Added new option for surface restoration for T,S (for long-term

large-sclae runs)

sample_inputs/param.nml

@@ -657,6 +657,17 @@
 
   step_nu_tr = 86400. !time step [sec] in all [MOD]_nu.nc (for inu_[MOD]=2)
 
+!-----------------------------------------------------------------------
+! Surface T,S restoration (for large-scale long-term runs). If invoked, 
+! the input is surface_restore.nc
+!-----------------------------------------------------------------------
+  iref_ts = 0 !on/off
+  ref_ts_restore_depth = 50. !restoration depth [m]
+  ref_ts_tscale = 365. !restoration time scale [days]
+  ref_ts_h1 = 100. !ramp-down depth 1 [m] (to turn off restoration in shallows)
+  ref_ts_h2 = 60. !ramp-down depth 2 [m]; must <ref_ts_h1
+  ref_ts_dt = 30. !time step in surface_restore.nc [days]
+
 !-----------------------------------------------------------------------
 ! Cut-off depth for cubic spline interpolation near bottom when computing horizontal gradients
 ! e.g. using hgrad_nodes() (radiation stress, and gradients of qnon and qhat in non-hydro model). 

src/Core/schism_glbl.F90

@@ -109,15 +109,16 @@ module schism_glbl
                       &xlsc0,rearth_pole,rearth_eq,hvis_coef0,disch_coef(10),hw_depth,hw_ratio, &
                       &slr_rate,rho0,shw,gen_wsett,turbinj,turbinjds,alphaw,h1_bcc,h2_bcc,vclose_surf_frac, &
                       &hmin_airsea_ex,hmin_salt_ex,shapiro0,loadtide_coef,h_massconsv,rinflation_icm, &
-                      &stemp_stc,stemp_dz(2)
+                      &stemp_stc,stemp_dz(2),ref_ts_h1,ref_ts_h2,ref_ts_restore_depth,ref_ts_tscale, &
+                      &ref_ts_dt
   real(rkind),save,allocatable :: veg_vert_z(:),veg_vert_scale_cd(:),veg_vert_scale_N(:),veg_vert_scale_D(:)
 
   ! Misc. variables shared between routines
   integer,save :: nz_r,ieqstate,kr_co, &
                   &ihconsv,isconsv,i_hmin_airsea_ex,i_hmin_salt_ex,ihdif,ntracers, & 
                   &ihydraulics,irouse_test,iwbl_itmax,nettype,nfltype, &
                   &ntetype,nsatype,ntrtype1(natrm),nettype2,nnode_et,nfltype2,nnode_fl, &
-                  &ntetype2,nsatype2,nnode_tr2(natrm),inu_tr(natrm), &
+                  &ntetype2,nsatype2,nnode_tr2(natrm),inu_tr(natrm),iref_ts, &
                   &nvar_sta,nout_sta,ntip,nbfr,itr_met,if_source,mass_source,nsources,nsinks, &
                   &max_flreg,irange_tr(2,natrm),nea_wwm,mnei_wwm,ne_wwm,neg_wwm, &
                   &max_iadjust_mass_consv,nsteps_from_cold
@@ -126,7 +127,7 @@ module schism_glbl
                       &vis_coe1,vis_coe2,h_bcc1,velmin_btrack,h_tvd,rmaxvel1,rmaxvel2, &
                       &difnum_max_l2,wtime1,wtime2,cmiu0, &
                       &cpsi2,rpub,rmub,rnub,cpsi1,psimin,eps_min,tip_dp,veg_di0,veg_h0,veg_nv0, &
-                      &veg_cd0,dtb_min_transport,bounds_lon(2)
+                      &veg_cd0,dtb_min_transport,bounds_lon(2),time_ref_ts
 
 !  logical,save :: lm2d !2D or 3D model
   logical,save :: lhas_quad=.false. !existence of quads
@@ -164,7 +165,7 @@ module schism_glbl
   character(len= 4),save :: a_4
   integer,save :: ncid_nu(natrm),ncid_tr3D(natrm),ncid_elev2D,ncid_uv3D,irec0_schout, &
  &istack0_schout,ncid_source,ncid_schout(7),ncid_schout_2(7),nrec_schout,nstride_schout, &
- &ncid_atmos
+ &ncid_atmos,ncid_ref_ts
 
   ! ADT for global-to-local linked-lists
   type :: llist_type
@@ -494,6 +495,7 @@ module schism_glbl
   logical,save :: lice_free_gb
 
   real(4),save,dimension(:,:,:),allocatable :: trnd_nu1,trnd_nu2,trnd_nu
+  real(4),save,dimension(:,:),allocatable :: ref_ts1,ref_ts2,ref_ts
   integer,save,allocatable :: iadv(:),iwater_type(:) 
 
   !weno>

src/Hydro/misc_subs.F90

@@ -98,16 +98,17 @@ subroutine other_hot_init(time)
 
       real(rkind), intent(in) :: time
 
-      integer :: it_now,it,i,j,k,m,mm,ntr_l,ninv,nd,itmp,itmp1,itmp2,ntmp,istat,ip,icount,n1,n2,kl
+      integer :: it_now,it,i,j,k,m,mm,ntr_l,ninv,nd,itmp,itmp1,itmp2,ntmp, &
+                 &istat,ip,icount,n1,n2,kl,nwild(2)
       real :: floatout 
       real(rkind) :: tmp,wx1,wx2,wy1,wy2,wtratio,ttt,dep,eqstate
       character(len=48) :: inputfile
       real(rkind), allocatable :: swild(:)
       real(4), allocatable :: swild9(:,:) !used in tracer nudging
       real(4), allocatable :: rwild(:,:) !used in nws=4
 
-      allocate(swild9(nvrt,mnu_pts),swild(nsa+nvrt+12+ntracers),stat=istat)
-      if(istat/=0) call parallel_abort('MISC: swild9')
+      allocate(swild(nsa+nvrt+12+ntracers),stat=istat)
+      if(istat/=0) call parallel_abort('MISC: swild')
       if(nws==4) then
         allocate(rwild(7,np_global),stat=istat)
         if(istat/=0) call parallel_abort('MISC: failed to alloc. (71)')
@@ -419,6 +420,9 @@ subroutine other_hot_init(time)
 #endif      
 
 !...  Nudging 
+      allocate(swild9(nvrt,mnu_pts),stat=istat)
+      if(istat/=0) call parallel_abort('MISC: swild9')
+
       !Shared variables for inu_tr=2 (not used if none of inu_tr=2)
       ntmp=time/step_nu_tr+1
       time_nu_tr=real(ntmp,rkind)*step_nu_tr !points to next time pt
@@ -477,6 +481,56 @@ subroutine other_hot_init(time)
           enddo !m
         endif !inu_tr(k)
       enddo !k
+      deallocate(swild9)
+
+!...  Surface TS restore
+      if(iref_ts/=0) then
+        allocate(swild9(np_global,1),stat=istat)
+        if(istat/=0) call parallel_abort('MISC: swild9(2)')
+
+        !Shared variables
+        ntmp=time/ref_ts_dt/86400.d0+1 !next time record
+        time_ref_ts=real(ntmp,rkind)*ref_ts_dt*86400.d0 ![sec]; points to next time pt
+        ref_ts1=-9999.; ref_ts2=-9999. !init
+
+        if(myrank==0) then
+          j=nf90_inq_varid(ncid_ref_ts, "reference_sst",nwild(1))
+          if(j/=NF90_NOERR) call parallel_abort('MISC: ref SST')
+          j=nf90_inq_varid(ncid_ref_ts, "reference_sss",nwild(2))
+          if(j/=NF90_NOERR) call parallel_abort('MISC: ref SSS')
+        endif 
+
+        do m=1,2 !T,S
+          swild9=-9999.
+          if(myrank==0) then
+            j=nf90_get_var(ncid_ref_ts,nwild(m),swild9(1:np_global,1), &
+     &(/1,ntmp/),(/np_global,1/))
+            if(j/=NF90_NOERR) call parallel_abort('MISC: surface relax (2)')
+          endif !myrank
+          call mpi_bcast(swild9,np_global,mpi_real,0,comm,istat)
+          do i=1,np_global
+            if(ipgl(i)%rank==myrank) then
+              ip=ipgl(i)%id
+              ref_ts1(ip,m)=swild9(i,1)
+            endif 
+          enddo !i
+
+          swild9=-9999.
+          if(myrank==0) then
+            j=nf90_get_var(ncid_ref_ts,nwild(m),swild9(1:np_global,1), &
+     &(/1,ntmp+1/),(/np_global,1/))
+            if(j/=NF90_NOERR) call parallel_abort('MISC: surface relax(2.2)')
+          endif !myrank
+          call mpi_bcast(swild9,np_global,mpi_real,0,comm,istat)
+          do i=1,np_global
+            if(ipgl(i)%rank==myrank) then
+              ip=ipgl(i)%id
+              ref_ts2(ip,m)=swild9(i,1)
+            endif
+          enddo !i
+        enddo !m: T,S
+        deallocate(swild9)
+      endif !iref_ts/=0
 
 !     The following to init th_dt*, th_time* and ath* is only done by
 !     rank 0, not bcast'ed, b/c in _step we'll continue the reading
@@ -909,7 +963,7 @@ subroutine other_hot_init(time)
 
 
       if(allocated(rwild)) deallocate(rwild)
-      deallocate(swild,swild9)
+      deallocate(swild)
 
       end subroutine other_hot_init
 

src/Hydro/schism_init.F90

@@ -195,7 +195,8 @@ subroutine schism_init(iorder,indir,iths,ntime)
      &ibcc_mean,flag_ic,start_year,start_month,start_day,start_hour,utc_start, &
      &itr_met,h_tvd,eps1_tvd_imp,eps2_tvd_imp,ip_weno, &
      &courant_weno,ntd_weno,nquad,epsilon1,i_epsilon2,epsilon2,epsilon3,ielad_weno,small_elad, &
-     &i_prtnftl_weno,inu_tr,step_nu_tr,vnh1,vnh2,vnf1,vnf2, &
+     &i_prtnftl_weno,inu_tr,step_nu_tr,vnh1,vnh2,vnf1,vnf2,iref_ts, &
+     &ref_ts_h1,ref_ts_h2,ref_ts_restore_depth,ref_ts_tscale,ref_ts_dt, &
      &moitn0,mxitn0,rtol0,iflux,inter_mom,h_bcc1,inu_elev,inu_uv, &
      &ihhat,kr_co,rmaxvel,velmin_btrack,btrack_nudge,ibtrack_test,irouse_test, &
      &inunfl,shorewafo,ic_elev,nramp_elev,inv_atm_bnd,prmsl_ref,s1_mxnbt,s2_mxnbt, &
@@ -471,6 +472,8 @@ subroutine schism_init(iorder,indir,iths,ntime)
       courant_weno=0.5_rkind; ntd_weno=1; nquad=2; epsilon1=1.d-15; i_epsilon2=1; epsilon2=1.d-10; epsilon3=1.d-25; 
       ielad_weno=0; small_elad=1.d-4; i_prtnftl_weno=0;
       inu_tr(:)=0; step_nu_tr=86400._rkind; vnh1=400._rkind; vnh2=500._rkind; vnf1=0._rkind; vnf2=0._rkind;
+      iref_ts=0; ref_ts_h1=100.d0; ref_ts_h2=60.d0; ref_ts_restore_depth=50.d0 
+      ref_ts_tscale=365.d0; ref_ts_dt=30.d0
       moitn0=50; mxitn0=1500; rtol0=1.d-12; iflux=0; inter_mom=0; 
       h_bcc1=100._rkind; inu_elev=0; inu_uv=0; 
       ihhat=1; kr_co=1; rmaxvel=5._rkind; velmin_btrack=1.d-4; btrack_nudge=9.013d-3; 
@@ -938,6 +941,20 @@ subroutine schism_init(iorder,indir,iths,ntime)
         call parallel_abort(errmsg)
       endif
 
+!...  Surface T,S relax for long-term simulations
+      if(iref_ts/=0.and.iref_ts/=1) then
+        write(errmsg,*)'Wrong iref_ts:',iref_ts
+        call parallel_abort(errmsg)
+      endif
+      if(iref_ts/=0.and.isconsv==0) then
+        write(errmsg,*)'Surface relax requires air-sea ex:',iref_ts,isconsv
+        call parallel_abort(errmsg)
+      endif
+
+      if(ref_ts_h1<=ref_ts_h2.or.ref_ts_restore_depth<=0.d0.or.ref_ts_tscale<=0.d0.or.ref_ts_dt<=0.d0) then
+        write(errmsg,*)'Wrong surface relax:',ref_ts_h1,ref_ts_h2,ref_ts_restore_depth,ref_ts_tscale,ref_ts_dt
+        call parallel_abort(errmsg)
+      endif
 
 !...  input information about hot start output
       if(nhot/=0.and.nhot/=1.or.nhot*mod(nhot_write,ihfskip)/=0) then
@@ -1417,6 +1434,11 @@ subroutine schism_init(iorder,indir,iths,ntime)
       endif
       if(istat/=0) call parallel_abort('INIT: alloc sdbt failure')
 
+      if(iref_ts/=0) then
+        allocate(ref_ts1(npa,2),ref_ts2(npa,2),ref_ts(npa,2),stat=itmp)
+        if(itmp/=0) call parallel_abort('INIT: alloc failed (57)')
+      endif
+
 !     Offline transport
       if(itransport_only/=0) then
         allocate(ts_offline(4,nvrt,nea),stat=istat)
@@ -3755,6 +3777,12 @@ subroutine schism_init(iorder,indir,iths,ntime)
         endif
       enddo !k
 
+!     Surface T,S restoration: open nc handle
+      if(iref_ts/=0.and.myrank==0) then
+        j=nf90_open(in_dir(1:len_in_dir)//'surface_restore.nc',OR(NF90_NETCDF4,NF90_NOWRITE),ncid_ref_ts)
+        if(j/=NF90_NOERR) call parallel_abort('init: surface_restore.nc not found')
+      endif !iref_ts
+
 !     Vegetation inputs: veg_*.gr3
       veg_alpha0=0.d0 !=D*Nv*Cdv/2; init; D is diameter or leaf width; Cdv is form drag (veg_cd)
       veg_h=0.d0 !veg height; not used at 2D sides

src/Hydro/schism_step.F90

@@ -297,9 +297,6 @@ subroutine schism_step(it)
      &dr_dxy(2,nvrt,nea),bcc(2,nvrt,nsa),stat=istat)
       if(istat/=0) call parallel_abort('STEP: other allocation failure')
 
-      allocate(swild9(nvrt,mnu_pts),stat=istat)
-      if(istat/=0) call parallel_abort('STEP: alloc failure (3)')
-
 !     Source
       if(if_source/=0) then
         allocate(msource(ntracers,nea),stat=istat)
@@ -1049,6 +1046,9 @@ subroutine schism_step(it)
       if(myrank==0) write(16,*)'done adjusting wind stress ...'
 
 !...  Read in tracer nudging
+      allocate(swild9(nvrt,mnu_pts),stat=istat)
+      if(istat/=0) call parallel_abort('STEP: alloc failure (3)')
+
       if(time>time_nu_tr) then
         icount3=time/step_nu_tr+2 !time record #
         do k=1,natrm
@@ -1123,6 +1123,54 @@ subroutine schism_step(it)
 !$OMP end parallel workshare
         endif !inu_tr(k)
       enddo !k
+      deallocate(swild9)
+
+!...  Read in surface relax
+      if(iref_ts/=0) then
+        allocate(swild9(np_global,1),stat=istat)
+        if(istat/=0) call parallel_abort('STEP: alloc failure (3.0)')
+        if(time>time_ref_ts) then
+          icount3=time/ref_ts_dt/86400.d0+2 !next time record #
+          ref_ts1=ref_ts2
+          if(myrank==0) then
+            j=nf90_inq_varid(ncid_ref_ts,"reference_sst",nwild(1))
+            if(j/=NF90_NOERR) call parallel_abort('STEP: surf relax (1)')
+            j=nf90_inq_varid(ncid_ref_ts,"reference_sss",nwild(2))
+            if(j/=NF90_NOERR) call parallel_abort('STEP: surf relax (2)')
+          endif
+
+          do k=1,2 !T,S
+            swild9=-9999.
+            if(myrank==0) then
+              j=nf90_get_var(ncid_ref_ts,nwild(k),swild9(1:np_global,1), &
+     &(/1,icount3/),(/np_global,1/))
+              if(j/=NF90_NOERR) call parallel_abort('STEP: surf relax(2.1)')
+            endif !myrank
+            call mpi_bcast(swild9,np_global,mpi_real,0,comm,istat)
+            do i=1,np_global
+              if(ipgl(i)%rank==myrank) then
+                ip=ipgl(i)%id
+                ref_ts2(ip,k)=swild9(i,1)
+                !Debug
+                !write(12,*)'Step nu:',i,nd,swild9(i,1)
+              endif
+            enddo !i
+          enddo !k
+          time_ref_ts=time_ref_ts+ref_ts_dt*86400.d0 ![sec]; shared among all tracers
+        endif !time>time_nu_tr
+
+!       Compute tracer
+        rat=(time_ref_ts-time)/ref_ts_dt/86400.d0
+        if(rat<0.d0.or.rat>1.d0) then
+          write(errmsg,*)'Impossible 82.2:',rat
+          call parallel_abort(errmsg)
+        endif
+!$OMP parallel workshare default(shared)
+        !may be junk (check later)
+        ref_ts=rat*ref_ts1+(1.d0-rat)*ref_ts2
+!$OMP end parallel workshare
+        deallocate(swild9)
+      endif !iref_ts/=0
 
 !...  Compute hydraulic transfer blocks together with reading in flux values
 !...  in case the blocks are taken out
@@ -7375,7 +7423,7 @@ subroutine schism_step(it)
 !...    Initialize S,T as flags
 !        tr_nd(1:2,:,:)=-99 !flags
 
-!$OMP parallel default(shared) private(i,evap,precip,sflux_e,itmp,rr,d_1,d_2,k,dp1,dp2,l,srad1,srad2,j)
+!$OMP parallel default(shared) private(i,evap,precip,sflux_e,itmp,rr,d_1,d_2,k,dp1,dp2,l,srad1,srad2,j,tmp,tmp2)
 
 !$OMP   workshare
         bdy_frc=0.d0; flx_sf=0.d0; flx_bt=0.d0
@@ -7393,15 +7441,19 @@ subroutine schism_step(it)
               if(ze(nvrt,i)-ze(kbe(i),i)<hmin_salt_ex) cycle
             endif
 
-!#ifdef      IMPOSE_NET_FLUX
-!              precip=sum(fluxprc(elnode(1:i34(i),i)))/real(i34(i),rkind) !P-E
-!              flx_sf(2,i)=tr_el(2,nvrt,i)*(-precip)/rho0
-!#else
             evap=sum(fluxevp(elnode(1:i34(i),i)))/real(i34(i),rkind)
             precip=sum(fluxprc(elnode(1:i34(i),i)))/real(i34(i),rkind)
             flx_sf(2,i)=tr_el(2,nvrt,i)*(evap-precip)/rho0
-!            endif !impose_net_flux
-!#endif
+
+            !Virtual flux (surface restoration)
+            if(iref_ts/=0) then
+              tmp=sum(ref_ts(elnode(1:i34(i),i),2))/real(i34(i),rkind)
+              if(tmp>0.d0) then
+                tmp2=max(0.d0,min(1.d0,(dpe(i)-ref_ts_h2)/(ref_ts_h1-ref_ts_h2)))
+                flx_sf(2,i)=flx_sf(2,i)+ref_ts_restore_depth/ref_ts_tscale/86400.d0*tmp2* &
+                        &(tmp-tr_el(2,nvrt,i))
+              endif !tmp>
+            endif !iref_ts/
           enddo !i
 !$OMP     end do
         endif !isconsv/=0
@@ -7423,6 +7475,16 @@ subroutine schism_step(it)
             sflux_e=sum(sflux(elnode(1:i34(i),i)))/real(i34(i),rkind)
             flx_sf(1,i)=sflux_e/rho0/shw
 
+            !Virtual flux (surface restoration)
+            if(iref_ts/=0) then
+              tmp=sum(ref_ts(elnode(1:i34(i),i),1))/real(i34(i),rkind)
+              if(tmp>-99.d0) then
+                tmp2=max(0.d0,min(1.d0,(dpe(i)-ref_ts_h2)/(ref_ts_h1-ref_ts_h2)))
+                flx_sf(1,i)=flx_sf(1,i)+ref_ts_restore_depth/ref_ts_tscale/86400.d0*tmp2* &
+                        &(tmp-tr_el(1,nvrt,i))
+              endif !tmp>
+            endif !iref_ts/
+
 !           Solar
 !           Calculate water type
 !           solar flux= R*exp(z/d_1))+(1-R)*exp(z/d_2) (d_[1,2] are attentuation depths; smaller values for muddier water)
@@ -10609,8 +10671,6 @@ subroutine schism_step(it)
       deallocate(hp_int,uth,vth,d2uv,dr_dxy,bcc)
       if(allocated(rwild)) deallocate(rwild)
       if(allocated(rwild6)) deallocate(rwild6)
-      deallocate(swild9)
-      !if(allocated(ts_offline)) deallocate(ts_offline)
 
 #ifdef USE_NAPZD
       deallocate(Bio_bdefp)

src/Readme.beta_notes

@@ -9,6 +9,7 @@ This beta notes are divided into 5 part:
 
 Github versions:
 
+- `` : added surfac T,S restoration (for large-scale long-term runs); related parameters are iref_ts,ref_ts_h1,ref_ts_h2,ref_ts_restore_depth,ref_ts_tscale,ref_ts_dt, and the input is surface_restore.nc;
 - `ab71be44` (26 Aug 2024): ptrack4 added biofouling option; new parameter ibiofoul and related values; 
 - `2f88fc5` (7 Aug 2024): changed horizontal diffusion method to filter; added an optional
                           parameter niter_hdif, and hdif.gr3 now specifies the filter strength (<=0.2);