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gyacomo/src/diagnose.F90
222b08e4a12egather_output

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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
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, dims(1) = (/0/)
CHARACTER(len=256) :: str, fname
!_____________________________________________________________________________
! 1. Initial diagnostics
IF ((kstep .EQ. 0)) THEN
! jobnum is either 0 from initialization or some integer values read from chkrst(0)
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
! 1.1 Initial run
IF (write_doubleprecision) THEN
CALL creatf(resfile, fidres, real_prec='d')
ELSE
CALL creatf(resfile, fidres)
END IF
WRITE(*,'(3x,a,a)') TRIM(resfile), ' created'
call flush(6)
! Data group
CALL creatg(fidres, "/data", "data")
CALL creatg(fidres, "/data/var2d", "2d profiles")
CALL creatg(fidres, "/data/var5d", "5d profiles")
! Initialize counter of number of saves for each category
IF (cstep==0) THEN
iframe2d=0
ENDIF
CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
IF (cstep==0) THEN
iframe5d=0
END IF
CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
! File group
CALL creatg(fidres, "/files", "files")
CALL attach(fidres, "/files", "jobnum", jobnum)
! var2d group (electro. pot., Ni00 moment)
rank = 0
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_Na00) THEN
CALL creatg(fidres, "/data/var2d/Ne00", "Ne00")
CALL putarr(fidres, "/data/var2d/Ne00/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var2d/Ne00/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
CALL creatg(fidres, "/data/var2d/Ni00", "Ni00")
CALL putarr(fidres, "/data/var2d/Ni00/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var2d/Ni00/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
END IF
IF (write_phi) THEN
CALL creatg(fidres, "/data/var2d/phi", "phi")
CALL putarr(fidres, "/data/var2d/phi/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var2d/phi/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
END IF
! var5d group (moments)
rank = 0
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_moments) THEN
CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
CALL putarr(fidres, "/data/var5d/moments_e/coordp", parray_e(ips_e:ipe_e), "p_e",ionode=0)
CALL putarr(fidres, "/data/var5d/moments_e/coordj", jarray_e(ijs_e:ije_e), "j_e",ionode=0)
CALL putarr(fidres, "/data/var5d/moments_e/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var5d/moments_e/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
CALL putarr(fidres, "/data/var5d/moments_i/coordp", parray_i(ips_i:ipe_i), "p_i",ionode=0)
CALL putarr(fidres, "/data/var5d/moments_i/coordj", jarray_i(ijs_i:ije_i), "j_i",ionode=0)
CALL putarr(fidres, "/data/var5d/moments_i/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var5d/moments_i/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
END IF
IF (write_non_lin) THEN
CALL creatg(fidres, "/data/var5d/Sepj", "Sepj")
CALL putarr(fidres, "/data/var5d/Sepj/coordp", parray_e(ips_e:ipe_e), "p_e",ionode=0)
CALL putarr(fidres, "/data/var5d/Sepj/coordj", jarray_e(ijs_e:ije_e), "j_e",ionode=0)
CALL putarr(fidres, "/data/var5d/Sepj/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var5d/Sepj/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
CALL creatg(fidres, "/data/var5d/Sipj", "Sipj")
CALL putarr(fidres, "/data/var5d/Sipj/coordp", parray_i(ips_i:ipe_i), "p_i",ionode=0)
CALL putarr(fidres, "/data/var5d/Sipj/coordj", jarray_i(ijs_i:ije_i), "j_i",ionode=0)
CALL putarr(fidres, "/data/var5d/Sipj/coordkr", krarray(ikrs:ikre), "kr*rho_s0",ionode=0)
CALL putarr(fidres, "/data/var5d/Sipj/coordkz", kzarray(ikzs:ikze), "kz*rho_s0",ionode=0)
END IF
! Add input namelist variables as attributes of /data/input, defined in srcinfo.h
WRITE(*,*) 'VERSION=', VERSION
WRITE(*,*) 'BRANCH=', BRANCH
WRITE(*,*) 'AUTHOR=', AUTHOR
WRITE(*,*) 'HOST=', HOST
WRITE(str,'(a,i2.2)') "/data/input"
rank=0
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_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 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) THEN
WRITE(*,"(F5.0,A,F5.0)") time,"/",tmax
ENDIF
! 2.1 0d history arrays
IF (nsave_0d .NE. 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 .NE. 0) THEN
IF (MOD(cstep, nsave_2d) == 0) THEN
CALL diagnose_2d
END IF
END IF
! 2.4 3d profiles
IF (nsave_5d .NE. 0) THEN
IF (MOD(cstep, nsave_5d) == 0) THEN
CALL diagnose_5d
END IF
END IF
! 2.5 Backups
nsave_cp = INT(5/dt)
IF (MOD(cstep, nsave_cp) == 0) THEN
CALL checkpoint_save
ENDIF
!_____________________________________________________________________________
! 3. Final diagnostics
ELSEIF (kstep .EQ. -1) THEN
CALL cpu_time(finish)
CALL attach(fidres, "/data/input","cpu_time",finish-start)
! Close all diagnostic files
CALL closef(fidres)
END IF
END SUBROUTINE diagnose
SUBROUTINE diagnose_0d
USE basic
USE futils, ONLY: append
USE diagnostics_par
USE prec_const
IMPLICIT NONE
WRITE(*,'(a,1x,i7.7,a1,i7.7,20x,a,1pe10.3,10x,a,1pe10.3)') &
'*** Timestep (this run/total) =', step, '/', cstep, 'Time =', time, 'dt =', dt
WRITE(*,*)
! flush stdout of all ranks. Usually ONLY rank 0 should write, but error messages might be written from other ranks as well
CALL FLUSH(stdout)
END SUBROUTINE diagnose_0d
SUBROUTINE diagnose_2d
USE basic
USE futils, ONLY: append, getatt, attach, putarrnd
USE fields
USE time_integration
USE diagnostics_par
USE prec_const
IMPLICIT NONE
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) THEN
CALL write_field2d(phi(:,:), 'phi')
END IF
IF (write_Na00) THEN
CALL write_field2d(moments_e(1,1,:,:,updatetlevel), 'Ne00')
CALL write_field2d(moments_i(1,1,:,:,updatetlevel), 'Ni00')
END IF
CONTAINS
SUBROUTINE write_field2d(field, text)
USE futils, ONLY: attach, putarr
USE grid, ONLY: ikrs,ikre, ikzs,ikze
USE prec_const
IMPLICIT NONE
COMPLEX(dp), DIMENSION(ikrs:ikre, ikzs:ikze), INTENT(IN) :: field
CHARACTER(*), INTENT(IN) :: text
CHARACTER(LEN=50) :: dset_name
WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var2d", TRIM(text), iframe2d
CALL putarr(fidres, dset_name, field(ikrs:ikre, ikzs:ikze),ionode=0)
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_moments) THEN
CALL write_field5d_e(moments_e(:,:,:,:,updatetlevel), 'moments_e')
CALL write_field5d_i(moments_i(:,:,:,:,updatetlevel), 'moments_i')
END IF
IF (write_non_lin) THEN
CALL write_field5d_e(Sepj, 'Sepj')
CALL write_field5d_i(Sipj, 'Sipj')
END IF
CONTAINS
SUBROUTINE write_field5d_e(field, text)
USE futils, ONLY: attach, putarr
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
CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze),ionode=0)
CALL attach(fidres, dset_name, "time", time)
END SUBROUTINE write_field5d_e
SUBROUTINE write_field5d_i(field, text)
USE futils, ONLY: attach, putarr
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
CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze),ionode=0)
CALL attach(fidres, dset_name, "time", time)
END SUBROUTINE write_field5d_i
END SUBROUTINE diagnose_5d
SUBROUTINE checkpoint_save
USE basic
USE grid
USE diagnostics_par
USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf
USE model
USE initial_par
USE fields
USE time_integration
IMPLICIT NONE
WRITE(rstfile,'(a,a1,i2.2,a3)') TRIM(rstfile0),'_',jobnum,'.h5'
CALL creatf(rstfile, fidrst, real_prec='d')
CALL creatg(fidrst, '/Basic', 'Basic data')
CALL attach(fidrst, '/Basic', 'cstep', cstep)
CALL attach(fidrst, '/Basic', 'time', time)
CALL attach(fidrst, '/Basic', 'jobnum', jobnum)
CALL attach(fidrst, '/Basic', 'dt', dt)
CALL attach(fidrst, '/Basic', 'iframe2d', iframe2d)
CALL attach(fidrst, '/Basic', 'iframe5d', iframe5d)
! Write state of system to restart file
CALL putarr(fidrst, '/Basic/moments_e', moments_e(ips_e:ipe_e,ijs_e:ije_e,&
ikrs:ikre,ikzs:ikze,1),ionode=0)
CALL putarr(fidrst, '/Basic/moments_i', moments_i(ips_i:ipe_i,ijs_i:ije_i,&
ikrs:ikre,ikzs:ikze,1),ionode=0)
CALL closef(fidrst)
WRITE(*,'(3x,a)') "Checkpoint file "//TRIM(rstfile)//" saved"
END SUBROUTINE checkpoint_save
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