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Diffusion FENNECS: Finite Element Non-Neutral Electron Cloud Simulator (geom_testmumps) Browse

fennecs/src/diagnose.f90
e4669700ed0dgeom_testmumps

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diagnose.f90
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SUBROUTINE diagnose(kstep)
!
! Diagnostics
!
USE basic
USE futils
USE hashtable
Use maxwsrce
Use neutcol
USE beam, ONLY : partslist, epot, ekin, etot, etot0, Nplocs_all, collectparts
#if USE_X == 1
USE xg, ONLY : initw, updt_xg_var
#endif
USE fields, ONLY: phi_spline
USE celldiag
USE mpi
Use geometry
Use splinebound
Use weighttypes
IMPLICIT NONE
!
INTEGER, INTENT(in) :: kstep
!
! Local vars and arrays
INTEGER, PARAMETER :: BUFSIZE = 20
CHARACTER(len=128) :: str, fname, grpname
INTEGER:: Ntotal ! Total number of simulated particles remaining in the simulation
INTEGER:: partsrank, partsdim(2)
INTEGER:: Nplocs_all_save(64)
INTEGER:: i
!________________________________________________________________________________
! 1. Initial diagnostics
IF( kstep .EQ. 0 .and. mpirank .eq. 0) THEN
! Only process 0 should save on file
!
WRITE(*,'(a)') ' Initial diagnostics'
!
! 1.1 Initial run or when NEWRES set to .TRUE.
!
IF( .NOT. nlres .OR. newres) THEN
CALL creatf(resfile, fidres, 'Espic2d result file', real_prec='d')
WRITE(*,'(3x,a,a)') TRIM(resfile), ' created'
!
! Label the run
IF( LEN_TRIM(label1).GT.0 ) CALL attach(fidres, "/", "label1", TRIM(label1))
IF( LEN_TRIM(label2).GT.0 ) CALL attach(fidres, "/", "label2", TRIM(label2))
IF( LEN_TRIM(label3).GT.0 ) CALL attach(fidres, "/", "label3", TRIM(label3))
IF( LEN_TRIM(label4).GT.0 ) CALL attach(fidres, "/", "label4", TRIM(label4))
!
! Job number
jobnum = 0
!
! Data group
CALL creatg(fidres, "/data", "data")
CALL creatg(fidres, "/data/var0d", "0d history arrays")
CALL creatg(fidres, "/data/var1d","1d history arrays")
CALL creatg(fidres, "/data/part", "part phase space")
CALL creatg(fidres, "/data/fields", "Electro static potential and Er Ez fields")
!
! File group
CALL creatg(fidres, "/files", "files")
CALL attach(fidres, "/files", "jobnum", jobnum)
CALL putarr(fidres, "/data/var1d/rgrid", rgrid)
CALL putarr(fidres, "/data/var1d/zgrid", zgrid)
CALL creatd(fidres, 1, (/ 64 /), "/data/var0d/Nplocs_all", "Nplocs_all")
CALL creatd(fidres, 1, (/3/), "/data/var0d/nudcol", "nudcol")
! Part and fields vectors
! Initialize time-dependent particle variables
CALL creatd(fidres, 1, SHAPE(partslist(1)%R), "/data/part/R", "R",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%Z), "/data/part/Z", "Z",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%Z), "/data/part/THET", "THET",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%UZ), "/data/part/UR", "UZ",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%UR), "/data/part/UZ", "UR",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%UTHET), "/data/part/UTHET", "UTHET",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%Rindex), "/data/part/Rindex", "Rindex",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%Zindex), "/data/part/Zindex", "Zindex",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%partindex), "/data/part/partindex", "partindex",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 1, SHAPE(partslist(1)%pot), "/data/part/pot", "pot",compress=.true.,chunking=SHAPE(partslist(1)%R))
CALL creatd(fidres, 0, SHAPE(time), "/data/part/time", "time" )
CALL creatd(fidres, 0, SHAPE(Ntotal), "/data/part/Nparts", "number of remaining parts in the simulation space")
CALL creatd(fidres, 1, (/7/), "/data/part/nbchange", "number of added parts, lost parts zm,zp,rm,rp, and collisions per type io, ela")
CALL attach(fidres,'/data/part', "q", partslist(1)%q)
CALL attach(fidres,'/data/part', "m", partslist(1)%m)
CALL attach(fidres,'/data/part', "weight", partslist(1)%weight)
CALL creatd(fidres, 1, SHAPE(pot), "/data/fields/pot", "pot")
CALL creatd(fidres, 1, SHAPE(Er), "/data/fields/Er", "Er")
CALL creatd(fidres, 1, SHAPE(Ez), "/data/fields/Ez", "Ez")
CALL creatd(fidres, 1, SHAPE(phi_spline), "/data/fields/phi", "spline form of Phi")
CALL creatd(fidres, 2, SHAPE(moments), "/data/fields/moments", "moments",compress=.true.,chunking=(/1,nrank(1)*nrank(2)/))
!CALL creatd(fidres, 2, SHAPE(moments), "/data/fields/moments", "moments")
CALL creatd(fidres, 0, SHAPE(time), "/data/fields/time", "time" )
CALL putarr(fidres, "/data/fields/Br", Br)
CALL putarr(fidres, "/data/fields/Bz", Bz)
CALL putarr(fidres, "/data/fields/Athet", Athet)
CALL putarr(fidres, "/data/fields/volume", Volume)
!
! 1.2 Restart run
!
ELSE
CALL cp2bk(resfile) ! backup previous result file
CALL openf(resfile, fidres, real_prec='d')
WRITE(*,'(3x,a,a)') TRIM(resfile), ' open'
CALL getatt(fidres, "/files", "jobnum", jobnum)
jobnum = jobnum+1
WRITE(*,'(3x,a,i3)') "Current Job Number =", jobnum
CALL attach(fidres, "/files", "jobnum", jobnum)
END IF
!
! Add input namelist variables as attributes of /data/input
WRITE(str,'(a,i2.2)') "/data/input.",jobnum
CALL creatg(fidres, TRIM(str))
CALL attach(fidres, TRIM(str), "job_time", job_time)
CALL attach(fidres, TRIM(str), "extra_time", extra_time)
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), "nlres", nlres)
CALL attach(fidres, TRIM(str), "nlsave", nlsave)
CALL attach(fidres, TRIM(str), "newres", newres)
CALL attach(fidres, TRIM(str), "nz", nz)
CALL putarr(fidres, TRIM(str)//"/lz", lz)
CALL attach(fidres, TRIM(str), "nplasma", nplasma)
CALL attach(fidres, TRIM(str), "potinn", potinn)
CALL attach(fidres, TRIM(str), "potout", potout)
CALL attach(fidres, TRIM(str), "B0", B0)
CALL attach(fidres, TRIM(str), "Rcurv", Rcurv)
CALL attach(fidres, TRIM(str), "width", width)
CALL attach(fidres, TRIM(str), "n0", n0)
CALL attach(fidres, TRIM(str), "temp", partslist(1)%temperature)
CALL attach(fidres, TRIM(str), "it0d", it0d)
CALL attach(fidres, TRIM(str), "it2d", it2d)
CALL attach(fidres, TRIM(str), "itparts", itparts)
CALL attach(fidres, TRIM(str), "nlclassical", nlclassical)
CALL attach(fidres, TRIM(str), "nlPhis", nlPhis)
CALL attach(fidres, TRIM(str), "qsim", partslist(1)%q*partslist(1)%weight)
CALL attach(fidres, TRIM(str), "msim", partslist(1)%m*partslist(1)%weight)
CALL attach(fidres, TRIM(str), "startstep", cstep)
CALL attach(fidres, TRIM(str), "H0", partslist(1)%H0)
CALL attach(fidres, TRIM(str), "P0", partslist(1)%P0)
CALL putarr(fidres, TRIM(str)//"/femorder", femorder)
CALL putarr(fidres, TRIM(str)//"/ngauss", ngauss)
CALL putarr(fidres, TRIM(str)//"/nnr", nnr)
CALL putarr(fidres, TRIM(str)//"/radii", radii)
CALL putarr(fidres, TRIM(str)//"/plasmadim", plasmadim)
CALL attach(fidres, TRIM(str), "rawparts", .true.)
CALL attach(fidres, TRIM(str), "nbspecies", nbspecies)
CALL putarr(fidres, TRIM(str)//"/potxt", potxt)
CALL putarr(fidres, TRIM(str)//"/Erxt", Erxt)
CALL putarr(fidres, TRIM(str)//"/Ezxt", Ezxt)
! Save geometry parameters for non conforming boundary conditions
Call geom_diag(fidres,str,rnorm)
! Save geometry parameters for non conforming boundary conditions using b-spline curves
call splinebound_diag(fidres, str, the_domain)
! Save Maxwellsource parameters for the ad-hoc source
Call maxwsrce_diag(fidres,str,vnorm)
! Save neutcol parameters for the electron collisions with neutrals
Call neutcol_diag(fidres,str,vnorm)
if(.not. isdataset(fidres,'/data/var0d/nudcol'))then
CALL creatd(fidres, 1, (/3/), "/data/var0d/nudcol", "nudcol")
end if
! Save STDIN of this run
WRITE(str,'(a,i2.2)') "/files/STDIN.",jobnum
INQUIRE(unit=lu_in, name=fname)
CALL putfile(fidres, TRIM(str), TRIM(fname))
! Prepare hdf5 file for storing test particles
DO i=2,nbspecies
IF ( partslist(i)%is_test) THEN
WRITE(grpname,'(a,i2)')'/data/part/',i
call create_parts_group(partslist(i),trim(grpname),time)
END IF
END DO
CALL attach(fidres, "/data/part", "nbspecies", nbspecies)
!
! Initialize buffers for 0d history arrays
CALL htable_init(hbuf0, BUFSIZE)
CALL set_htable_fileid(hbuf0, fidres, "/data/var0d")
!
! Initialize Xgrafix
#if USE_X == 1
IF(nlxg) THEN
CALL initw
END IF
#endif
END IF
IF(kstep .EQ. 0) THEN
! Initialize particle cell diagnostic
CALL celldiag_init(lu_in, fidres)
CLOSE(lu_in)
END IF
!________________________________________________________________________________
! 2. Periodic diagnostics
IF( kstep .NE. -1) THEN
IF(modulo(step,ittracer) .eq. 0 .or. nlend) THEN
! We gather the traced particles on the mpi host
DO i=1,nbspecies
IF(partslist(i)%is_test) CALL collectparts(partslist(i))
END DO
END IF
IF(modulo(step,itrestart) .eq. 0 .or. modulo(step,itparts) .eq. 0 .or. nlend) THEN
! We gather the traced particles on the mpi host
DO i=1,nbspecies
CALL collectparts(partslist(i))
END DO
END IF
IF(modulo(step,ittext) .eq. 0 .or. nlend) THEN
! We gather the number of gained and lost particles on the mpi host
do i=1,nbspecies
IF(mpirank .eq.0 ) THEN
CALL MPI_REDUCE(MPI_IN_PLACE, partslist(i)%nbadded, 1, MPI_INTEGER, MPI_SUM, &
& 0, MPI_COMM_WORLD, ierr)
CALL MPI_REDUCE(MPI_IN_PLACE, partslist(i)%nblost, 4, MPI_INTEGER, MPI_SUM, &
& 0, MPI_COMM_WORLD, ierr)
CALL MPI_REDUCE(MPI_IN_PLACE, partslist(i)%nbcolls, 2, MPI_INTEGER, MPI_SUM, &
& 0, MPI_COMM_WORLD, ierr)
ELSE
CALL MPI_REDUCE(partslist(i)%nbadded, partslist(i)%nbadded, 1, MPI_INTEGER, MPI_SUM, &
& 0, MPI_COMM_WORLD, ierr)
CALL MPI_REDUCE(partslist(i)%nblost, partslist(i)%nblost, 4, MPI_INTEGER, MPI_SUM, &
& 0, MPI_COMM_WORLD, ierr)
CALL MPI_REDUCE(partslist(i)%nbcolls, partslist(i)%nbcolls, 2, MPI_INTEGER, MPI_SUM, &
& 0, MPI_COMM_WORLD, ierr)
partslist(i)%nbadded=0
partslist(i)%nblost=0
partslist(i)%nbcolls=0
END IF
end do
end if
!
! Only process 0 should save on file
IF(mpirank .ne. 0) RETURN
!
IF (mpisize .gt. 1) THEN
partslist(1)%Nptot=sum(Nplocs_all)
END IF
!
IF(modulo(step,ittext).eq. 0 .or. nlend) THEN
WRITE(*,'(a,1x,i8.8,a1,i8.8,20x,a,1pe10.3)') '*** Timestep (this run/total) =', &
& step, '/', cstep, 'Time =', time
if( abs(etot).gt. 0) then
WRITE(*,'(a,6(1pe12.4),1x,i8.8,a1,i8.8)') 'Epot, Ekin, Etot, Etot0, Eerr, Eerr rel, Nbparts/Ntotal', epot, ekin, etot, etot0, etot-etot0,(etot-etot0)/etot, partslist(1)%Nptot,'/',nplasma
else
WRITE(*,'(a,4(1pe12.4),1x,i8.8,a1,i8.8)') 'Epot, Ekin, Etot, Eerr, Nbparts/Ntotal', epot, ekin, etot, etot-etot0, partslist(1)%Nptot,'/',nplasma
end if
IF(mpisize .gt. 1 ) then
WRITE(*,'(a,64i10.7)') 'Nbparts per proc', Nplocs_all
end if
Write(*,'(a)')"speci, added, zmloss, zploss, rmloss, rploss, iocoll, elacoll, tot var, tot"
do i=1,nbspecies
WRITE(*,'(i04,9i9.7)') i, partslist(i)%nbadded,-partslist(i)%nblost,partslist(i)%nbcolls,partslist(i)%nbadded-sum(partslist(i)%nblost), partslist(i)%Nptot
partslist(i)%nbadded=0
partslist(i)%nblost=0
partslist(i)%nbcolls=0
end do
END IF
!________________________________________________________________________________
!
! 2.1 0d history arrays
!
IF(modulo(step,it0d).eq. 0 .or. nlend) THEN
CALL add_record(hbuf0, "time", "simulation time", time)
CALL add_record(hbuf0, "epot", "potential energy", epot)
CALL add_record(hbuf0, "ekin", "kinetic energy", ekin)
CALL add_record(hbuf0, "etot", "total energy", etot)
CALL add_record(hbuf0, "etot0", "theoretical total energy", etot0)
CALL add_record(hbuf0, "nbparts", "number of remaining parts in the simulation space", REAL(partslist(1)%Nptot,kind=db))
CALL htable_endstep(hbuf0)
Nplocs_all_save=0
Nplocs_all_save(1:mpisize)=Nplocs_all(0:mpisize-1)
CALL append(fidres, "/data/var0d/Nplocs_all", REAL(Nplocs_all_save,kind=db))
CALL append(fidres, "/data/var0d/nudcol", partslist(1)%nudcol/dt)
END IF
!
! 2.2 2d profiles
IF(modulo(step,it2d).eq. 0 .or. nlend) THEN
CALL append(fidres, "/data/fields/time", time)
CALL append(fidres, "/data/fields/pot", pot*phinorm)
CALL append(fidres, "/data/fields/Er", Er*enorm)
CALL append(fidres, "/data/fields/Ez", Ez*enorm)
CALL append(fidres, "/data/fields/phi", phi_spline*phinorm)
CALL append(fidres, "/data/fields/moments", moments)
END IF
!
! 2.3 main specie quantities
IF(modulo(step,itparts).eq. 0 .or. nlend) THEN
!PRINT*, 'write particles to file_____________________'
CALL append(fidres, "/data/part/time", time)
CALL append(fidres, "/data/part/Nparts", REAL(partslist(1)%Nptot,kind=db))
!CALL append(fidres, "/data/part/nbchange", REAL((/partslist(1)%nbadded,partslist(1)%nblost,partslist(1)%nbcolls/),kind=db))
IF ( isdataset(fidres,'/data/part/R') ) THEN
CALL getdims(fidres, '/data/part/R', partsrank, partsdim)
partsdim(1)=min(size(partslist(1)%R,1), partsdim(1))
CALL append(fidres, "/data/part/R", partslist(1)%R(1:partsdim(1))*rnorm)
CALL append(fidres, "/data/part/Z", partslist(1)%Z(1:partsdim(1))*rnorm)
CALL append(fidres, "/data/part/THET", partslist(1)%THET(1:partsdim(1)))
CALL append(fidres, "/data/part/UZ", 0.5*(partslist(1)%UZ(1:partsdim(1))/partslist(1)%gamma(1:partsdim(1))+partslist(1)%UZold(1:partsdim(1))/partslist(1)%gammaold(1:partsdim(1))))
CALL append(fidres, "/data/part/UR", 0.5*(partslist(1)%UR(1:partsdim(1))/partslist(1)%gamma(1:partsdim(1))+partslist(1)%URold(1:partsdim(1))/partslist(1)%gammaold(1:partsdim(1))))
CALL append(fidres, "/data/part/UTHET", 0.5*(partslist(1)%UTHET(1:partsdim(1))/partslist(1)%gamma(1:partsdim(1))+partslist(1)%UTHETold(1:partsdim(1))/partslist(1)%gammaold(1:partsdim(1))))
CALL append(fidres, "/data/part/pot", partslist(1)%pot(1:partsdim(1))*phinorm)
CALL append(fidres, "/data/part/Rindex", REAL(partslist(1)%Rindex(1:partsdim(1)),kind=db))
CALL append(fidres, "/data/part/Zindex", REAL(partslist(1)%Zindex(1:partsdim(1)),kind=db))
CALL append(fidres, "/data/part/partindex", REAL(partslist(1)%partindex(1:partsdim(1)),kind=db))
END IF
END IF
!
! 2.4 Tracer quantities
IF(modulo(step,ittracer).eq. 0 .or. nlend) THEN
!PRINT*, 'write particles to file_____________________'
DO i=2,nbspecies
IF ( .not. partslist(i)%is_test) CYCLE
WRITE(grpname,'(a,i2,a)')'/data/part/',i,'/'
CALL append(fidres, trim(grpname) // "time", time)
CALL append(fidres, trim(grpname) //"Nparts", REAL(partslist(i)%Nptot,kind=db))
!CALL append(fidres, trim(grpname) //"nbchange", REAL((/partslist(i)%nbadded,partslist(i)%nblost,partslist(i)%nbcolls/),kind=db))
IF ( isdataset(fidres,trim(grpname)//'R') ) THEN
CALL getdims(fidres, trim(grpname) // 'R', partsrank, partsdim)
partsdim(1)=min(size(partslist(i)%R,1), partsdim(1))
CALL append(fidres, trim(grpname) // "R", partslist(i)%R(1:partsdim(1))*rnorm)
CALL append(fidres, trim(grpname) // "Z", partslist(i)%Z(1:partsdim(1))*rnorm)
CALL append(fidres, trim(grpname) // "THET", partslist(i)%THET(1:partsdim(1)))
CALL append(fidres, trim(grpname) // "UZ", 0.5*(partslist(i)%UZ(1:partsdim(1))/partslist(i)%gamma(1:partsdim(1)) + partslist(i)%UZold(1:partsdim(1))/partslist(i)%gammaold(1:partsdim(1))))
CALL append(fidres, trim(grpname) // "UR", 0.5*(partslist(i)%UR(1:partsdim(1))/partslist(i)%gamma(1:partsdim(1)) + partslist(i)%URold(1:partsdim(1))/partslist(i)%gammaold(1:partsdim(1))))
CALL append(fidres, trim(grpname) // "UTHET", 0.5*(partslist(i)%UTHET(1:partsdim(1))/partslist(i)%gamma(1:partsdim(1)) + partslist(i)%UTHETold(1:partsdim(1))/partslist(i)%gammaold(1:partsdim(1))))
CALL append(fidres, trim(grpname) // "pot", partslist(i)%pot(1:partsdim(1))*phinorm)
CALL append(fidres, trim(grpname) // "Rindex", REAL(partslist(i)%Rindex(1:partsdim(1)),kind=db))
CALL append(fidres, trim(grpname) // "Zindex", REAL(partslist(i)%Zindex(1:partsdim(1)),kind=db))
CALL append(fidres, trim(grpname) // "partindex", REAL(partslist(i)%partindex(1:partsdim(1)),kind=db))
END IF
END DO
!
END IF
! 2.5 3d profiles
!
!
! 2.6 Xgrafix
!
#if USE_X == 1
IF(nlxg .AND. modulo(kstep,itgraph) .eq. 0) THEN
call xgevent
CALL updt_xg_var
CALL xgupdate
END IF
#endif
!________________________________________________________________________________
! 3. Final diagnostics
ELSE
! Only process 0 should save on file
IF(mpirank .ne. 0) RETURN
!
! Flush 0d history array buffers
CALL htable_hdf5_flush(hbuf0)
!
! Close all diagnostic files
CALL closef(fidres)
!________________________________________________________________________________
END IF
!
CONTAINS
SUBROUTINE create_parts_group(p,grpname, time)
USE beam,ONLY: particles
type(particles):: p
real(kind=db):: time
character(len=*):: grpname
If(isgroup(fidres, trim(grpname))) return
CALL creatg(fidres, grpname, "specific specie phase space")
CALL creatd(fidres, 0, SHAPE(time), trim(grpname) // "/time", "time")
CALL creatd(fidres, 0, SHAPE(time), trim(grpname) //"/Nparts", "number of remaining parts")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/R", "radial pos")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/Z", "axial pos")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/THET", "azimuthal pos")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/UZ", "axial beta*gamma")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/UR", "radial beta*gamma")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/UTHET", "azimuthal beta*gamma")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/pot", "electric potential")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/Rindex", "radial grid index")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/Zindex", "axial grid index")
CALL creatd(fidres, 1, SHAPE(p%R), trim(grpname) // "/partindex", "particle index")
CALL creatd(fidres, 1, (/7/), trim(grpname) // "nbchange", "number of added parts, lost parts zm,zp,rm,rp, and collisions per type io, ela")
CALL attach(fidres,trim(grpname), "q", p%q)
CALL attach(fidres,trim(grpname), "m", p%m)
CALL attach(fidres,trim(grpname), "weight", p%weight)
END SUBROUTINE create_parts_group
END SUBROUTINE diagnose
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