full
+
+!!-------------- Auxiliary routines -----------------!!
+SUBROUTINE diagnose_0d
+
+ USE basic
+ USE futils, ONLY: append, attach, getatt
+ USE diagnostics_par
+ USE prec_const
+ USE processing
+ USE model, ONLY: KIN_E
+
+ IMPLICIT NONE
+ ! Time measurement data
+ CALL append(fidres, "/profiler/Tc_rhs", tc_rhs,ionode=0)
+ CALL append(fidres, "/profiler/Tc_adv_field", tc_adv_field,ionode=0)
+ CALL append(fidres, "/profiler/Tc_clos", tc_clos,ionode=0)
+ CALL append(fidres, "/profiler/Tc_ghost", tc_ghost,ionode=0)
+ CALL append(fidres, "/profiler/Tc_coll", tc_coll,ionode=0)
+ CALL append(fidres, "/profiler/Tc_poisson", tc_poisson,ionode=0)
+ CALL append(fidres, "/profiler/Tc_Sapj", tc_Sapj,ionode=0)
+ CALL append(fidres, "/profiler/Tc_checkfield",tc_checkfield,ionode=0)
+ CALL append(fidres, "/profiler/Tc_diag", tc_diag,ionode=0)
+ CALL append(fidres, "/profiler/Tc_process", tc_process,ionode=0)
+ CALL append(fidres, "/profiler/Tc_step", tc_step,ionode=0)
+ CALL append(fidres, "/profiler/time", time,ionode=0)
+ ! Processing data
+ CALL append(fidres, "/data/var0d/time", time,ionode=0)
+ CALL append(fidres, "/data/var0d/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidres, "/data/var0d/", "frames",iframe2d)
+ iframe0d=iframe0d+1
+ CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
+ ! Ion transport data
+ IF (write_gamma) THEN
+ CALL compute_radial_ion_transport
+ CALL append(fidres, "/data/var0d/gflux_ri",gflux_ri,ionode=0)
+ CALL append(fidres, "/data/var0d/pflux_ri",pflux_ri,ionode=0)
+ ENDIF
+ IF (write_hf) THEN
+ CALL compute_radial_heatflux
+ CALL append(fidres, "/data/var0d/hflux_x",hflux_x,ionode=0)
+ ENDIF
+END SUBROUTINE diagnose_0d
+
+SUBROUTINE diagnose_3d
+
+ USE basic
+ USE futils, ONLY: append, getatt, attach, putarrnd, putarr
+ USE fields
+ USE array
+ 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
+ USE parallel, ONLY : gather_xyz
+ USE model, ONLY: KIN_E
+
+ IMPLICIT NONE
+
+ INTEGER :: i_, root, world_rank, world_size
+ CHARACTER(256) :: dset_name
+ 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_kykxz(phi (ikys:ikye,ikxs:ikxe,izs:ize), 'phi')
+ IF (write_phi) THEN
+ CALL gather_xyz(phi(ikys:ikye,1:Nkx,izs:ize),phi_full(1:Nky,1:Nkx,1:Nz))
+ WRITE(dset_name, "(A, '/', i6.6)") "/data/var3d/phi_gatherv", iframe3d
+ CALL putarr(fidres, dset_name, phi_full(1:Nky,1:Nkx,1:Nz), ionode=0)
+ CALL attach(fidres, dset_name, "time", time)
+ ENDIF
+
+ IF (write_Na00) THEN
+ IF(KIN_E)THEN
+ IF (ips_e .EQ. 1) &
+ Ne00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_e(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
+ CALL write_field3d_kykxz(Ne00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ne00')
+ ENDIF
+ IF (ips_i .EQ. 1) &
+ Ni00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_i(ips_i,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
+ CALL write_field3d_kykxz(Ni00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ni00')
+
+ IF (ips_i .EQ. 1) &
+ CALL gather_xyz(Ni00(ikys:ikye,1:Nkx,izs:ize),Ni00_full(1:Nky,1:Nkx,1:Nz))
+ WRITE(dset_name, "(A, '/', i6.6)") "/data/var3d/Ni00_gatherv", iframe3d
+ CALL putarr(fidres, dset_name, Ni00_full(1:Nky,1:Nkx,1:Nz), ionode=0)
+ CALL attach(fidres, dset_name, "time", time)
+
+ ! CALL compute_Napjz_spectrum
+ ! IF(KIN_E) &
+ ! CALL write_field3d_pjz_e(Nepjz(ips_e:ipe_e,ijs_e:ije_e,izs:ize), 'Nepjz')
+ ! CALL write_field3d_pjz_i(Nipjz(ips_i:ipe_i,ijs_i:ije_i,izs:ize), 'Nipjz')
+ ENDIF
+
+ !! Fuid moments
+ IF (write_dens .OR. write_fvel .OR. write_temp) &
+ CALL compute_fluid_moments
+
+ IF (write_dens) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(dens_e(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_e')
+ CALL write_field3d_kykxz(dens_i(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_i')
+ ENDIF
+
+ IF (write_fvel) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(upar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_e')
+ CALL write_field3d_kykxz(upar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(uper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_e')
+ CALL write_field3d_kykxz(uper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_i')
+ ENDIF
+
+ IF (write_temp) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(Tpar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_e')
+ CALL write_field3d_kykxz(Tpar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(Tper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_e')
+ CALL write_field3d_kykxz(Tper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(temp_e(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_e')
+ CALL write_field3d_kykxz(temp_i(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_i')
+ ENDIF
+
+ CONTAINS
+
+ SUBROUTINE write_field3d_kykxz(field, text)
+ IMPLICIT NONE
+ COMPLEX(dp), DIMENSION(ikys:ikye,ikxs:ikxe, izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(256) :: dset_name
+ 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(ikys:ikye,ikxs:ikxe, izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), (/1, 1, 3/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field3d_kykxz
+
+ SUBROUTINE write_field3d_pjz_i(field, text)
+ IMPLICIT NONE
+ REAL(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(LEN=50) :: dset_name
+ 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(ips_i:ipe_i,ijs_i:ije_i,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), (/1, 0, 3/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field3d_pjz_i
+
+ SUBROUTINE write_field3d_pjz_e(field, text)
+ IMPLICIT NONE
+ REAL(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(LEN=50) :: dset_name
+ 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(ips_e:ipe_e,ijs_e:ije_e,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), (/1, 0, 3/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field3d_pjz_e
+
+END SUBROUTINE diagnose_3d
+
+SUBROUTINE diagnose_5d
+
+ USE basic
+ USE futils, ONLY: append, getatt, attach, putarrnd
+ USE fields
+ USE array!, ONLY: Sepj, Sipj
+ USE grid, ONLY: ips_e,ipe_e, ips_i, ipe_i, &
+ ijs_e,ije_e, ijs_i, ije_i, &
+ ikxs,ikxe,ikys,ikye,izs,ize
+ USE time_integration
+ USE diagnostics_par
+ USE prec_const
+ USE model, ONLY: KIN_E
+ IMPLICIT NONE
+
+ CALL append(fidres, "/data/var5d/time", time,ionode=0)
+ CALL append(fidres, "/data/var5d/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidres, "/data/var5d/", "frames",iframe5d)
+ iframe5d=iframe5d+1
+ CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
+
+ IF (write_Napj) THEN
+ IF(KIN_E)&
+ CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_e')
+ CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_i')
+ ENDIF
+
+ IF (write_Sapj) THEN
+ IF(KIN_E)&
+ CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), 'Sepj')
+ CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), '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, ikxs,ikxe, ikys,ikye, izs,ize
+ USE prec_const
+ IMPLICIT NONE
+
+ COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,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,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
+ ENDIF
+ CALL attach(fidres, dset_name, 'cstep', cstep)
+ CALL attach(fidres, dset_name, 'time', time)
+ CALL attach(fidres, dset_name, 'jobnum', jobnum)
+ CALL attach(fidres, dset_name, 'dt', dt)
+ CALL attach(fidres, dset_name, 'iframe2d', iframe2d)
+ CALL attach(fidres, dset_name, 'iframe5d', iframe5d)
+
+ END SUBROUTINE write_field5d_e
+
+ SUBROUTINE write_field5d_i(field, text)
+ USE futils, ONLY: attach, putarr, putarrnd
+ 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,ikys:ikye,ikxs:ikxe,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,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
+ ENDIF
+ CALL attach(fidres, dset_name, 'cstep', cstep)
+ CALL attach(fidres, dset_name, 'time', time)
+ CALL attach(fidres, dset_name, 'jobnum', jobnum)
+ CALL attach(fidres, dset_name, 'dt', dt)
+ CALL attach(fidres, dset_name, 'iframe2d', iframe2d)
+ CALL attach(fidres, dset_name, 'iframe5d', iframe5d)
+
+ END SUBROUTINE write_field5d_i
+END SUBROUTINE diagnose_5d
diff --git a/src/grid_mod.F90 b/src/grid_mod.F90
index 139cd0abe9a60444394d846263bcadad61a73266..62154f9db49ee8960da2c38eafd673824c3c1f5e 100644
--- a/src/grid_mod.F90
+++ b/src/grid_mod.F90
@@ -58,8 +58,8 @@ MODULE grid
INTEGER, PUBLIC :: local_np_e, local_np_i
INTEGER, PUBLIC :: total_np_e, total_np_i
integer(C_INTPTR_T), PUBLIC :: local_np_e_offset, local_np_i_offset
- INTEGER, DIMENSION(:), ALLOCATABLE, PUBLIC :: counts_np_e, counts_np_i
- INTEGER, DIMENSION(:), ALLOCATABLE, PUBLIC :: displs_np_e, displs_np_i
+ INTEGER, DIMENSION(:), ALLOCATABLE, PUBLIC :: rcv_p_e, rcv_p_i
+ INTEGER, DIMENSION(:), ALLOCATABLE, PUBLIC :: dsp_p_e, dsp_p_i
! "" for z
INTEGER, PUBLIC :: local_nz
INTEGER, PUBLIC :: total_nz
@@ -179,17 +179,17 @@ CONTAINS
ipgs_e = ips_e - 2/deltape; ipge_e = ipe_e + 2/deltape;
ipgs_i = ips_i - 2/deltapi; ipge_i = ipe_i + 2/deltapi;
! List of shift and local numbers between the different processes (used in scatterv and gatherv)
- ALLOCATE(counts_np_e (1:num_procs_p))
- ALLOCATE(counts_np_i (1:num_procs_p))
- ALLOCATE(displs_np_e (1:num_procs_p))
- ALLOCATE(displs_np_i (1:num_procs_p))
+ ALLOCATE(rcv_p_e (1:num_procs_p))
+ ALLOCATE(rcv_p_i (1:num_procs_p))
+ ALLOCATE(dsp_p_e (1:num_procs_p))
+ ALLOCATE(dsp_p_i (1:num_procs_p))
DO in = 0,num_procs_p-1
CALL decomp1D(total_np_e, num_procs_p, in, istart, iend)
- counts_np_e(in+1) = iend-istart+1
- displs_np_e(in+1) = istart-1
+ rcv_p_e(in+1) = iend-istart+1
+ dsp_p_e(in+1) = istart-1
CALL decomp1D(total_np_i, num_procs_p, in, istart, iend)
- counts_np_i(in+1) = iend-istart+1
- displs_np_i(in+1) = istart-1
+ rcv_p_i(in+1) = iend-istart+1
+ dsp_p_i(in+1) = istart-1
ENDDO
! local grid computation
diff --git a/src/memory.F90 b/src/memory.F90
index 6fbaafde7c7e5da897214c00c1ad177272a12fdc..3c313f5394e3c4e996f7140ef8e53677fccfc9fb 100644
--- a/src/memory.F90
+++ b/src/memory.F90
@@ -58,6 +58,7 @@ SUBROUTINE memory
!Ions arrays
CALL allocate_array( Ni00, ikys,ikye, ikxs,ikxe, izs,ize)
+ CALL allocate_array( Ni00_full, 1,Nky, 1,Nkx, 1,Nz)
CALL allocate_array( dens_i, ikys,ikye, ikxs,ikxe, izs,ize)
CALL allocate_array( upar_i, ikys,ikye, ikxs,ikxe, izs,ize)
CALL allocate_array( uper_i, ikys,ikye, ikxs,ikxe, izs,ize)
@@ -125,4 +126,7 @@ SUBROUTINE memory
ENDIF
CALL allocate_array( Ciipj, 1,(pmaxi+1)*(jmaxi+1), 1,(pmaxi+1)*(jmaxi+1), 1,1, 1,1, 1,1)
ENDIF
+
+ !____________DIAGNOSTIC PURPOSE ONLY ARRAYS_______________
+
END SUBROUTINE memory
diff --git a/src/parallel_mod.F90 b/src/parallel_mod.F90
index 1598bf33d380e50a2d6211b770856d68b00bbe87..522337748a7d42b2a16dc4498322a13528d01d6f 100644
--- a/src/parallel_mod.F90
+++ b/src/parallel_mod.F90
@@ -1,18 +1,25 @@
MODULE parallel
USE basic
- USE grid, ONLY: Nkx,Nky,Nz, ikys,ikye, izs,ize, local_nky, local_nz
+ USE grid, ONLY: Nkx,Nky,Nz, ikys,ikye, izs,ize, local_nky, local_nz, &
+ local_np_e, local_np_i, total_np_e, total_np_i, &
+ pmaxi, pmaxe, ips_e, ipe_e, ips_i, ipe_i, &
+ jmaxi, jmaxe, ijs_e, ije_e, ijs_i, ije_i, &
+ rcv_p_e, rcv_p_i, dsp_p_e, dsp_p_i
use prec_const
IMPLICIT NONE
! recieve and displacement counts for gatherv
- INTEGER, DIMENSION(:), ALLOCATABLE :: rcv_z, rcv_y, dsp_z, dsp_y
+ INTEGER, DIMENSION(:), ALLOCATABLE :: rcv_y, dsp_y, rcv_zy, dsp_zy
+ INTEGER, DIMENSION(:), ALLOCATABLE :: rcv_zp_e, dsp_zp_e
+ INTEGER, DIMENSION(:), ALLOCATABLE :: rcv_zp_i, dsp_zp_i
PUBLIC :: manual_0D_bcast, manual_3D_bcast, init_parallel_var, &
- gather_xyz!, gather_pjz, gather_pjxyz
+ gather_xyz, gather_pjz_e, gather_pjz_i!, gather_pjxyz
CONTAINS
SUBROUTINE init_parallel_var
INTEGER :: i_
+ !!!!!! XYZ gather variables
!! Y reduction at constant x and z
! number of points recieved and displacement for the y reduction
ALLOCATE(rcv_y(0:num_procs_ky-1),dsp_y(0:num_procs_ky-1)) !Displacement sizes for balance diagnostic
@@ -23,18 +30,44 @@ CONTAINS
DO i_=1,num_procs_ky-1
dsp_y(i_) =dsp_y(i_-1) + rcv_y(i_-1)
END DO
- print*, rcv_y, dsp_y
!! Z reduction for full slices of y data but constant x
! number of points recieved and displacement for the z reduction
- ALLOCATE(rcv_z(0:num_procs_z-1),dsp_z(0:num_procs_z-1)) !Displacement sizes for balance diagnostic
+ ALLOCATE(rcv_zy(0:num_procs_z-1),dsp_zy(0:num_procs_z-1)) !Displacement sizes for balance diagnostic
! all processes share their local number of points
- CALL MPI_ALLGATHER(local_nz*Nky,1,MPI_INTEGER,rcv_z,1,MPI_INTEGER,comm_z,ierr)
+ CALL MPI_ALLGATHER(local_nz*Nky,1,MPI_INTEGER,rcv_zy,1,MPI_INTEGER,comm_z,ierr)
! the displacement array can be build from each local_np as
- dsp_z(0)=0
+ dsp_zy(0)=0
DO i_=1,num_procs_z-1
- dsp_z(i_) =dsp_z(i_-1) + rcv_z(i_-1)
+ dsp_zy(i_) =dsp_zy(i_-1) + rcv_zy(i_-1)
END DO
- print*, rcv_z, dsp_z
+ print*, rcv_zy, dsp_zy
+
+ !!!!! PJZ gather variables
+ ! ELECTRONS
+ ! P variables are already defined in grid module (see rcv_p_a, dsp_p_a)
+ !! Z reduction for full slices of p data but constant j
+ ! number of points recieved and displacement for the z reduction
+ ALLOCATE(rcv_zp_e(0:num_procs_z-1),dsp_zp_e(0:num_procs_z-1)) !Displacement sizes for balance diagnostic
+ ! all processes share their local number of points
+ CALL MPI_ALLGATHER(local_nz*total_np_e,1,MPI_INTEGER,rcv_zp_e,1,MPI_INTEGER,comm_z,ierr)
+ ! the displacement array can be build from each local_np as
+ dsp_zp_e(0)=0
+ DO i_=1,num_procs_z-1
+ dsp_zp_e(i_) =dsp_zp_e(i_-1) + dsp_zp_e(i_-1)
+ END DO
+ ! IONS
+ ! P variables are already defined in grid module (see rcv_p_a, dsp_p_a)
+ !! Z reduction for full slices of p data but constant j
+ ! number of points recieved and displacement for the z reduction
+ ALLOCATE(rcv_zp_i(0:num_procs_z-1),dsp_zp_i(0:num_procs_z-1)) !Displacement sizes for balance diagnostic
+ ! all processes share their local number of points
+ CALL MPI_ALLGATHER(local_nz*total_np_i,1,MPI_INTEGER,rcv_zp_i,1,MPI_INTEGER,comm_z,ierr)
+ ! the displacement array can be build from each local_np as
+ dsp_zp_i(0)=0
+ DO i_=1,num_procs_z-1
+ dsp_zp_i(i_) =dsp_zp_i(i_-1) + dsp_zp_i(i_-1)
+ END DO
+
END SUBROUTINE init_parallel_var
!!!!! Gather a field in spatial coordinates on rank 0 !!!!!
@@ -45,26 +78,28 @@ CONTAINS
COMPLEX(dp), DIMENSION( 1:Nky ) :: buffer_fy_cz !full y, constant z
COMPLEX(dp), DIMENSION( 1:Nky, izs:ize ) :: buffer_fy_lz !full y, local z
COMPLEX(dp), DIMENSION( 1:Nky, 1:Nz ) :: buffer_fy_fz !full y, full z
- INTEGER :: send_count, root_p, root_z, root_ky, ix, iz
+ INTEGER :: snd_y, snd_z, root_p, root_z, root_ky, ix, iz
+
+ snd_y = local_nky ! Number of points to send along y (per z)
+ snd_z = Nky*local_nz ! Number of points to send along z (full y)
root_p = 0; root_z = 0; root_ky = 0
IF(rank_p .EQ. root_p) THEN
DO ix = 1,Nkx
DO iz = izs,ize
! fill a buffer to contain a slice of data at constant kx and z
- print*,iz
buffer_ly_cz(ikys:ikye) = field_sub(ikys:ikye,ix,iz)
- CALL MPI_GATHERV(buffer_ly_cz,local_nky,MPI_DOUBLE_COMPLEX, &
+ CALL MPI_GATHERV(buffer_ly_cz, snd_y, MPI_DOUBLE_COMPLEX, &
buffer_fy_cz, rcv_y, dsp_y, MPI_DOUBLE_COMPLEX, &
- root_ky, comm_ky)
+ root_ky, comm_ky, ierr)
buffer_fy_lz(1:Nky,iz) = buffer_fy_cz(1:Nky)
ENDDO
- ! send the full line on y contained by root_ky
+ ! send the full line on y contained by root_kyas
IF(rank_ky .EQ. 0) THEN
- CALL MPI_GATHERV(buffer_fy_lz,Nky*local_nz,MPI_DOUBLE_COMPLEX, &
- buffer_fy_fz, rcv_z, dsp_z, MPI_DOUBLE_COMPLEX, &
- root_z, comm_z)
+ CALL MPI_GATHERV(buffer_fy_lz, snd_z, MPI_DOUBLE_COMPLEX, &
+ buffer_fy_fz, rcv_zy, dsp_zy, MPI_DOUBLE_COMPLEX, &
+ root_z, comm_z, ierr)
ENDIF
! ID 0 (the one who output) rebuild the whole array
IF(my_id .EQ. 0) &
@@ -74,6 +109,81 @@ CONTAINS
END SUBROUTINE gather_xyz
!!!!! Gather a field in kinetic + z coordinates on rank 0 !!!!!
+ SUBROUTINE gather_pjz_e(field_sub,field_full)
+ COMPLEX(dp), DIMENSION(ips_e:ipe_e, ijs_e:ije_e, izs:ize), INTENT(IN) :: field_sub
+ COMPLEX(dp), DIMENSION( 1:pmaxe+1, 1:jmaxe+1, 1:Nz), INTENT(INOUT) :: field_full
+ COMPLEX(dp), DIMENSION(ips_e:ipe_e) :: buffer_lp_cz !local p, constant z
+ COMPLEX(dp), DIMENSION( 1:pmaxe+1 ) :: buffer_fp_cz !full p, constant z
+ COMPLEX(dp), DIMENSION( 1:pmaxe+1, izs:ize ) :: buffer_fp_lz !full p, local z
+ COMPLEX(dp), DIMENSION( 1:pmaxe+1, 1:Nz ) :: buffer_fp_fz !full p, full z
+ INTEGER :: snd_p, snd_z, root_p, root_z, root_ky, ij, iz, Npe
+
+ Npe = pmaxe+1 ! total number of hermite moments
+ snd_p = local_np_e ! Number of points to send along y (per z)
+ snd_z = Npe*local_nz ! Number of points to send along z (full y)
+
+ root_p = 0; root_z = 0; root_ky = 0
+ IF(rank_ky .EQ. root_ky) THEN
+ DO ij = 1,jmaxe+1
+ DO iz = izs,ize
+ ! fill a buffer to contain a slice of data at constant kx and z
+ buffer_lp_cz(ips_e:ipe_e) = field_sub(ips_e:ipe_e,ij,iz)
+ CALL MPI_GATHERV(buffer_lp_cz, snd_p, MPI_DOUBLE_COMPLEX, &
+ buffer_fp_cz, rcv_p_e, dsp_p_e, MPI_DOUBLE_COMPLEX, &
+ root_p, comm_p, ierr)
+ buffer_fp_lz(1:Npe,iz) = buffer_fp_cz(1:Npe)
+ ENDDO
+
+ ! send the full line on y contained by root_kyas
+ IF(rank_p .EQ. 0) THEN
+ CALL MPI_GATHERV(buffer_fp_lz, snd_z, MPI_DOUBLE_COMPLEX, &
+ buffer_fp_fz, rcv_zp_e, dsp_zp_e, MPI_DOUBLE_COMPLEX, &
+ root_z, comm_z, ierr)
+ ENDIF
+ ! ID 0 (the one who output) rebuild the whole array
+ IF(my_id .EQ. 0) &
+ field_full(1:Npe,ij,1:Nz) = buffer_fp_fz(1:Npe,1:Nz)
+ ENDDO
+ ENDIF
+ END SUBROUTINE gather_pjz_e
+
+ SUBROUTINE gather_pjz_i(field_sub,field_full)
+ COMPLEX(dp), DIMENSION(ips_i:ipe_i, ijs_i:ije_i, izs:ize), INTENT(IN) :: field_sub
+ COMPLEX(dp), DIMENSION( 1:pmaxi+1, 1:jmaxi+1, 1:Nz), INTENT(INOUT) :: field_full
+ COMPLEX(dp), DIMENSION(ips_i:ipe_i) :: buffer_lp_cz !local p, constant z
+ COMPLEX(dp), DIMENSION( 1:pmaxi+1 ) :: buffer_fp_cz !full p, constant z
+ COMPLEX(dp), DIMENSION( 1:pmaxi+1, izs:ize ) :: buffer_fp_lz !full p, local z
+ COMPLEX(dp), DIMENSION( 1:pmaxi+1, 1:Nz ) :: buffer_fp_fz !full p, full z
+ INTEGER :: snd_p, snd_z, root_p, root_z, root_ky, ij, iz, Npi
+
+ Npi = pmaxi+1 ! total number of hermite moments
+ snd_p = local_np_i ! Number of points to send along y (per z)
+ snd_z = Npi*local_nz ! Number of points to send along z (full y)
+
+ root_p = 0; root_z = 0; root_ky = 0
+ IF(rank_ky .EQ. root_ky) THEN
+ DO ij = 1,jmaxi+1
+ DO iz = izs,ize
+ ! fill a buffer to contain a slice of data at constant kx and z
+ buffer_lp_cz(ips_i:ipe_i) = field_sub(ips_i:ipe_i,ij,iz)
+ CALL MPI_GATHERV(buffer_lp_cz, snd_p, MPI_DOUBLE_COMPLEX, &
+ buffer_fp_cz, rcv_p_i, dsp_p_i, MPI_DOUBLE_COMPLEX, &
+ root_p, comm_p, ierr)
+ buffer_fp_lz(1:Npi,iz) = buffer_fp_cz(1:Npi)
+ ENDDO
+
+ ! send the full line on y contained by root_kyas
+ IF(rank_p .EQ. 0) THEN
+ CALL MPI_GATHERV(buffer_fp_lz, snd_z, MPI_DOUBLE_COMPLEX, &
+ buffer_fp_fz, rcv_zp_i, dsp_zp_i, MPI_DOUBLE_COMPLEX, &
+ root_z, comm_z, ierr)
+ ENDIF
+ ! ID 0 (the one who output) rebuild the whole array
+ IF(my_id .EQ. 0) &
+ field_full(1:Npi,ij,1:Nz) = buffer_fp_fz(1:Npi,1:Nz)
+ ENDDO
+ ENDIF
+ END SUBROUTINE gather_pjz_i
!!!!! Gather a field in kinetic + spatial coordinates on rank 0 !!!!!
diff --git a/src/ppinit.F90 b/src/ppinit.F90
index f103cdd91a65fd818c6e5ae63b8df2df5fe261c1..1863dcf9852c2e85ab2a9fe87e1627bb8de368c4 100644
--- a/src/ppinit.F90
+++ b/src/ppinit.F90
@@ -50,7 +50,7 @@ SUBROUTINE ppinit
periods(3)=.TRUE.
CALL MPI_CART_CREATE(MPI_COMM_WORLD, ndims, dims, periods, reorder, comm0, ierr)
- CALL MPI_COMM_GROUP(comm0,group0)
+ CALL MPI_COMM_GROUP(comm0,group0, ierr)
CALL MPI_COMM_RANK(comm0, rank_0, ierr)
CALL MPI_CART_COORDS(comm0,rank_0,ndims,coords,ierr)
@@ -81,12 +81,12 @@ SUBROUTINE ppinit
CALL MPI_CART_SHIFT(comm0, 2, 1, nbr_D, nbr_U, ierr) !down up neighbours
! Create the communicator for groups used in gatherv
- CALL MPI_COMM_GROUP(comm0,group_ky0)
- ALLOCATE(rank2include(0:num_procs_ky))
- DO r_ = 0,rank_0
- IF(rank_y .EQ. 0) &
- rank2exclude
- ENDDO
- CALL MPI_COMM_CREATE_GROUPE(comm0, group_p0, comm_ky0)
+ ! CALL MPI_COMM_GROUP(comm0,group_ky0)
+ ! ALLOCATE(rank2include(0:num_procs_ky))
+ ! DO r_ = 0,rank_0
+ ! IF(rank_y .EQ. 0) &
+ ! rank2exclude
+ ! ENDDO
+ ! CALL MPI_COMM_CREATE_GROUPE(comm0, group_p0, comm_ky0)
END SUBROUTINE ppinit
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index 84d0bd3a46788d6242e6427ed69717a87bed7bc1..248577edb2e8d35d9b2ab1847bccc821dd23c31a 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -53,7 +53,7 @@ options.PLAN = 'xy';
% options.PLAN = 'sx';
options.COMP = 9;
% options.TIME = dat.Ts5D;
-options.TIME = 920:1:1250;
+options.TIME = 920:1:1100;
data.EPS = 0.1;
data.a = data.EPS * 2000;
create_film(data,options,'.gif')
@@ -71,11 +71,11 @@ options.NAME = 'N_i^{00}';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'xy';
+options.PLAN = 'xz';
% options.NAME = 'f_i';
% options.PLAN = 'sx';
-options.COMP = 'avg';
-options.TIME = [900 923 927 990];
+options.COMP = 9;
+options.TIME = [900 1000 1100];
data.a = data.EPS * 2e3;
fig = photomaton(data,options);
save_figure(data,fig)
diff --git a/wk/analysis_header.m b/wk/analysis_header.m
index 28d53d9fa75886538543945efe5d064f42bbe4b1..4be2eb2fc0261d6acaba7b7a6e070ebc0fc09c12 100644
--- a/wk/analysis_header.m
+++ b/wk/analysis_header.m
@@ -5,9 +5,9 @@ helazdir = '/home/ahoffman/HeLaZ/';
outfile ='';
outfile ='';
outfile ='';
-% outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
+outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
% outfile ='shearless_cyclone/128x128x16xdmax_L_120_CBC_1.0';
-outfile ='shearless_cyclone/linear_CBC_100_D_16';
+% outfile ='shearless_cyclone/linear_CBC_100_D_16';
% outfile ='quick_run/CLOS_1_64x64_5x3_L_120_kN_2.0_kT_0.5_nu_1e-01_SGGK';
% outfile ='pedestal/64x64x16x2x1_L_300_LnT_20_nu_0.1';
% outfile ='quick_run/32x32x16_5x3_L_300_q0_2.5_e_0.18_kN_20_kT_20_nu_1e-01_DGGK';
diff --git a/wk/debug_script.m b/wk/debug_script.m
new file mode 100644
index 0000000000000000000000000000000000000000..3954d02070ab844e0f79b33fc7dbbd7364d1ef6a
--- /dev/null
+++ b/wk/debug_script.m
@@ -0,0 +1,18 @@
+system('cd ../results/debug/test_diag; mpirun -np 8 ./helaz3_dbg 2 2 2; cd $HOME/HeLaZ/wk');
+
+
+filename = '../results/debug/test_diag/outputs_00.h5';
+
+f_ = h5read(filename,'/data/var3d/phi/000004/');
+f_gatherv = h5read(filename,'/data/var3d/phi_gatherv/000004/');
+f_ = f_.real + 1i*f_.imaginary;
+f_gatherv = f_gatherv.real + 1i*f_gatherv.imaginary;
+err = sum(sum(sum(abs(f_-f_gatherv))))/sum(sum(sum(abs(f_))));
+disp(['error_phi = ',sprintf('%2.2e',err)]);
+
+f_ = h5read(filename,'/data/var3d/Ni00/000004/');
+f_gatherv = h5read(filename,'/data/var3d/Ni00_gatherv/000004/');
+f_ = f_.real + 1i*f_.imaginary;
+f_gatherv = f_gatherv.real + 1i*f_gatherv.imaginary;
+err = sum(sum(sum(abs(f_-f_gatherv))))/sum(sum(sum(abs(f_))));
+disp(['error_Ni00 = ',sprintf('%2.2e',err)]);