SUBROUTINE diagnose(kstep)
! Diagnostics, writing simulation state to disk
USE basic, ONLY: lu_in, chrono_runt, cstep, dt, time, tmax, display_h_min_s
USE diagnostics_par, ONLY: input_fname
USE processing, ONLY: pflux_x, hflux_x
USE parallel, ONLY: my_id
IMPLICIT NONE
INTEGER, INTENT(in) :: kstep
!! Basic diagnose loop for reading input file, displaying advancement and ending
IF ((kstep .EQ. 0)) THEN
INQUIRE(unit=lu_in, name=input_fname)
CLOSE(lu_in)
ENDIF
!! End diag
IF (kstep .EQ. -1) THEN
! Display total run time
CALL display_h_min_s(chrono_runt%ttot)
! Show last state transport values
IF (my_id .EQ. 0) &
WRITE(*,"(A,G10.2,A8,G10.2,A)") 'Final transport values : | Gxi = ',pflux_x(1),'| Qxi = ',hflux_x(1),'|'
END IF
!! Specific diagnostic calls
CALL diagnose_full(kstep)
! Terminal info
IF ((kstep .GE. 0) .AND. (MOD(cstep, INT(1.0/dt)) == 0) .AND. (my_id .EQ. 0)) THEN
WRITE(*,"(A,F6.0,A1,F6.0,A8,G10.2,A8,G10.2,A)")'|t/tmax = ', time,"/",tmax,'| Gxi = ',pflux_x(1),'| Qxi = ',hflux_x(1),'|'
ENDIF
END SUBROUTINE diagnose
SUBROUTINE init_outfile(comm,file0,file,fid)
USE diagnostics_par, ONLY: write_doubleprecision, diag_par_outputinputs, input_fname
USE basic, ONLY: speak, jobnum, basic_outputinputs
USE grid, ONLY: grid_outputinputs
USE geometry, ONLY: geometry_outputinputs
USE model, ONLY: model_outputinputs
USE closure, ONLY: closure_outputinputs
USE species, ONLY: species_outputinputs
USE collision, ONLY: coll_outputinputs
USE initial_par, ONLY: initial_outputinputs
USE time_integration,ONLY: time_integration_outputinputs
USE futils, ONLY: creatf, creatg, creatd, attach, putfile
IMPLICIT NONE
!input
INTEGER, INTENT(IN) :: comm
CHARACTER(len=256), INTENT(IN) :: file0
CHARACTER(len=256), INTENT(OUT) :: file
INTEGER, INTENT(OUT) :: fid
CHARACTER(len=256) :: str
INCLUDE 'srcinfo.h'
! Writing output filename
WRITE(file,'(a,a1,i2.2,a3)') TRIM(file0) ,'_',jobnum,'.h5'
! 1.1 Initial run
! Main output file creation
IF (write_doubleprecision) THEN
CALL creatf(file, fid, real_prec='d', mpicomm=comm)
ELSE
CALL creatf(file, fid, mpicomm=comm)
END IF
CALL speak(TRIM(file)//' created')
! basic data group
CALL creatg(fid, "/data", "data")
! File group
CALL creatg(fid, "/files", "files")
CALL attach(fid, "/files", "jobnum", jobnum)
! Add the code info and parameters to the file
CALL creatg(fid, "/data/input", "input")
CALL creatd(fid, 0,(/0/),"/data/input/codeinfo",'Code Information')
CALL attach(fid, "/data/input/codeinfo", "version", VERSION) !defined in srcinfo.h
CALL attach(fid, "/data/input/codeinfo", "branch", BRANCH) !defined in srcinfo.h
CALL attach(fid, "/data/input/codeinfo", "author", AUTHOR) !defined in srcinfo.h
CALL attach(fid, "/data/input/codeinfo", "execdate", EXECDATE) !defined in srcinfo.h
CALL attach(fid, "/data/input/codeinfo", "host", HOST) !defined in srcinfo.h
CALL basic_outputinputs(fid)
CALL grid_outputinputs(fid)
CALL geometry_outputinputs(fid)
CALL diag_par_outputinputs(fid)
CALL model_outputinputs(fid)
CALL closure_outputinputs(fid)
CALL species_outputinputs(fid)
CALL coll_outputinputs(fid)
CALL initial_outputinputs(fid)
CALL time_integration_outputinputs(fid)
! Save STDIN (input file) of this run
IF(jobnum .LE. 99) THEN
WRITE(str,'(a,i2.2)') "/files/STDIN.",jobnum
ELSE
WRITE(str,'(a,i3.2)') "/files/STDIN.",jobnum
END IF
CALL putfile(fid, TRIM(str), TRIM(input_fname),ionode=0)
END SUBROUTINE init_outfile
SUBROUTINE diagnose_full(kstep)
USE basic, ONLY: speak,chrono_runt,&
cstep,iframe0d,iframe3d,iframe5d,crashed
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
USE diagnostics_par
USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf, putarrnd
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
INTEGER, INTENT(in) :: kstep
INTEGER, parameter :: BUFSIZE = 2
INTEGER :: rank = 0, ierr
INTEGER :: dims(1) = (/0/)
!____________________________________________________________________________
! 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_poisson", "cumulative poisson computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_Sapj", "cumulative Sapj computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_coll", "cumulative collision computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_grad", "cumulative grad computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_nadiab", "cumulative nadiab moments computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_adv_field", "cumulative adv. fields computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_ghost", "cumulative communication time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_clos", "cumulative closure 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_step", "cumulative total step computation time")
CALL creatd(fidres, 0, dims, "/profiler/time", "current simulation time")
#ifdef TEST_SVD
CALL creatd(fidres, 0, (/0/), "/profiler/Tc_DLRA", "cumulative total DLRA computation time")
#endif
! 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" , parray_full, "p", ionode=0)
CALL putarr(fidres, "/data/grid/coordj" , jarray_full, "j", ionode=0)
! Metric info
CALL creatg(fidres, "/data/metric", "Metric data")
CALL putarrnd(fidres, "/data/metric/gxx", gxx((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/gxy", gxy((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/gxz", gxz((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/gyy", gyy((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/gyz", gyz((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/gzz", gzz((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/hatR", hatR((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/hatZ", hatZ((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/hatB", hatB((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/dBdx", dBdx((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/dBdy", dBdy((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/dBdz", dBdz((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/Jacobian", Jacobian((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/gradz_coeff", gradz_coeff((1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 1/))
CALL putarrnd(fidres, "/data/metric/Ckxky", Ckxky(1:local_nky,1:local_nkx,(1+ngz/2):(local_nz+ngz/2),:), (/1, 1, 3/))
CALL putarrnd(fidres, "/data/metric/kernel", kernel(1,(1+ngj/2):(local_nj+ngj/2),1:local_nky,1:local_nkx,(1+ngz/2):(local_nz+ngz/2),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_x", "Radial gyro transport")
CALL creatd(fidres, rank, dims, "/data/var0d/pflux_x", "Radial part transport")
ENDIF
IF (write_hf) THEN
CALL creatd(fidres, rank, dims, "/data/var0d/hflux_x", "Radial part heat flux")
ENDIF
IF (cstep==0) THEN
iframe0d=0
ENDIF
CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
END IF
! var2d group (gyro transport)
IF (nsave_0d .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")
#ifdef TEST_SVD
CALL creatg(fidres, "/data/var2d/sv_ky_pj", "singular values of the moment ky/pj cut")
#endif
ENDIF
! var3d group (phi,psi, fluid moments, Ni00, Napjz)
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.AND.EM) CALL creatg(fidres, "/data/var3d/psi", "psi")
IF (write_Na00) THEN
CALL creatg(fidres, "/data/var3d/Na00", "gyrocenter density ")
CALL creatg(fidres, "/data/var3d/Napjz", "pj(z) moment spectrum ")
ENDIF
IF (write_dens) THEN
CALL creatg(fidres, "/data/var3d/dens", "density ")
ENDIF
IF (write_fvel) THEN
CALL creatg(fidres, "/data/var3d/upar", "parallel fluid velocity ")
CALL creatg(fidres, "/data/var3d/uper", "perpendicular fluid velocity ")
ENDIF
IF (write_temp) THEN
CALL creatg(fidres, "/data/var3d/Tper", "perpendicular temperature ")
CALL creatg(fidres, "/data/var3d/Tpar", "parallel temperature ")
CALL creatg(fidres, "/data/var3d/temp", "tiotal temperature ")
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
CALL creatg(fidres, "/data/var5d/moments", "full moments array")
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 2d profiles
IF (nsave_2d .GT. 0) THEN
IF (MOD(cstep, nsave_2d) == 0) THEN
CALL diagnose_2d
ENDIF
ENDIF
! 2.3 3d profiles
IF (nsave_3d .GT. 0) THEN
IF (MOD(cstep, nsave_3d) == 0) THEN
CALL diagnose_3d
! Looks at the folder if the file check_phi exists and spits a snapshot
! of the current electrostatic potential in a basic text file
CALL spit_snapshot_check
ENDIF
ENDIF
! 2.4 5d profiles
IF (nsave_5d .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",chrono_runt%ttot)
! 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, creatd
USE diagnostics_par
USE prec_const
USE processing
USE model, ONLY: Na
IMPLICIT NONE
! 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)
CALL append(fidres, "/profiler/Tc_clos", REAL(chrono_clos%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_ghost", REAL(chrono_ghst%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_coll", REAL(chrono_coll%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_poisson", REAL(chrono_pois%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_Sapj", REAL(chrono_sapj%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_checkfield",REAL(chrono_chck%ttot,dp),ionode=0)
CALL append(fidres, "/profiler/Tc_diag", REAL(chrono_diag%ttot,dp),ionode=0)
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 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)
CALL append(fidres, "/data/var0d/cstep", real(cstep,dp),ionode=0)
CALL getatt(fidres, "/data/var0d/", "frames",iframe0d)
iframe0d=iframe0d+1
CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
! Ion transport data
IF (write_gamma) THEN
CALL compute_radial_transport
CALL append(fidres, "/data/var0d/gflux_x",REAL(gflux_x,dp),ionode=0)
CALL append(fidres, "/data/var0d/pflux_x",REAL(pflux_x,dp),ionode=0)
ENDIF
IF (write_hf) THEN
CALL compute_radial_heatflux
CALL append(fidres, "/data/var0d/hflux_x",REAL(hflux_x,dp),ionode=0)
ENDIF
END SUBROUTINE diagnose_0d
SUBROUTINE diagnose_2d
USE prec_const
USE basic
USE diagnostics_par
USE futils, ONLY: putarr, append
#ifdef TEST_SVD
USE DLRA, ONLY: Sf
#endif
IMPLICIT NONE
CHARACTER(50) :: dset_name
iframe2d=iframe2d+1
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
SUBROUTINE diagnose_3d
USE basic
USE futils, ONLY: append, getatt, attach, putarrnd, putarr
USE fields, ONLY: phi, psi, moments
USE array, ONLY: Napjz,dens,upar,uper,Tpar,Tper,temp
USE grid, ONLY: CONTAINSp0, ip0,ij0, local_na, total_na,&
total_np, total_nj, total_nky, total_nkx, total_nz, &
local_np, local_nj, local_nky, local_nkx, local_nz, &
ngz
USE time_integration, ONLY: updatetlevel
USE diagnostics_par
USE prec_const
USE processing, ONLY: compute_fluid_moments, compute_Napjz_spectrum
USE model, ONLY: EM
USE parallel, ONLY: manual_3D_bcast
IMPLICIT NONE
COMPLEX(xp), DIMENSION(local_na,local_nky,local_nkx,local_nz) :: Na00_
! 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)
CALL getatt(fidres, "/data/var3d/", "frames",iframe3d)
iframe3d=iframe3d+1
CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
! Write current EM fields
IF (write_phi) CALL write_field3d_kykxz(phi (:,:,(1+ngz/2):(local_nz+ngz/2)), 'phi')
IF (write_phi.AND.EM) CALL write_field3d_kykxz(psi (:,:,(1+ngz/2):(local_nz+ngz/2)), 'psi')
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_field3da_kykxz(Na00_, 'Na00')
! <<Napj>x>y spectrum
CALL write_field3da_pjz(Napjz, 'Napjz')
ENDIF
!! Fuid moments
IF (write_dens .OR. write_fvel .OR. write_temp) &
CALL compute_fluid_moments
IF (write_dens) THEN
CALL write_field3da_kykxz(dens, 'dens')
ENDIF
IF (write_fvel) THEN
CALL write_field3da_kykxz(upar, 'upar')
CALL write_field3da_kykxz(uper, 'uper')
ENDIF
IF (write_temp) THEN
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(:,:,:), 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/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)
CALL putarr(fidres, dset_name, field_full, ionode=0)
ENDIF
END SUBROUTINE write_field3d_kykxz
SUBROUTINE write_field3da_kykxz(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/var3d", TRIM(text), iframe3d
IF (num_procs .EQ. 1) THEN ! no data distribution
CALL putarr(fidres, dset_name, field, 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, ionode=0)
ENDIF
END SUBROUTINE write_field3da_kykxz
SUBROUTINE write_field3da_pjz(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/var3d", TRIM(text), iframe3d
IF (num_procs .EQ. 1) THEN ! no data distribution
CALL putarr(fidres, dset_name, field, 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, ionode=0)
ENDIF
CALL attach(fidres, dset_name, "time", time)
END SUBROUTINE write_field3da_pjz
END SUBROUTINE diagnose_3d
SUBROUTINE diagnose_5d
USE basic, ONLY: time, iframe5d,cstep
USE futils, ONLY: append, getatt, attach, putarrnd, putarr
USE fields, ONLY: moments
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 diagnostics_par
USE prec_const, ONLY: xp,dp
IMPLICIT NONE
CALL append(fidres, "/data/var5d/time", REAL(time,dp),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
CALL write_field5d(moments, 'moments')
ENDIF
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
IMPLICIT NONE
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),1)
field_full = 0;
WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
IF (num_procs .EQ. 1) THEN
CALL putarr(fidres, dset_name, field_sub, ionode=0)
ELSEIF(GATHERV_OUTPUT) THEN ! output using one node (gatherv)
CALL gather_pjxyz(field_sub,field_full,total_na,local_np,total_np,total_nj,local_nky,total_nky,total_nkx,local_nz,total_nz)
CALL putarr(fidres, dset_name, field_full, ionode=0)
ELSE
CALL putarrnd(fidres, dset_name, field_sub, (/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, 'iframe5d', iframe5d)
END SUBROUTINE write_field5d
END SUBROUTINE diagnose_5d
SUBROUTINE spit_snapshot_check
USE fields, ONLY: phi
USE grid, ONLY: total_nkx,total_nky,total_nz,&
local_nky,local_nz, ngz
USE parallel, ONLY: gather_xyz, my_id
USE basic
USE prec_const, ONLY: xp
IMPLICIT NONE
LOGICAL :: file_exist
INTEGER :: fid_check, ikx, iky, iz
CHARACTER(256) :: check_filename
COMPLEX(xp), DIMENSION(total_nky,total_nkx,total_nz) :: field_to_check
!! Spit a snapshot of PHI if requested (triggered by creating a file named "check_phi")
INQUIRE(file='check_phi', exist=file_exist)
IF( file_exist ) THEN
IF(my_id.EQ. 0) WRITE(*,*) 'Check file found -> gather phi..'
CALL gather_xyz(phi(:,:,(1+Ngz/2):(local_nz+Ngz/2)), field_to_check,local_nky,total_nky,total_nkx,local_nz,total_nz)
IF(my_id.EQ. 0) THEN
WRITE(check_filename,'(a16)') 'check_phi.out'
OPEN(fid_check, file=check_filename, form='formatted')
WRITE(*,*) 'Check file found -> output phi ..'
WRITE(fid_check,*) total_nky, total_nkx, total_nz
DO iky = 1,total_nky; DO ikx = 1, total_nkx; DO iz = 1,total_nz
WRITE(fid_check,*) real(field_to_check(iky,ikx,iz)), ',' , imag(field_to_check(iky,ikx,iz))
ENDDO; ENDDO; ENDDO
CLOSE(fid_check)
WRITE(*,*) 'Check file found -> done.'
! delete the check_phi flagfile
OPEN(fid_check, file='check_phi')
CLOSE(fid_check, status='delete')
ENDIF
ENDIF
END SUBROUTINE spit_snapshot_check