Homec4science
Diffusion GYACOMO (OBSOLETE: LATEST VERSION ON gitlab.epfl.ch) (shear_version) Browse

gyacomo/src/diagnose.F90
784baff12d6dshear_version

Last Change
Raw File

diagnose.F90
View Options

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/)
INTEGER :: cp_counter = 0
CHARACTER(len=256) :: str, fname,test_
!_____________________________________________________________________________
! 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=MPI_COMM_WORLD)
ELSE
CALL creatf(resfile, fidres, mpicomm=MPI_COMM_WORLD)
END IF
IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') TRIM(resfile), ' created'
! Checkpoint file creation
IF (nsave_cp .GT. 0) THEN
WRITE(rstfile,'(a,a1,i2.2,a3)') TRIM(rstfile0),'_',jobnum,'.h5'
CALL creatf(rstfile, fidrst, real_prec='d', mpicomm=MPI_COMM_WORLD)
CALL creatg(fidrst, '/Basic', 'Basic data')
CALL creatg(fidrst, '/Basic/moments_e', 'electron moments')
CALL creatg(fidrst, '/Basic/moments_i', 'ion moments')
CALL creatg(fidrst, '/Basic/phi', 'ES potential')
! Attaching informations about moments
CALL attach(fidrst,"/Basic/moments_e/" , "pmaxe", pmaxe)
CALL attach(fidrst,"/Basic/moments_e/" , "jmaxe", jmaxe)
CALL attach(fidrst,"/Basic/moments_e/" , "Trunc", CLOS)
CALL attach(fidrst,"/Basic/moments_i/" , "pmaxi", pmaxi)
CALL attach(fidrst,"/Basic/moments_i/" , "jmaxi", jmaxi)
CALL attach(fidrst,"/Basic/moments_i/" , "Trunc", CLOS)
IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') TRIM(rstfile), ' created'
CALL flush(6)
ELSE
IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') 'No checkpoint'
ENDIF
! 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)
! 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_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")
! 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 (nsave_2d .GT. 0) THEN
CALL creatg(fidres, "/data/var2d/Ne00", "Ne00")
CALL creatg(fidres, "/data/var2d/Ni00", "Ni00")
CALL creatg(fidres, "/data/var2d/phi", "phi")
IF (num_procs .EQ. 1) THEN
CALL putarr(fidres, "/data/var2d/Ne00/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var2d/Ni00/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var2d/phi/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
ELSE
CALL putarr(fidres, "/data/var2d/Ne00/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
CALL putarr(fidres, "/data/var2d/Ni00/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
CALL putarr(fidres, "/data/var2d/phi/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
ENDIF
CALL putarr(fidres, "/data/var2d/Ne00/coordkz", kzarray(ikzs:ikze), "kz*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var2d/Ni00/coordkz", kzarray(ikzs:ikze), "kz*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 (nsave_5d .GT. 0) THEN
CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
CALL creatg(fidres, "/data/var5d/Sepj", "Sepj")
CALL creatg(fidres, "/data/var5d/Sipj", "Sipj")
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_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/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/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)
IF (num_procs .EQ. 1) THEN
CALL putarr(fidres, "/data/var5d/moments_e/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var5d/moments_i/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var5d/Sepj/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var5d/Sipj/coordkr", krarray(ikrs:ikre), "kr*rho_s0", ionode=0)
ELSE
CALL putarr(fidres, "/data/var5d/moments_e/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
CALL putarr(fidres, "/data/var5d/moments_i/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
CALL putarr(fidres, "/data/var5d/Sepj/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
CALL putarr(fidres, "/data/var5d/Sipj/coordkr", krarray(ikrs:ikre), "kr*rho_s0", pardim=1)
ENDIF
CALL putarr(fidres, "/data/var5d/moments_e/coordkz", kzarray(ikzs:ikze), "kz*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var5d/moments_i/coordkz", kzarray(ikzs:ikze), "kz*rho_s0", ionode=0)
CALL putarr(fidres, "/data/var5d/Sepj/coordkz", kzarray(ikzs:ikze), "kz*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
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"
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 attach(fidres, TRIM(str), "cpu_time", -1)
CALL attach(fidres, TRIM(str), "Nproc",num_procs)
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) THEN
IF (MOD(cstep, nsave_5d) == 0) THEN
CALL diagnose_5d
END IF
END IF
! 2.5 Backups
IF (nsave_cp .GT. 0) THEN
IF (MOD(cstep, nsave_cp) == 0) THEN
CALL checkpoint_save(cp_counter)
cp_counter = cp_counter + 1
ENDIF
ENDIF
!_____________________________________________________________________________
! 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)
IF ((nsave_cp .GT. 0) .AND. (.NOT. crashed)) THEN
CALL checkpoint_save(cp_counter)
CALL closef(fidrst)
ENDIF
END IF
END SUBROUTINE diagnose
SUBROUTINE diagnose_0d
USE basic
USE futils, ONLY: append
USE diagnostics_par
USE prec_const
IMPLICIT NONE
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_step", tc_step,ionode=0)
CALL append(fidres, "/profiler/time", time,ionode=0)
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)
CALL write_field2d(phi(:,:), 'phi')
CALL write_field2d(moments_e(1,1,:,:,updatetlevel), 'Ne00')
CALL write_field2d(moments_i(1,1,:,:,updatetlevel), 'Ni00')
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
IF (num_procs .EQ. 1) THEN
CALL putarr(fidres, dset_name, field(ikrs:ikre, ikzs:ikze), ionode=0)
ELSE
CALL putarr(fidres, dset_name, field(ikrs:ikre, ikzs:ikze), pardim=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)
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')
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')
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
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 putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), pardim=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
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 putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), pardim=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
SUBROUTINE checkpoint_save(cp_step)
USE basic
USE grid, ONLY: ips_i,ipe_i, ijs_i,ije_i, ips_e,ipe_e, ijs_e,ije_e, ikrs,ikre, ikzs,ikze
USE diagnostics_par
USE futils, ONLY: putarr,attach
USE model
USE initial_par
USE fields
USE time_integration
IMPLICIT NONE
INTEGER, INTENT(IN) :: cp_step
CHARACTER(LEN=50) :: dset_name
! Write state of system to restart file
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/moments_e", cp_step
IF (num_procs .EQ. 1) THEN
CALL putarr(fidrst, dset_name, moments_e(ips_e:ipe_e,ijs_e:ije_e,&
ikrs:ikre,ikzs:ikze,1), ionode=0)
ELSE
CALL putarr(fidrst, dset_name, moments_e(ips_e:ipe_e,ijs_e:ije_e,&
ikrs:ikre,ikzs:ikze,1), pardim=3)
ENDIF
CALL attach(fidrst, dset_name, 'cstep', cstep)
CALL attach(fidrst, dset_name, 'time', time)
CALL attach(fidrst, dset_name, 'jobnum', jobnum)
CALL attach(fidrst, dset_name, 'dt', dt)
CALL attach(fidrst, dset_name, 'iframe2d', iframe2d)
CALL attach(fidrst, dset_name, 'iframe5d', iframe5d)
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/moments_i", cp_step
IF (num_procs .EQ. 1) THEN
CALL putarr(fidrst, dset_name, moments_i(ips_i:ipe_i,ijs_i:ije_i,&
ikrs:ikre,ikzs:ikze,1), ionode=0)
ELSE
CALL putarr(fidrst, dset_name, moments_i(ips_i:ipe_i,ijs_i:ije_i,&
ikrs:ikre,ikzs:ikze,1), pardim=3)
ENDIF
CALL attach(fidrst, dset_name, 'cstep', cstep)
CALL attach(fidrst, dset_name, 'time', time)
CALL attach(fidrst, dset_name, 'jobnum', jobnum)
CALL attach(fidrst, dset_name, 'dt', dt)
CALL attach(fidrst, dset_name, 'iframe2d', iframe2d)
CALL attach(fidrst, dset_name, 'iframe5d', iframe5d)
! Write state of system to restart file
WRITE(dset_name, "(A, '/', i6.6)") "/Basic/phi", cp_step
IF (num_procs .EQ. 1) THEN
CALL putarr(fidrst, dset_name, phi(ikrs:ikre,ikzs:ikze), ionode=0)
ELSE
CALL putarr(fidrst, dset_name, phi(ikrs:ikre,ikzs:ikze), pardim=1)
ENDIF
CALL attach(fidrst, dset_name, 'cstep', cstep)
CALL attach(fidrst, dset_name, 'time', time)
CALL attach(fidrst, dset_name, 'jobnum', jobnum)
CALL attach(fidrst, dset_name, 'dt', dt)
CALL attach(fidrst, dset_name, 'iframe2d', iframe2d)
CALL attach(fidrst, dset_name, 'iframe5d', iframe5d)
IF (my_id .EQ. 0) THEN
WRITE(*,'(3x,a)') "Checkpoint file "//TRIM(rstfile)//" updated"
ENDIF
END SUBROUTINE checkpoint_save
c4science · Help