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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 grid
USE diagnostics_par
USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf, putarrnd
USE model
USE initial_par
USE fields
USE time_integration
USE prec_const
IMPLICIT NONE
INCLUDE 'srcinfo.h'
INTEGER, INTENT(in) :: kstep
INTEGER, parameter :: BUFSIZE = 2
INTEGER :: rank = 0
INTEGER :: dims(1) = (/0/)
INTEGER :: cp_counter = 0
CHARACTER(len=256) :: str, fname,test_
! putarr(...,pardim=1) does not work for 2D domain decomposition
! so we need to gather non 5D data on one proc to output it
INTEGER :: parray_e_full(1:pmaxe+1), parray_i_full(1:pmaxi+1)
INTEGER :: jarray_e_full(1:jmaxe+1), jarray_i_full(1:jmaxi+1)
REAL(dp) :: krarray_full(1:nkr), kzarray_full(1:nkz)
CALL cpu_time(t0_diag) ! Measuring time
!_____________________________________________________________________________
! 1. Initial diagnostics
IF ((kstep .EQ. 0)) THEN
! Writing output filename
WRITE(resfile,'(a,a1,i2.2,a3)') TRIM(resfile0),'_',jobnum,'.h5'
! 1.1 Initial run
! Main output file creation
IF (write_doubleprecision) THEN
CALL creatf(resfile, fidres, real_prec='d', mpicomm=comm0)
ELSE
CALL creatf(resfile, fidres, mpicomm=comm0)
END IF
IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') TRIM(resfile), ' created'
! Data group
CALL creatg(fidres, "/data", "data")
! File group
CALL creatg(fidres, "/files", "files")
CALL attach(fidres, "/files", "jobnum", jobnum)
! 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_comm", "cumulative communication 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_diag", "cumulative sym computation time")
CALL creatd(fidres, 0, dims, "/profiler/Tc_checkfield", "cumulative checkfield 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")
! Build the full grids on process 0 to diagnose it without comm
IF (my_id .EQ. 0) THEN
! P
DO ip = 1,pmaxe+1; parray_e_full(ip) = (ip-1); END DO
DO ip = 1,pmaxi+1; parray_i_full(ip) = (ip-1); END DO
! J
DO ij = 1,jmaxe+1; jarray_e_full(ij) = (ij-1); END DO
DO ij = 1,jmaxi+1; jarray_i_full(ij) = (ij-1); END DO
! Kr
DO ikr = 1,Nkr
krarray_full(ikr) = REAL(ikr-1,dp) * deltakr
END DO
! Kz
IF (Nkz .GT. 1) THEN
DO ikz = 1,Nkz
kzarray_full(ikz) = deltakz*(MODULO(ikz-1,Nkz/2)-Nkz/2*FLOOR(2.*real(ikz-1)/real(Nkz)))
if (ikz .EQ. Nz/2+1) kzarray(ikz) = -kzarray(ikz)
END DO
ELSE
kzarray_full(1) = 0
endif
ENDIF
! Grid info
CALL creatg(fidres, "/data/grid", "Grid data")
CALL putarr(fidres, "/data/grid/coordkr", krarray_full(1:nkr),"kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/grid/coordkz", kzarray_full(1:nkz),"kz*rho_s0", ionode=0)
CALL putarr(fidres, "/data/grid/coordp_e" , parray_e_full(1:pmaxe+1), "p_e", ionode=0)
CALL putarr(fidres, "/data/grid/coordj_e" , jarray_e_full(1:jmaxe+1), "j_e", ionode=0)
CALL putarr(fidres, "/data/grid/coordp_i" , parray_i_full(1:pmaxe+1), "p_i", ionode=0)
CALL putarr(fidres, "/data/grid/coordj_i" , jarray_i_full(1:jmaxe+1), "j_i", ionode=0)
! 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 (cstep==0) THEN
iframe0d=0
ENDIF
CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
END IF
! var2d group (electro. pot., Ni00 moment)
IF (nsave_2d .GT. 0) THEN
CALL creatg(fidres, "/data/var2d", "2d profiles")
CALL creatd(fidres, rank, dims, "/data/var2d/time", "Time t*c_s/R")
CALL creatd(fidres, rank, dims, "/data/var2d/cstep", "iteration number")
IF (write_phi) CALL creatg(fidres, "/data/var2d/phi", "phi")
IF (write_Na00) THEN
CALL creatg(fidres, "/data/var2d/Ne00", "Ne00")
CALL creatg(fidres, "/data/var2d/Ni00", "Ni00")
ENDIF
IF (cstep==0) THEN
iframe2d=0
ENDIF
CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
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_e", "moments_e")
CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
ENDIF
IF (write_Sapj) THEN
CALL creatg(fidres, "/data/var5d/moments_e", "Sipj")
CALL creatg(fidres, "/data/var5d/moments_i", "Sepj")
ENDIF
IF (cstep==0) THEN
iframe5d=0
END IF
CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
END IF
! Add input namelist variables as attributes of /data/input, defined in srcinfo.h
IF (my_id .EQ. 0) WRITE(*,*) 'VERSION=', VERSION
IF (my_id .EQ. 0) WRITE(*,*) 'BRANCH=', BRANCH
IF (my_id .EQ. 0) WRITE(*,*) 'AUTHOR=', AUTHOR
IF (my_id .EQ. 0) WRITE(*,*) 'HOST=', HOST
WRITE(str,'(a,i2.2)') "/data/input"
CALL creatd(fidres, rank,dims,TRIM(str),'Input parameters')
CALL attach(fidres, TRIM(str), "version", VERSION) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "branch", BRANCH) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "author", AUTHOR) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "execdate", EXECDATE) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "host", HOST) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "start_time", time)
CALL attach(fidres, TRIM(str), "start_cstep", cstep-1)
CALL attach(fidres, TRIM(str), "start_iframe0d", iframe0d)
CALL attach(fidres, TRIM(str), "start_iframe2d", iframe2d)
CALL attach(fidres, TRIM(str), "start_iframe5d", iframe5d)
CALL attach(fidres, TRIM(str), "dt", dt)
CALL attach(fidres, TRIM(str), "tmax", tmax)
CALL attach(fidres, TRIM(str), "nrun", nrun)
CALL attach(fidres, TRIM(str), "cpu_time", -1)
CALL attach(fidres, TRIM(str), "Nproc", num_procs)
CALL attach(fidres, TRIM(str), "Np_p" , num_procs_p)
CALL attach(fidres, TRIM(str), "Np_kr",num_procs_kr)
CALL attach(fidres, TRIM(str), "write_gamma",write_gamma)
CALL attach(fidres, TRIM(str), "write_phi",write_phi)
CALL attach(fidres, TRIM(str), "write_Na00",write_Na00)
CALL attach(fidres, TRIM(str), "write_Napj",write_Napj)
CALL attach(fidres, TRIM(str), "write_Sapj",write_Sapj)
CALL grid_outputinputs(fidres, str)
CALL output_par_outputinputs(fidres, str)
CALL model_outputinputs(fidres, str)
CALL initial_outputinputs(fidres, str)
CALL time_integration_outputinputs(fidres, 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
INQUIRE(unit=lu_in, name=fname)
CLOSE(lu_in)
CALL putfile(fidres, TRIM(str), TRIM(fname),ionode=0)
ELSEIF((kstep .EQ. 0)) THEN
IF(jobnum .LE. 99) THEN
WRITE(resfile,'(a,a1,i2.2,a3)') TRIM(resfile0),'_',jobnum,'.h5'
ELSE
WRITE(resfile,'(a,a1,i3.2,a3)') TRIM(resfile0),'_',jobnum,'.h5'
END IF
CALL openf(resfile,fidres, 'D');
ENDIF
!_____________________________________________________________________________
! 2. Periodic diagnostics
!
IF (kstep .GE. 0) THEN
! Terminal info
IF (MOD(cstep, INT(1.0/dt)) == 0 .AND. (my_id .EQ. 0)) THEN
WRITE(*,"(F5.0,A,F5.0)") time,"/",tmax
ENDIF
! 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
IF (nsave_2d .GT. 0) THEN
IF (MOD(cstep, nsave_2d) == 0) THEN
CALL diagnose_2d
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 cpu_time(finish)
CALL attach(fidres, "/data/input","cpu_time",finish-start)
! Display computational time cost
IF (my_id .EQ. 0) CALL display_h_min_s(finish-start)
! Close all diagnostic files
CALL closef(fidres)
END IF
CALL cpu_time(t1_diag); tc_diag = tc_diag + (t1_diag - t0_diag)
END SUBROUTINE diagnose
SUBROUTINE diagnose_0d
USE basic
USE futils, ONLY: append, attach, getatt
USE diagnostics_par
USE prec_const
USE processing
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_poisson", tc_poisson,ionode=0)
CALL append(fidres, "/profiler/Tc_Sapj", tc_Sapj,ionode=0)
CALL append(fidres, "/profiler/Tc_diag", tc_diag,ionode=0)
CALL append(fidres, "/profiler/Tc_checkfield",tc_checkfield,ionode=0)
CALL append(fidres, "/profiler/Tc_comm", tc_comm,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
END SUBROUTINE diagnose_0d
SUBROUTINE diagnose_2d
USE basic
USE futils, ONLY: append, getatt, attach, putarrnd
USE fields
USE array, ONLY: Ne00, Ni00
USE grid, ONLY: ikrs,ikre, ikzs,ikze, nkr, nkz, local_nkr, ikr, ikz, ips_e, ips_i
USE time_integration
USE diagnostics_par
USE prec_const
IMPLICIT NONE
COMPLEX(dp) :: buffer(ikrs:ikre,ikzs:ikze)
INTEGER :: i_, root, world_rank, world_size
CALL append(fidres, "/data/var2d/time", time,ionode=0)
CALL append(fidres, "/data/var2d/cstep", real(cstep,dp),ionode=0)
CALL getatt(fidres, "/data/var2d/", "frames",iframe2d)
iframe2d=iframe2d+1
CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
IF (write_phi) CALL write_field2d(phi (:,:), 'phi')
IF (write_Na00) THEN
IF ( (ips_e .EQ. 1) .AND. (ips_i .EQ. 1) ) THEN
Ne00(ikrs:ikre,ikzs:ikze) = moments_e(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
Ni00(ikrs:ikre,ikzs:ikze) = moments_i(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
ENDIF
root = 0
!!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
CALL MPI_COMM_RANK(commp,world_rank,ierr)
CALL MPI_COMM_SIZE(commp,world_size,ierr)
IF (world_size .GT. 1) THEN
!! Broadcast phi to the other processes on the same k range (communicator along p)
IF (world_rank .EQ. root) THEN
! Fill the buffer
DO ikr = ikrs,ikre
DO ikz = ikzs,ikze
buffer(ikr,ikz) = Ne00(ikr,ikz)
ENDDO
ENDDO
! Send it to all the other processes
DO i_ = 0,num_procs_p-1
IF (i_ .NE. world_rank) &
CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, commp, ierr)
ENDDO
ELSE
! Recieve buffer from root
CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, commp, MPI_STATUS_IGNORE, ierr)
! Write it in phi
DO ikr = ikrs,ikre
DO ikz = ikzs,ikze
Ne00(ikr,ikz) = buffer(ikr,ikz)
ENDDO
ENDDO
ENDIF
ENDIF
CALL write_field2d(Ne00(ikrs:ikre,ikzs:ikze), 'Ne00')
!!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
CALL MPI_COMM_RANK(commp,world_rank,ierr)
CALL MPI_COMM_SIZE(commp,world_size,ierr)
IF (world_size .GT. 1) THEN
!! Broadcast phi to the other processes on the same k range (communicator along p)
IF (world_rank .EQ. root) THEN
! Fill the buffer
DO ikr = ikrs,ikre
DO ikz = ikzs,ikze
buffer(ikr,ikz) = Ni00(ikr,ikz)
ENDDO
ENDDO
! Send it to all the other processes
DO i_ = 0,num_procs_p-1
IF (i_ .NE. world_rank) &
CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, commp, ierr)
ENDDO
ELSE
! Recieve buffer from root
CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, commp, MPI_STATUS_IGNORE, ierr)
! Write it in phi
DO ikr = ikrs,ikre
DO ikz = ikzs,ikze
Ni00(ikr,ikz) = buffer(ikr,ikz)
ENDDO
ENDDO
ENDIF
ENDIF
CALL write_field2d(Ni00(ikrs:ikre,ikzs:ikze), 'Ni00')
ENDIF
CONTAINS
SUBROUTINE write_field2d(field, text)
USE futils, ONLY: attach, putarr
USE grid, ONLY: ikrs,ikre, ikzs,ikze, nkr, nkz, local_nkr
USE prec_const
USE basic, ONLY : commr, num_procs_p, rank_p
IMPLICIT NONE
COMPLEX(dp), DIMENSION(ikrs:ikre, ikzs:ikze), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
COMPLEX(dp) :: buffer_dist(ikrs:ikre,ikzs:ikze)
COMPLEX(dp) :: buffer_full(1:nkr,1:nkz)
INTEGER :: scount, rcount
CHARACTER(LEN=50) :: dset_name
scount = (ikre-ikrs+1) * (ikze-ikzs+1)
rcount = scount
WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var2d", TRIM(text), iframe2d
IF (num_procs .EQ. 1) THEN ! no data distribution
CALL putarr(fidres, dset_name, field(ikrs:ikre, ikzs:ikze), ionode=0)
ELSE
CALL putarrnd(fidres, dset_name, field(ikrs:ikre, ikzs:ikze), (/1, 1/))
ENDIF
CALL attach(fidres, dset_name, "time", time)
END SUBROUTINE write_field2d
END SUBROUTINE diagnose_2d
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
USE time_integration
USE diagnostics_par
USE prec_const
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
CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel), 'moments_e')
CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel), 'moments_i')
ENDIF
IF (write_Sapj) THEN
CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,:,:), 'Sepj')
CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,:,:), '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, ikrs,ikre, ikzs,ikze
USE prec_const
IMPLICIT NONE
COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), 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,ikrs:ikre,ikzs:ikze), ionode=0)
ELSE
CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), (/1,3/))
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, ikrs,ikre, ikzs,ikze
USE prec_const
IMPLICIT NONE
COMPLEX(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), 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,ikrs:ikre,ikzs:ikze), ionode=0)
ELSE
CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), (/1,3/))
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
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