! $Id$ ! ! subroutines in the chosen set of physics modules. ! module Equ ! use Cdata use Messages use Boundcond use Mpicomm use Grid, only: calc_pencils_grid, get_grid_mn ! implicit none ! private ! public :: pde, debug_imn_arrays, initialize_pencils public :: impose_floors_ceilings ! contains !*********************************************************************** include 'pencil_init.inc' ! defines subroutine initialize_pencils() !*********************************************************************** subroutine pde(f,df,p) ! ! Call the different evolution equations. ! ! 10-sep-01/axel: coded ! 12-may-12/MR: call of density_before_boundary added for boussinesq; ! moved call of timing after call of anelastic_after_mn ! 26-aug-13/MR: added call of diagnostic for imaginary parts ! 9-jun-15/MR: call of gravity_after_boundary added ! 24-sep-16/MR: added offset manipulation for second derivatives in complete one-sided fornulation. ! 5-jan-17/MR: removed mn-offset manipulation ! 14-feb-17/MR: adaptations for use of GPU kernels in calculating the rhss of the pde ! use Chiral use Chemistry use Density use Detonate, only: detonate_before_boundary use Diagnostics use Dustdensity use Energy use EquationOfState use Forcing, only: forcing_after_boundary ! ! To check ghost cell consistency, please uncomment the following line: ! use Ghost_check, only: check_ghosts_consistency use General, only: ioptest, loptest use GhostFold, only: fold_df, fold_df_3points use Gpu use Gravity use Hydro use Interstellar, only: interstellar_before_boundary, check_SN use Magnetic use Hypervisc_strict, only: hyperviscosity_strict use Hyperresi_strict, only: hyperresistivity_strict use NSCBC use Particles_main use Poisson use Pscalar use PointMasses use Polymer use Radiation use Selfgravity use Shear use Shock, only: calc_shock_profile, calc_shock_profile_simple use Solid_Cells, only: update_solid_cells, freeze_solid_cells, & dsolid_dt_integrate use Special, only: special_before_boundary,special_after_boundary use Sub use Testfield use Testflow use Testscalar use Viscosity, only: viscosity_after_boundary use Grid, only: coarsegrid_interp ! real, dimension (mx,my,mz,mfarray) :: f real, dimension (mx,my,mz,mvar) :: df type (pencil_case) :: p ! intent(inout):: f ! inout due to lshift_datacube_x, ! density floor, or velocity ceiling intent(out) :: df,p ! logical :: early_finalize real, dimension(nx) :: pfreeze,pfreeze_int,pfreeze_ext real, dimension(1) :: mass_per_proc integer :: iv logical, dimension(npencils) :: lpenc_loc ! ! Print statements when they are first executed. ! headtt = headt .and. lfirst .and. lroot ! if (headtt.or.ldebug) print*,'pde: ENTER' if (headtt) call svn_id( & "$Id$") ! ! Initialize counter for calculating and communicating print results. ! Do diagnostics only in the first of the 3 (=itorder) substeps. ! ldiagnos =lfirst.and.lout l1davgfirst=lfirst.and.l1davg l2davgfirst=lfirst.and.l2davg ! ! Derived diagnostics switches. ! l1dphiavg=lcylinder_in_a_box.and.l1davgfirst ! ! For chemistry with LSODE ! lchemonly=.false. ! ! Record times for diagnostic and 2d average output. ! if (ldiagnos ) tdiagnos =t ! (diagnostics are for THIS time) if (l1davgfirst) t1ddiagnos =t ! (1-D averages are for THIS time) if (l2davgfirst) then t2davgfirst=t ! (2-D averages are for THIS time) ! ! [AB: Isn't it true that not all 2-D averages use rcyl_mn? ! lwrite_phiaverages=T is required, and perhaps only that.] ! [BD: add also the z_mn dependency] ! lpencil(i_rcyl_mn)=.true. lpencil(i_z_mn)=.true. endif ! ! Shift entire data cube by one grid point at the beginning of each ! time-step. Useful for smearing out possible x-dependent numerical ! diffusion, e.g. in a linear shear flow. ! if (lfirst .and. lshift_datacube_x) then call boundconds_x(f) do n=n1,n2; do m=m1,m2 f(:,m,n,:)=cshift(f(:,m,n,:),1,1) enddo; enddo endif ! ! Need to finalize communication early either for test purposes, or ! when radiation transfer of global ionization is calculated. ! This could in principle be avoided (but it not worth it now) ! early_finalize=test_nonblocking.or. & leos_ionization.or.lradiation_ray.or. & lhyperviscosity_strict.or.lhyperresistivity_strict.or. & ltestscalar.or.ltestfield.or.ltestflow.or. & lparticles_spin.or.lsolid_cells.or. & lchemistry.or.lweno_transport .or. lbfield .or. & ! lslope_limit_diff .or. lvisc_smag .or. & lvisc_smag .or. & lyinyang .or. & !!!.or.lgpu & ncoarse>1 ! ! Write crash snapshots to the hard disc if the time-step is very low. ! The user must have set crash_file_dtmin_factor>0.0 in &run_pars for ! this to be done. ! if (crash_file_dtmin_factor > 0.0) call output_crash_files(f) ! ! For debugging purposes impose minimum or maximum value on certain variables. ! call impose_floors_ceilings(f) ! ! Apply global boundary conditions to particle positions and communicate ! migrating particles between the processors. ! if (lparticles) call particles_boundconds(f) if (lpointmasses) call boundconds_pointmasses ! ! Calculate the potential of the self gravity. Must be done before ! communication in order to be able to take the gradient of the potential ! later. ! call calc_selfpotential(f) ! ! Check for dust grain mass interval overflows ! (should consider having possibility for all modules to fiddle with the ! f array before boundary conditions are sent) ! if (.not. lchemistry) then if (ldustdensity) call null_dust_vars(f) if (ldustdensity .and. lmdvar .and. lfirst) call redist_mdbins(f) endif ! ! Call "before_boundary" hooks (for f array precalculation) ! if (linterstellar) call interstellar_before_boundary(f) if (ldensity.or.lboussinesq) call density_before_boundary(f) if (lhydro.or.lhydro_kinematic) call hydro_before_boundary(f) if (lmagnetic) call magnetic_before_boundary(f) call energy_before_boundary(f) if (lshear) call shear_before_boundary(f) if (lchiral) call chiral_before_boundary(f) if (lspecial) call special_before_boundary(f) if (ltestflow) call testflow_before_boundary(f) if (ltestfield) call testfield_before_boundary(f) if (lparticles) call particles_before_boundary(f) if (ldetonate) call detonate_before_boundary(f) ! ! Fetch fp to the special module. ! if (lparticles.and.lspecial) call particles_special_bfre_bdary(f) ! ! Initiate shock profile calculation and use asynchronous to handle ! communication along processor/periodic boundaries. ! if (lshock) call calc_shock_profile(f) ! ! Prepare x-ghost zones; required before f-array communication ! AND shock calculation ! call boundconds_x(f) ! ! Initiate (non-blocking) communication and do boundary conditions. ! Required order: ! 1. x-boundaries (x-ghost zones will be communicated) - done above ! 2. communication ! 3. y- and z-boundaries ! if (ldebug) print*,'pde: before initiate_isendrcv_bdry' call initiate_isendrcv_bdry(f) if (early_finalize) then call finalize_isendrcv_bdry(f) if (lcoarse) call coarsegrid_interp(f) ! after boundconds_x??? call boundconds_y(f) call boundconds_z(f) endif ! ! Remove unphysical values of the mass fractions. This must be done ! before the call to update_solid_cells in order to avoid corrections ! within the solid structure. ! if (lsolid_cells .and. lchemistry) & call chemspec_normalization_N2(f) ! ! update solid cell "ghost points". This must be done in order to get the ! correct boundary layer close to the solid geometry, i.e. no-slip conditions. ! call update_solid_cells(f) ! ! For sixth order momentum-conserving, symmetric hyperviscosity with positive ! definite heating rate we need to precalculate the viscosity term. The ! restivitity term for sixth order hyperresistivity with positive definite ! heating rate must also be precalculated. ! if (lhyperviscosity_strict) call hyperviscosity_strict(f) if (lhyperresistivity_strict) call hyperresistivity_strict(f) ! ! Dynamically set the (hyper-)diffusion coefficients ! if (ldynamical_diffusion) call set_dyndiff_coeff(f) ! ! Calculate the characteristic velocity ! for slope limited diffusion ! ! if (lslope_limit_diff.and.lfirst) then ! f(2:mx-2,2:my-2,2:mz-2,iFF_char_c)=0. !print*,'vor magnetic:', maxval(f(2:mx-2,2:my-2,2:mz-2,iFF_char_c)) ! call update_char_vel_energy(f) ! call update_char_vel_magnetic(f) ! call update_char_vel_hydro(f) !call update_char_vel_density(f) !f(2:mx-2,2:my-2,2:mz-2,iFF_char_c)=sqrt(f(2:mx-2,2:my-2,2:mz-2,iFF_char_c)) ! JW: for hydro it is done without sqrt !if (ldiagnos) print*, 'max(char_c)=', maxval(f(2:mx-2,2:my-2,2:mz-2,iFF_char_c)) ! endif ! ! For calculating the pressure gradient directly from the pressure (which is ! derived from the basic thermodynamical variables), we need to fill in the ! pressure in the f array. ! call fill_farray_pressure(f) ! ! Set inverse timestep to zero before entering loop over m and n. ! If we want to have a logarithmic time advance, we want set this here ! as the maximum. All other routines can then still make it shorter. ! if (lfirst.and.ldt) then if (dtmax/=0.0) then if (lfractional_tstep_advance) then dt1_max=1./(dt_incr*t) else dt1_max=1./dtmax endif else dt1_max=0.0 endif endif ! ! Calculate ionization degree (needed for thermodynamics) ! Radiation transport along rays. If lsingle_ray, then this ! is only used for visualization and only needed when lvideo ! (but this is decided in radtransfer itself) ! if (leos_ionization.or.leos_temperature_ionization) call ioncalc(f) if (lradiation_ray) call radtransfer(f) ! ! Calculate shock profile (simple). ! if (lshock) call calc_shock_profile_simple(f) ! ! Call "after" hooks (for f array precalculation). This may imply ! calculating averages (some of which may only be required for certain ! settings in hydro of the testfield procedure (only when lsoca=.false.), ! for example. They used to be or are still called hydro_after_boundary etc, ! and will soon be renamed to hydro_after_boundary. ! ! Important to note that the processor boundaries are not full updated ! at this point, even if the name 'after_boundary' suggesting this. ! Use early_finalize in this case. ! MR+joern+axel, 8.10.2015 ! call timing('pde','before hydro_after_boundary') ! if (lhydro) call hydro_after_boundary(f) if (lviscosity) call viscosity_after_boundary(f) if (lmagnetic) call magnetic_after_boundary(f) if (lenergy) call energy_after_boundary(f) if (lgrav) call gravity_after_boundary(f) if (lforcing) call forcing_after_boundary(f) if (lpolymer) call calc_polymer_after_boundary(f) if (ltestscalar) call testscalar_after_boundary(f) if (ltestfield) call testfield_after_boundary(f) !AB: quick fix !if (ltestfield) call testfield_after_boundary(f,p) if (lpscalar) call pscalar_after_boundary(f) if (ldensity) call density_after_boundary(f) if (ltestflow) call calc_ltestflow_nonlin_terms(f,df) if (lspecial) call special_after_boundary(f) ! ! Calculate quantities for a chemical mixture ! if (lchemistry .and. ldustdensity) then call chemspec_normalization(f) ! call dustspec_normalization(f) endif if (lchemistry .and. ldensity) call calc_for_chem_mixture(f) call timing('pde','after calc_for_chem_mixture') ! if (lgpu) then call rhs_gpu(f,itsub,early_finalize) if (ldiagnos.or.l1davgfirst.or.l1dphiavg.or.l2davgfirst) then call copy_farray_from_GPU(f) call calc_all_module_diagnostics(f,p) endif else call rhs_cpu(f,df,p,mass_per_proc,early_finalize) endif ! ! earliest call to check_SN that does not break the pencil chece! ! if (linterstellar) call check_SN(f) ! ! Finish the job for the anelastic approximation ! if (lanelastic) call anelastic_after_mn(f,p,df,mass_per_proc) ! call timing('pde','at the end of the mn_loop') ! ! Integrate diagnostics related to solid cells (e.g. drag and lift). ! if (lsolid_cells) call dsolid_dt_integrate ! ! Calculate the gradient of the potential if there is room allocated in the ! f-array. ! if (igpotselfx/=0) then call initiate_isendrcv_bdry(f,igpotselfx,igpotselfz) call finalize_isendrcv_bdry(f,igpotselfx,igpotselfz) call boundconds_x(f,igpotselfx,igpotselfz) call boundconds_y(f,igpotselfx,igpotselfz) call boundconds_z(f,igpotselfx,igpotselfz) endif ! ! Change df and dfp according to the chosen particle modules. ! if (lparticles) then call particles_pde_blocks(f,df) call particles_pde(f,df,p) endif ! if (lpointmasses) call pointmasses_pde(f,df) ! ! Electron inertia: our df(:,:,:,iax:iaz) so far is ! (1 - l_e^2\Laplace) daa, thus to get the true daa, we need to invert ! that operator. ! [wd-aug-2007: This should be replaced by the more general stuff with the ! Poisson solver (so l_e can be non-constant), so at some point, we can ! remove/replace this] ! ! if (lelectron_inertia .and. inertial_length/=0.) then ! do iv = iax,iaz ! call inverse_laplacian_semispectral(df(:,:,:,iv), H=linertial_2) ! enddo ! df(:,:,:,iax:iaz) = -df(:,:,:,iax:iaz) * linertial_2 ! endif ! ! Take care of flux-limited diffusion ! This is now commented out, because we always use radiation_ray instead. ! !-- if (lradiation_fld) f(:,:,:,idd)=DFF_new ! ! Fold df from first ghost zone into main df. ! if (lfold_df) then if (lhydro .and. (.not. lpscalar) .and. (.not. lchemistry)) then call fold_df(df,iux,iuz) else call fold_df(df,iux,mvar) endif endif if (lfold_df_3points) then call fold_df_3points(df,iux,mvar) endif ! ! ------------------------------------------------------------- ! NO CALLS MODIFYING DF BEYOND THIS POINT (APART FROM FREEZING) ! ------------------------------------------------------------- ! ! Freezing must be done after the full (m,n) loop, as df may be modified ! outside of the considered pencil. ! do imn=1,ny*nz n=nn(imn) m=mm(imn) !if (imn_array(m,n)==0) cycle ! ! Recalculate grid/geometry related pencils. The r_mn and rcyl_mn are requested ! in pencil_criteria_grid. Unfortunately we need to recalculate them here. ! if (any(lfreeze_varext).or.any(lfreeze_varint)) then lpenc_loc=.false. if (lcylinder_in_a_box.or.lcylindrical_coords) then lpenc_loc(i_rcyl_mn)=.true. else lpenc_loc(i_r_mn)=.true. endif call calc_pencils_grid(f,p,lpenc_loc) ! ! Set df=0 for r_mnr_ext. ! if (any(lfreeze_varext)) then if (headtt) print*, 'pde: freezing variables for r > ', rfreeze_ext, & ' : ', lfreeze_varext if (lcylinder_in_a_box.or.lcylindrical_coords) then if (wfreeze_ext==0.0) then where (p%rcyl_mn>=rfreeze_ext) pfreeze_ext=0.0 elsewhere pfreeze_ext=1.0 endwhere else pfreeze_ext=1.0-quintic_step(p%rcyl_mn,rfreeze_ext,wfreeze_ext, & SHIFT=fshift_ext) endif else if (wfreeze_ext==0.0) then where (p%r_mn>=rfreeze_ext) pfreeze_ext=0.0 elsewhere pfreeze_ext=1.0 endwhere else pfreeze_ext=1.0-quintic_step(p%r_mn,rfreeze_ext,wfreeze_ext, & SHIFT=fshift_ext) endif endif ! do iv=1,nvar if (lfreeze_varext(iv)) & df(l1:l2,m,n,iv) = pfreeze_ext*df(l1:l2,m,n,iv) enddo endif endif ! ! Set df=0 inside square. ! if (any(lfreeze_varsquare)) then if (headtt) print*, 'pde: freezing variables inside square : ', & lfreeze_varsquare pfreeze=1.0-quintic_step(x(l1:l2),xfreeze_square,wfreeze,SHIFT=-1.0)*& quintic_step(spread(y(m),1,nx),yfreeze_square,-wfreeze,SHIFT=-1.0) ! do iv=1,nvar if (lfreeze_varsquare(iv)) df(l1:l2,m,n,iv) = pfreeze*df(l1:l2,m,n,iv) enddo endif ! ! Freeze components of variables in boundary slice if specified by boundary ! condition 'f' ! ! Freezing boundary conditions in x. ! if (lfrozen_bcs_x) then ! are there any frozen vars at all? ! ! Only need to do this for nonperiodic x direction, on left/right-most ! processor and in left/right--most pencils ! if (.not. lperi(1)) then if (lfirst_proc_x) where (lfrozen_bot_var_x(1:nvar)) df(l1,m,n,1:nvar) = 0. if (llast_proc_x) where (lfrozen_top_var_x(1:nvar)) df(l2,m,n,1:nvar) = 0. endif ! endif ! ! Freezing boundary conditions in y. ! if (lfrozen_bcs_y) then ! are there any frozen vars at all? ! ! Only need to do this for nonperiodic y direction, on bottom/top-most ! processor and in bottom/top-most pencils. ! if (.not. lperi(2)) then if (lfirst_proc_y .and. (m == m1)) then do iv=1,nvar if (lfrozen_bot_var_y(iv)) df(l1:l2,m,n,iv) = 0. enddo endif if (llast_proc_y .and. (m == m2)) then do iv=1,nvar if (lfrozen_top_var_y(iv)) df(l1:l2,m,n,iv) = 0. enddo endif endif endif ! ! Freezing boundary conditions in z. ! if (lfrozen_bcs_z) then ! are there any frozen vars at all? ! ! Only need to do this for nonperiodic z direction, on bottom/top-most ! processor and in bottom/top-most pencils. ! if (.not. lperi(3)) then if (lfirst_proc_z .and. (n == n1)) then do iv=1,nvar if (lfrozen_bot_var_z(iv)) df(l1:l2,m,n,iv) = 0. enddo endif if (llast_proc_z .and. (n == n2)) then do iv=1,nvar if (lfrozen_top_var_z(iv)) df(l1:l2,m,n,iv) = 0. enddo endif endif endif ! ! Set df=0 for all solid cells. ! call freeze_solid_cells(df) ! enddo ! ! Boundary treatment of the df-array. ! ! This is a way to impose (time- ! dependent) boundary conditions by solving a so-called characteristic ! form of the fluid equations on the boundaries, as opposed to setting ! actual values of the variables in the f-array. The method is called ! Navier-Stokes characteristic boundary conditions (NSCBC). ! ! The treatment should be done after the y-z-loop, but before the Runge- ! Kutta solver adds to the f-array. ! if (lnscbc) call nscbc_boundtreat(f,df) ! ! 0-D Diagnostics. ! if (ldiagnos) then call diagnostic(fname,nname) call diagnostic(fname_keep,nname,lcomplex=.true.) endif ! ! 1-D diagnostics. ! if (l1davgfirst) then if (lwrite_xyaverages) call xyaverages_z if (lwrite_xzaverages) call xzaverages_y if (lwrite_yzaverages) call yzaverages_x endif if (l1dphiavg) call phizaverages_r ! ! 2-D averages. ! if (l2davgfirst) then if (lwrite_yaverages) call yaverages_xz if (lwrite_zaverages) call zaverages_xy if (lwrite_phiaverages) call phiaverages_rz endif ! ! Note: zaverages_xy are also needed if bmx and bmy are to be calculated ! (of course, yaverages_xz does not need to be calculated for that). ! if (.not.l2davgfirst.and.ldiagnos.and.ldiagnos_need_zaverages) then if (lwrite_zaverages) call zaverages_xy endif ! ! Calculate mean fields and diagnostics related to mean fields. ! if (ldiagnos) then if (lmagnetic) call calc_mfield if (lhydro) call calc_mflow if (lpscalar) call calc_mpscalar endif ! ! Calculate rhoccm and cc2m (this requires that these are set in print.in). ! Broadcast result to other processors. This is needed for calculating PDFs. ! ! if (idiag_rhoccm/=0) then ! if (iproc==0) rhoccm=fname(idiag_rhoccm) ! call mpibcast_real(rhoccm) ! endif ! ! if (idiag_cc2m/=0) then ! if (iproc==0) cc2m=fname(idiag_cc2m) ! call mpibcast_real(cc2m) ! endif ! ! if (idiag_gcc2m/=0) then ! if (iproc==0) gcc2m=fname(idiag_gcc2m) ! call mpibcast_real(gcc2m) ! endif ! ! Reset lwrite_prof. ! lwrite_prof=.false. ! endsubroutine pde !**************************************************************************** subroutine calc_all_module_diagnostics(f,p) ! ! Calculates module diagnostics (so far only density, energy, hydro, magnetic) ! ! 10-sep-2019/MR: coded ! use Density, only: calc_diagnostics_density use Energy, only: calc_diagnostics_energy use Hydro, only: calc_diagnostics_hydro use Magnetic, only: calc_diagnostics_magnetic real, dimension (mx,my,mz,mfarray),intent(INOUT) :: f type (pencil_case) ,intent(INOUT) :: p integer :: nyz, imn nyz=ny*nz do imn=1,nyz n=nn(imn) m=mm(imn) ! ! Skip points not belonging to coarse grid. ! lcoarse_mn=lcoarse.and.mexts(1)<=m.and.m<=mexts(2) if (lcoarse_mn) then lcoarse_mn=lcoarse_mn.and.ninds(0,m,n)>0 if (ninds(0,m,n)<=0) cycle endif lfirstpoint=(imn==1) ! true for very first iteration of m-n loop llastpoint=(imn==nyz) ! true for very last iteration of m-n loop call calc_all_pencils(f,p) call calc_diagnostics_density(f,p) call calc_diagnostics_energy(f,p) call calc_diagnostics_hydro(f,p) call calc_diagnostics_magnetic(f,p) enddo endsubroutine calc_all_module_diagnostics !**************************************************************************** subroutine calc_all_pencils(f,p) use Diagnostics, only: calc_phiavg_profile use BorderProfiles, only: calc_pencils_borderprofiles use Chiral use Chemistry use Cosmicray use CosmicrayFlux use Density use Dustvelocity use Dustdensity use Energy use EquationOfState use Forcing, only: calc_pencils_forcing use Gravity use Heatflux use Hydro use Lorenz_gauge use Magnetic use NeutralDensity use NeutralVelocity use Particles_main use Pscalar use PointMasses use Polymer use Radiation use Selfgravity use Shear use Shock, only: calc_pencils_shock, calc_shock_profile, & calc_shock_profile_simple use Solid_Cells, only: update_solid_cells_pencil use Special, only: calc_pencils_special, dspecial_dt use Ascalar use Testfield use Testflow use Testscalar use Viscosity, only: calc_pencils_viscosity real, dimension (mx,my,mz,mfarray),intent(INOUT) :: f type (pencil_case) ,intent(INOUT) :: p ! ! The solid cells may have to be updated at the beginning of every ! pencil calculation. ! call update_solid_cells_pencil(f) ! ! Grid spacing. In case of equidistant grid and cartesian coordinates ! this is calculated before the (m,n) loop. ! if (.not. lcartesian_coords .or. .not.all(lequidist)) call get_grid_mn ! ! Calculate grid/geometry related pencils. ! call calc_pencils_grid(f,p) ! ! Calculate profile for phi-averages if needed. ! if ((l2davgfirst.and.lwrite_phiaverages ) .or. & (l1dphiavg .and.lwrite_phizaverages)) & call calc_phiavg_profile(p) ! ! Calculate pencils for the pencil_case. ! Note: some no-modules (e.g. nohydro) also calculate some pencils, ! so it would be wrong to check for lhydro etc in such cases. ! DM : in the formulation of lambda effect due to Kitchanov and Olemski, ! DM : we need to have dsdr to calculate lambda. Hence, the way it is done now, ! DM : we need to have energy pencils calculated before viscosity pencils. ! DM : This is *bad* practice and must be corrected later. ! To check ghost cell consistency, please uncomment the following 2 lines: ! if (.not. lpencil_check_at_work .and. necessary(imn)) & ! call check_ghosts_consistency (f, 'before calc_pencils_*') call calc_pencils_hydro(f,p) call calc_pencils_density(f,p) if (lpscalar) call calc_pencils_pscalar(f,p) if (lascalar) call calc_pencils_ascalar(f,p) call calc_pencils_eos(f,p) if (lshock) call calc_pencils_shock(f,p) if (lchemistry) call calc_pencils_chemistry(f,p) call calc_pencils_energy(f,p) if (lviscosity) call calc_pencils_viscosity(f,p) if (lforcing_cont) call calc_pencils_forcing(f,p) if (llorenz_gauge) call calc_pencils_lorenz_gauge(f,p) if (lmagnetic) call calc_pencils_magnetic(f,p) if (lpolymer) call calc_pencils_polymer(f,p) if (lgrav) call calc_pencils_gravity(f,p) if (lselfgravity) call calc_pencils_selfgravity(f,p) if (ldustvelocity) call calc_pencils_dustvelocity(f,p) if (ldustdensity) call calc_pencils_dustdensity(f,p) if (lneutralvelocity) call calc_pencils_neutralvelocity(f,p) if (lneutraldensity) call calc_pencils_neutraldensity(f,p) if (lcosmicray) call calc_pencils_cosmicray(f,p) if (lcosmicrayflux) call calc_pencils_cosmicrayflux(f,p) if (lchiral) call calc_pencils_chiral(f,p) if (lradiation) call calc_pencils_radiation(f,p) if (lshear) call calc_pencils_shear(f,p) if (lborder_profiles) call calc_pencils_borderprofiles(f,p) if (lpointmasses) call calc_pencils_pointmasses(f,p) if (lparticles) call particles_calc_pencils(f,p) if (lspecial) call calc_pencils_special(f,p) if (lheatflux) call calc_pencils_heatflux(f,p) endsubroutine calc_all_pencils !*********************************************************************** subroutine rhs_cpu(f,df,p,mass_per_proc,early_finalize) ! ! Calculates rhss of the PDEs. ! ! 14-feb-17/MR: Carved out from pde. ! 21-feb-17/MR: Moved all module-specific estimators of the (inverse) possible timestep ! to the individual modules. ! use Diagnostics use Chiral use Chemistry use Cosmicray use CosmicrayFlux use Density use Dustvelocity use Dustdensity use Energy use EquationOfState use Forcing, only: calc_pencils_forcing, calc_diagnostics_forcing use General, only: notanumber use GhostFold, only: fold_df, fold_df_3points use Gravity use Heatflux use Hydro use Lorenz_gauge use Magnetic use NeutralDensity use NeutralVelocity use Particles_main use Pscalar use PointMasses use Polymer use Radiation use Selfgravity use Shear use Shock, only: calc_pencils_shock, calc_shock_profile, & calc_shock_profile_simple use Solid_Cells, only: update_solid_cells_pencil, dsolid_dt use Special, only: calc_pencils_special, dspecial_dt use Sub, only: sum_mn use Ascalar use Testfield use Testflow use Testscalar use Viscosity, only: calc_pencils_viscosity real, dimension (mx,my,mz,mfarray),intent(INOUT) :: f real, dimension (mx,my,mz,mvar) ,intent(OUT ) :: df type (pencil_case) ,intent(INOUT) :: p real, dimension(1) ,intent(INOUT) :: mass_per_proc logical ,intent(IN ) :: early_finalize integer :: nyz real, dimension (nx,3) :: df_iuu_pencil real, dimension(nx) :: dt1_advec, dt1_diffus, dt1_src, dt1_reac real :: dt1_poly_relax, dt1_preac nyz=ny*nz mn_loop: do imn=1,nyz n=nn(imn) m=mm(imn) lfirstpoint=(imn==1) ! true for very first iteration of m-n loop llastpoint=(imn==nyz) ! true for very last iteration of m-n loop !if (imn_array(m,n)==0) cycle ! ! Skip points not belonging to coarse grid. ! lcoarse_mn=lcoarse.and.mexts(1)<=m.and.m<=mexts(2) if (lcoarse_mn) then lcoarse_mn=lcoarse_mn.and.ninds(0,m,n)>0 if (ninds(0,m,n)<=0) cycle endif ! ! Store the velocity part of df array in a temporary array ! while solving the anelastic case. ! call timing('pde','before lanelastic',mnloop=.true.) if (lanelastic) then df_iuu_pencil = df(l1:l2,m,n,iuu:iuu+2) df(l1:l2,m,n,iuu:iuu+2)=0.0 endif ! ! if (loptimise_ders) der_call_count=0 !DERCOUNT ! ! Make sure all ghost points are set. ! if (.not.early_finalize.and.necessary(imn)) then call finalize_isendrcv_bdry(f) call boundconds_y(f) call boundconds_z(f) endif call timing('pde','finished boundconds_z',mnloop=.true.) ! ! For each pencil, accumulate through the different modules ! advec_XX and diffus_XX, which are essentially the inverse ! advective and diffusive timestep for that module. ! (note: advec2 is an inverse _squared_ timesteps) ! Note that advec_cs2 should always be initialized when leos. ! if (lfirst.and.ldt.and.(.not.ldt_paronly)) then advec_cs2=0.0 maxadvec=0. if (lenergy.or.ldensity.or.lmagnetic.or.lradiation.or.lneutralvelocity.or.lcosmicray.or. & (ltestfield_z.and.iuutest>0)) & advec2=0. if (ldensity.or.lviscosity.or.lmagnetic.or.lenergy) & advec2_hypermesh=0.0 maxdiffus=0. maxdiffus2=0. maxdiffus3=0. maxsrc=0. endif call calc_all_pencils(f,p) ! ! -------------------------------------------------------- ! NO CALLS MODIFYING PENCIL_CASE PENCILS BEYOND THIS POINT ! -------------------------------------------------------- ! ! hydro, density, and entropy evolution ! Note that pressure gradient is added in denergy_dt of noentropy to momentum, ! even if lentropy=.false. ! call duu_dt(f,df,p) call dlnrho_dt(f,df,p) call denergy_dt(f,df,p) ! ! Magnetic field evolution ! if (lmagnetic) call daa_dt(f,df,p) ! ! Lorenz gauge evolution ! if (llorenz_gauge) call dlorenz_gauge_dt(f,df,p) ! ! Polymer evolution ! if (lpolymer) call dpoly_dt(f,df,p) ! ! Testscalar evolution ! if (ltestscalar) call dcctest_dt(f,df,p) ! ! Testfield evolution ! if (ltestfield) call daatest_dt(f,df,p) ! ! Testflow evolution ! if (ltestflow) call duutest_dt(f,df,p) ! ! Passive scalar evolution ! if (lpscalar) call dlncc_dt(f,df,p) ! ! Supersaturation evolution if (lascalar) call dacc_dt(f,df,p) ! ! Dust evolution ! if (ldustvelocity) call duud_dt(f,df,p) if (ldustdensity) call dndmd_dt(f,df,p) ! ! Neutral evolution ! if (lneutraldensity) call dlnrhon_dt(f,df,p) if (lneutralvelocity) call duun_dt(f,df,p) ! ! Add gravity, if present ! if (lgrav) then if (lhydro.or.ldustvelocity.or.lneutralvelocity) & call duu_dt_grav(f,df,p) endif ! ! Self-gravity ! if (lselfgravity) call duu_dt_selfgrav(f,df,p) ! ! Cosmic ray energy density ! if (lcosmicray) call decr_dt(f,df,p) ! ! Cosmic ray flux ! if (lcosmicrayflux) call dfcr_dt(f,df,p) ! ! Chirality of left and right handed aminoacids ! if (lchiral) call dXY_chiral_dt(f,df,p) ! ! Evolution of radiative energy ! if (lradiation_fld) call de_dt(f,df,p) ! ! Evolution of chemical species ! if (lchemistry) call dchemistry_dt(f,df,p) ! ! Evolution of heatflux vector ! if (lheatflux) call dheatflux_dt(f,df,p) ! ! Continuous forcing function (currently only for extra diagonstics) ! if (lforcing_cont) call calc_diagnostics_forcing(p) ! ! Add and extra 'special' physics ! if (lspecial) call dspecial_dt(f,df,p) ! ! Add radiative cooling and radiative pressure (for ray method) ! if (lradiation_ray.and.lenergy) then call radiative_cooling(f,df,p) call radiative_pressure(f,df,p) endif ! ! Find diagnostics related to solid cells (e.g. drag and lift). ! Integrating to the full result is done after loops over m and n. ! if (lsolid_cells) call dsolid_dt(f,df,p) ! ! Add shear if present ! if (lshear) call shearing(f,df,p) ! if (lparticles) call particles_pde_pencil(f,df,p) ! if (lpointmasses) call pointmasses_pde_pencil(f,df,p) ! ! Call diagnostics that involves the full right hand side ! This must be done at the end of all calls that might modify df. ! if (ldiagnos) then if (lhydro) call df_diagnos_hydro(df,p) if (lmagnetic) call df_diagnos_magnetic(df,p) endif ! ! General phiaverage quantities -- useful for debugging. ! MR: Result is constant in time, so why here? ! if (l2davgfirst) then call phisum_mn_name_rz(p%rcyl_mn,idiag_rcylmphi) call phisum_mn_name_rz(p%phi_mn,idiag_phimphi) call phisum_mn_name_rz(p%z_mn,idiag_zmphi) call phisum_mn_name_rz(p%r_mn,idiag_rmphi) endif ! ! Do the time integrations here, before the pencils are overwritten. ! if (ltime_integrals.and.llast.and..not.lgpu) then if (lhydro) call time_integrals_hydro(f,p) if (lmagnetic) call time_integrals_magnetic(f,p) endif ! ! In max_mn maximum values of u^2 (etc) are determined sucessively ! va2 is set in magnetic (or nomagnetic) ! In rms_mn sum of all u^2 (etc) is accumulated ! Calculate maximum advection speed for timestep; needs to be done at ! the first substep of each time step ! Note that we are (currently) accumulating the maximum value, ! not the maximum squared! ! ! The dimension of the run ndim (=0, 1, 2, or 3) enters the viscous time step. ! This has to do with the term on the diagonal, cdtv depends on order of scheme ! if (lfirst.and.ldt.and.(.not.ldt_paronly)) then ! ! sum or maximum of the advection terms? ! (lmaxadvec_sum=.false. by default) ! advec2=advec2+advec_cs2 if (lenergy.or.ldensity.or.lmagnetic.or.lradiation.or.lneutralvelocity.or.lcosmicray.or. & (ltestfield_z.and.iuutest>0)) & maxadvec=maxadvec+sqrt(advec2) if (ldensity.or.lhydro.or.lmagnetic.or.lenergy) & maxadvec=maxadvec+sqrt(advec2_hypermesh) ! ! Time step constraints from each module. ! (At the moment, magnetic and testfield use the same variable.) ! !if (n==n1 .and. m==m1) print*, 'equ:maxdiffus=', maxdiffus ! ! Exclude the frozen zones from the time-step calculation. ! if (any(lfreeze_varint)) then if (lcylinder_in_a_box.or.lcylindrical_coords) then where (p%rcyl_mn<=rfreeze_int) maxadvec=0.0 maxdiffus=0.0 endwhere else where (p%r_mn<=rfreeze_int) maxadvec=0.0 maxdiffus=0.0 endwhere endif endif ! if (any(lfreeze_varext)) then if (lcylinder_in_a_box.or.lcylindrical_coords) then where (p%rcyl_mn>=rfreeze_ext) maxadvec=0.0 maxdiffus=0.0 endwhere else where (p%r_mn>=rfreeze_ext) maxadvec=0.0 maxdiffus=0.0 endwhere endif endif ! ! cdt, cdtv, and cdtc are empirical non-dimensional coefficients ! dt1_advec = maxadvec/cdt ! ! Check for NaNs in the advection time-step. ! if (notanumber(dt1_advec)) & call fatal_error_local('pde','NaN in dt1_advec') ! dt1_diffus = maxdiffus/cdtv + maxdiffus2/cdtv2 + maxdiffus3/cdtv3 ! ! Timestep constraint from source terms. ! dt1_src = maxsrc/cdtsrc ! ! Timestep combination from advection and diffusion (and "source"). ! dt1_max = max(dt1_max, sqrt(dt1_advec**2 + dt1_diffus**2 + dt1_src**2)) ! ! time step constraint from the coagulation kernel ! if (ldustdensity) then dt1_reac = reac_dust/cdtc dt1_max = max(dt1_max,dt1_reac) endif ! ! time step constraint from speed of chemical reactions ! if (lchemistry .and. .not.llsode) then dt1_reac = reac_chem/cdtc ! dt1_preac= reac_pchem/cdtc dt1_max = max(dt1_max,dt1_reac) endif ! ! time step constraint from relaxation time of polymer ! if (lpolymer) then dt1_poly_relax = 1./(trelax_poly*cdt_poly) dt1_max = max(dt1_max,dt1_poly_relax) endif ! ! Diagnostics showing how close to advective and diffusive time steps we are ! if (ldiagnos.and.idiag_dtv/=0) & call max_mn_name(maxadvec/cdt,idiag_dtv,l_dt=.true.) if (ldiagnos.and.idiag_dtdiffus/=0) & call max_mn_name(maxdiffus/cdtv,idiag_dtdiffus,l_dt=.true.) if (ldiagnos.and.idiag_dtdiffus2/=0) & call max_mn_name(maxdiffus2/cdtv2,idiag_dtdiffus2,l_dt=.true.) if (ldiagnos.and.idiag_dtdiffus3/=0) & call max_mn_name(maxdiffus3/cdtv3,idiag_dtdiffus3,l_dt=.true.) ! ! Regular and hyperdiffusive mesh Reynolds numbers ! if (ldiagnos) then if (idiag_Rmesh/=0) & call max_mn_name(pi_1*maxadvec/(maxdiffus+tini),idiag_Rmesh) if (idiag_Rmesh3/=0) & call max_mn_name(pi5_1*maxadvec/(maxdiffus3+tini),idiag_Rmesh3) if (idiag_maxadvec/=0) & call max_mn_name(maxadvec,idiag_maxadvec) endif endif ! ! Display derivative info ! !debug if (loptimise_ders.and.lout) then !DERCOUNT !debug do iv=1,nvar !DERCOUNT !debug do ider=1,8 !DERCOUNT !debug do j=1,3 !DERCOUNT !debug do k=1,3 !DERCOUNT !debug if (der_call_count(iv,ider,j,k) > 1) then !DERCOUNT !debug print*,'DERCOUNT: '//varname(iv)//' derivative ', & !DERCOUNT !debug ider,j,k, & !DERCOUNT !debug ' called ', & !DERCOUNT !debug der_call_count(iv,ider,j,k), & !DERCOUNT !debug 'times!' !DERCOUNT !debug endif !DERCOUNT !debug enddo !DERCOUNT !debug enddo !DERCOUNT !debug enddo !DERCOUNT !debug enddo !DERCOUNT !debug if (maxval(der_call_count)>1) call fatal_error( & !DERCOUNT !debug 'pde','ONE OR MORE DERIVATIVES HAS BEEN DOUBLE CALLED') !DERCOUNT !debug endif ! ! Fill in the rhs of the poisson equation and restore the df(:,:,:,iuu) array ! for anelastic case ! if (lanelastic) then ! call calc_pencils_density(f,p) f(l1:l2,m,n,irhs) = p%rho*df(l1:l2,m,n,iuu) f(l1:l2,m,n,irhs+1) = p%rho*df(l1:l2,m,n,iuu+1) f(l1:l2,m,n,irhs+2) = p%rho*df(l1:l2,m,n,iuu+2) df(l1:l2,m,n,iuu:iuu+2) = df_iuu_pencil(1:nx,1:3) +& df(l1:l2,m,n,iuu:iuu+2) call sum_mn(p%rho,mass_per_proc(1)) endif call timing('pde','end of mn loop',mnloop=.true.) ! ! End of loops over m and n. ! headtt=.false. enddo mn_loop ! endsubroutine rhs_cpu !*********************************************************************** subroutine debug_imn_arrays ! ! For debug purposes: writes out the mm, nn, and necessary arrays. ! ! 23-nov-02/axel: coded ! open(1,file=trim(directory)//'/imn_arrays.dat') do imn=1,ny*nz if (necessary(imn)) write(1,'(a)') '----necessary=.true.----' write(1,'(4i6)') imn,mm(imn),nn(imn) enddo close(1) ! endsubroutine debug_imn_arrays !*********************************************************************** subroutine output_crash_files(f) ! ! Write crash snapshots when time-step is low. ! ! 15-aug-2007/anders: coded ! use Snapshot ! real, dimension(mx,my,mz,mfarray) :: f ! integer, save :: icrash=0 character (len=10) :: filename character (len=1) :: icrash_string ! if ( (it>1) .and. lfirst .and. (dt<=crash_file_dtmin_factor*dtmin) ) then write(icrash_string, fmt='(i1)') icrash filename='crash'//icrash_string//'.dat' call wsnap(filename,f,mvar_io,ENUM=.false.) if (lroot) then print*, 'Time-step is very low - writing '//trim(filename) print*, '(it, itsub=', it, itsub, ')' print*, '(t, dt=', t, dt, ')' endif ! ! Next crash index, cycling from 0-9 to avoid excessive writing of ! snapshots to the hard disc. ! icrash=icrash+1 icrash=mod(icrash,10) endif ! endsubroutine output_crash_files !*********************************************************************** subroutine set_dyndiff_coeff(f) ! ! Set dynamical diffusion coefficients. ! ! 18-jul-14/ccyang: coded. ! 03-apr-16/ccyang: add switch ldyndiff_useumax ! use Density, only: dynamical_diffusion use Energy, only: dynamical_thermal_diffusion use Magnetic, only: dynamical_resistivity use Sub, only: find_max_fvec, find_rms_fvec use Viscosity, only: dynamical_viscosity ! real, dimension(mx,my,mz,mfarray), intent(in) :: f ! real :: uc ! ! Find the characteristic speed, either the absolute maximum or the rms. ! if (ldyndiff_useumax) then uc = find_max_fvec(f, iuu) else uc = find_rms_fvec(f, iuu) endif ! ! Ask each module to set the diffusion coefficients. ! if (ldensity) call dynamical_diffusion(uc) if (lmagnetic .and. .not. lbfield) call dynamical_resistivity(uc) if (lenergy) call dynamical_thermal_diffusion(uc) if (lviscosity) call dynamical_viscosity(uc) ! endsubroutine set_dyndiff_coeff !*********************************************************************** subroutine impose_floors_ceilings(f) ! ! Impose floors or ceilings for implemented fields. ! ! 20-oct-14/ccyang: modularized from pde. ! use Cosmicray, only: impose_ecr_floor use Density, only: impose_density_floor,impose_density_ceiling use Dustdensity, only: impose_dustdensity_floor use Energy, only: impose_energy_floor use Hydro, only: impose_velocity_ceiling ! real, dimension(mx,my,mz,mfarray), intent(inout) :: f ! call impose_density_floor(f) call impose_density_ceiling(f) call impose_velocity_ceiling(f) call impose_energy_floor(f) call impose_dustdensity_floor(f) call impose_ecr_floor(f) ! endsubroutine impose_floors_ceilings !*********************************************************************** endmodule Equ