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gyacomo/src/diagnose.F90
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diagnose.F90
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SUBROUTINE diagnose(kstep)
! Diagnostics, writing simulation state to disk
USE basic
USE diagnostics_par
USE processing, ONLY: gflux_ri, hflux_xi
IMPLICIT NONE
INTEGER, INTENT(in) :: kstep
CALL cpu_time(t0_diag) ! Measuring time
!! 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
IF (kstep .GE. 0) THEN
! Terminal info
IF (MOD(cstep, INT(1.0/dt)) == 0 .AND. (my_id .EQ. 0)) THEN
! WRITE(*,"(F6.0,A,F6.0)") time,"/",tmax
WRITE(*,"(A,F6.0,A1,F6.0,A8,G10.2,A8,G10.2,A)")'|t/tmax = ', time,"/",tmax,'| Gxi = ',gflux_ri,'| Qxi = ',hflux_xi,'|'
ENDIF
ELSEIF (kstep .EQ. -1) THEN
CALL cpu_time(finish)
! Display computational time cost
IF (my_id .EQ. 0) CALL display_h_min_s(finish-start)
END IF
!! Specific diagnostic calls
CALL diagnose_full(kstep)
CALL cpu_time(t1_diag); tc_diag = tc_diag + (t1_diag - t0_diag)
END SUBROUTINE diagnose
SUBROUTINE init_outfile(comm,file0,file,fid)
USE diagnostics_par, ONLY : write_doubleprecision, diag_par_outputinputs, input_fname
USE basic, ONLY : my_id, jobnum, basic_outputinputs
USE grid, ONLY : grid_outputinputs
USE geometry, ONLY : geometry_outputinputs
USE model, ONLY : model_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
IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') 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
WRITE(str,'(a,i2.2)') "/data/input"
CALL creatd(fid, 0,(/0/),TRIM(str),'Input parameters')
CALL attach(fid, TRIM(str), "version", VERSION) !defined in srcinfo.h
CALL attach(fid, TRIM(str), "branch", BRANCH) !defined in srcinfo.h
CALL attach(fid, TRIM(str), "author", AUTHOR) !defined in srcinfo.h
CALL attach(fid, TRIM(str), "execdate", EXECDATE) !defined in srcinfo.h
CALL attach(fid, TRIM(str), "host", HOST) !defined in srcinfo.h
CALL basic_outputinputs(fid,str)
CALL grid_outputinputs(fid, str)
CALL geometry_outputinputs(fid, str)
CALL diag_par_outputinputs(fid, str)
CALL model_outputinputs(fid, str)
CALL coll_outputinputs(fid, str)
CALL initial_outputinputs(fid, str)
CALL time_integration_outputinputs(fid, str)
! 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
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/)
!____________________________________________________________________________
! 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_process", "cumulative process 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")
! 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/gxz", gxz(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/hatB_NL", hatB_NL(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")
IF(KIN_E) THEN
CALL creatd(fidres, rank, dims, "/data/var0d/gflux_re", "Radial gyro electron transport")
CALL creatd(fidres, rank, dims, "/data/var0d/pflux_re", "Radial part electron transport")
ENDIF
ENDIF
IF (write_hf) THEN
CALL creatd(fidres, rank, dims, "/data/var0d/hflux_xi", "Radial part ion heat flux")
IF(KIN_E) THEN
CALL creatd(fidres, rank, dims, "/data/var0d/hflux_xe", "Radial part electron heat flux")
ENDIF
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) CALL creatg(fidres, "/data/var3d/psi", "psi")
IF (write_Na00) THEN
IF(KIN_E)&
CALL creatg(fidres, "/data/var3d/Ne00", "Ne00")
CALL creatg(fidres, "/data/var3d/Ni00", "Ni00")
IF(KIN_E)&
CALL creatg(fidres, "/data/var3d/Nepjz", "Nepjz")
CALL creatg(fidres, "/data/var3d/Nipjz", "Nipjz")
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 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 .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)
IF(KIN_E) THEN
CALL compute_radial_electron_transport
CALL append(fidres, "/data/var0d/gflux_re",gflux_re,ionode=0)
CALL append(fidres, "/data/var0d/pflux_re",pflux_re,ionode=0)
ENDIF
ENDIF
IF (write_hf) THEN
CALL compute_radial_ion_heatflux
CALL append(fidres, "/data/var0d/hflux_xi",hflux_xi,ionode=0)
IF(KIN_E) THEN
CALL compute_radial_electron_heatflux
CALL append(fidres, "/data/var0d/hflux_xe",hflux_xe,ionode=0)
ENDIF
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 model, ONLY: KIN_E
IMPLICIT NONE
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) CALL write_field3d_kykxz(psi (ikys:ikye,ikxs:ikxe,izs:ize), 'psi')
IF (write_Na00) THEN
IF(KIN_E)THEN
IF (CONTAINS_ip0_e) &
Ne00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_e(ip0_e,ij0_e,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
CALL write_field3d_kykxz(Ne00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ne00')
ENDIF
IF (CONTAINS_ip0_i) &
Ni00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_i(ip0_i,ij0_i,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
CALL write_field3d_kykxz(Ni00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ni00')
! 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)
USE parallel, ONLY : gather_xyz
IMPLICIT NONE
COMPLEX(dp), DIMENSION(ikys:ikye,ikxs:ikxe, izs:ize), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
COMPLEX(dp), DIMENSION(1:Nky,1:Nkx,1:Nz) :: field_full
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)
ELSEIF(GATHERV_OUTPUT) THEN ! output using one node (gatherv)
CALL gather_xyz(field(ikys:ikye,1:Nkx,izs:ize),field_full(1:Nky,1:Nkx,1:Nz))
CALL putarr(fidres, dset_name, field_full(1:Nky,1:Nkx,1:Nz), ionode=0)
ELSE ! output using putarrnd (very slow on marconi)
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, putarr
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, &
Np_i, Nj_i, Np_e, Nj_e, Nky, Nkx, Nz, &
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 parallel, ONLY: gather_pjxyz_e
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
COMPLEX(dp), DIMENSION(1:Np_e,1:Nj_e,1:Nky,1:Nkx,1:Nz) :: field_full
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)
ELSEIF(GATHERV_OUTPUT) THEN ! output using one node (gatherv)
CALL gather_pjxyz_e(field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize),&
field_full(1:Np_e,1:Nj_e,1:Nky,1:Nkx,1:Nz))
CALL putarr(fidres, dset_name, field_full(1:Np_i,1:Nj_i,1:Nky,1:Nkx,1:Nz), 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 parallel, ONLY: gather_pjxyz_i
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
COMPLEX(dp), DIMENSION(1:Np_i,1:Nj_i,1:Nky,1:Nkx,1:Nz) :: field_full
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)
ELSEIF(GATHERV_OUTPUT) THEN ! output using one node (gatherv)
CALL gather_pjxyz_i(field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize),&
field_full(1:Np_i,1:Nj_i,1:Nky,1:Nkx,1:Nz))
CALL putarr(fidres, dset_name, field_full(1:Np_i,1:Nj_i,1:Nky,1:Nkx,1:Nz), 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
SUBROUTINE spit_snapshot_check
USE fields, ONLY: phi
USE grid, ONLY: ikxs,ikxe,Nkx,ikys,ikye,Nky,izs,ize,Nz
USE parallel, ONLY: gather_xyz
USE basic
IMPLICIT NONE
LOGICAL :: file_exist
INTEGER :: fid_check, ikx, iky, iz
CHARACTER(256) :: check_filename
COMPLEX(dp), DIMENSION(1:Nky,1:Nkx,1: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(ikys:ikye,ikxs:ikxe,izs:ize), field_to_check)
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,*) Nky, Nkx, Nz
DO iky = 1,Nky; DO ikx = 1, Nkx; DO iz = 1,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
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