id summary reporter owner description type status priority milestone component version resolution keywords cc 569 IMPORTANT: Active and Passive tracer and Limiting bottom stress arango arango "The following updates to the code were implemented: * Added the switch '''LtracerCLM''' to manage the tracer climatology field to process for active and passive tracers in all the standard input files ('''ocean_*.in''', biology, and sediment). For example, in '''ocean_*.in''' we have now: {{{ ! Logical switches (TRUE/FALSE) to specify which variables to process for ! tracers climatology: [1:NAT+NPT,Ngrids]. See glossary below for details. LtracerCLM == T T ! temperature, salinity, inert }}} This will allow us to only process and operate on the desired tracer climatology field. In biological tracers, it will make sense to operate on the nutrient climatology and not on the higher trophic level model constituents, for example. The tracer climatology '''tclm''' array will only contains the desired climatology fields to save memory usage. They are processed as follows to read and interpolate: {{{ ic=0 DO i=1,NT(ng) IF (LtracerCLM(i,ng)) THEN ic=ic+1 CALL get_3dfld (ng, iNLM, idTclm(i), CLM(ng)%ncid, & & 1, CLM(ng), update(1), & & LBi, UBi, LBj, UBj, 1, N(ng), 2, 1, & # ifdef MASKING & GRID(ng) % rmask, & # endif & CLIMA(ng) % tclmG(:,:,:,:,ic)) IF (exit_flag.ne.NoError) RETURN END IF END DO ... ic=0 DO itrc=1,NT(ng) IF (LtracerCLM(itrc,ng)) THEN ic=ic+1 CALL set_3dfld_tile (ng, tile, iNLM, idTclm(itrc), & & LBi, UBi, LBj, UBj, 1, N(ng), & & CLIMA(ng)%tclmG(:,:,:,:,ic), & & CLIMA(ng)%tclm (:,:,:,ic), & & update) IF (exit_flag.ne.NoError) RETURN END IF END DO }}} Notice that we have now the full tracer '''DO-'''loop. In '''step3d_t.F''', we now have: {{{ # if defined TCLM_NUDGING && defined TCLIMATOLOGY ! ! Nudge towards tracer climatology. ! IF (LtracerCLM(itrc,ng)) THEN ic=ic+1 DO k=1,N(ng) DO j=JstrR,JendR DO i=IstrR,IendR t(i,j,k,nnew,itrc)=t(i,j,k,nnew,itrc)+ & & dt(ng)*Tnudgcof(i,j,itrc)* & & (tclm(i,j,k,ic)-t(i,j,k,nnew,itrc)) END DO END DO END DO END IF # endif }}} * Added processing of all passive tracer quadratic terms: <'''t*t'''>, <'''u*t'''>, <'''v*t'''>, <'''Huon*t'''>, and <'''Hvom*t'''>. This will facilitate computing budgets for any passive tracer. The desired fields are processed and written into the average files according to the logical switches: {{{ Aout(idTTav) == F F ! temp2, ... quadratic tracer terms Aout(idUTav) == F F ! utemp, ... quadratic tracer terms Aout(idVTav) == F F ! vtemp, ... quadratic tracer terms Aout(iHUTav) == F F ! Huontemp, ... tracer volume flux, Aout(iHVTav) == F F ! Hvomtemp, ... tracer volume flux, }}} This also required changes to all the standard input files ('''ocean_*.in''', biology, and sediment). '''Warming:''' The file '''varinfo.dat''' was also modified for the generic quadratic tracers metadata: {{{ 'tracer2' ! Output 'time-averaged squared tracer' 'tracer2' ! [tracer2] 'tracer2, scalar, series' 'ocean_time' 'idTTav(itrc)' 'r3dvar' 1.0d0 'Huontracer' ! Output 'time-averaged tracer u-volume flux' 'meter3 second-1 tracer' ! [m3/s tracer] 'Huontracer, scalar, series' 'ocean_time' 'iHUTav(itrc)' 'u3dvar' 1.0d0 'utracer' ! Output 'time-averaged u-momentum times tracer' 'meter second-1 tracer' ! [m/s tracer] 'utracer, scalar, series' 'ocean_time' 'idUTav(itrc)' 'u3dvar' 1.0d0 'Hvomtracer' ! Output 'time-averaged tracer v-volume flux' 'meter3 second-1 tracer' ! [m3/s tracer] 'Hvomtracer, scalar, series' 'ocean_time' 'iHVTav(itrc)' 'v3dvar' 1.0d0 'vtracer' ! Output 'time-averaged v-momentum times tracer' 'meter second-1 tracer' ! [m/s tracer] 'vtracer, scalar, series' 'ocean_time' 'idVTav(itrc)' 'v3dvar' 1.0d0 }}} The metadata is processed in a generic way in '''mod_ncparam.F'''. Many thanks to John Wilkin and Aboozar Tabatabai for suggesting this capability. * Added the new C_preprocessing option '''LIMIT_BSTRESS''' to limit the bottom momentum stress in '''set_vbc.F''' to preserve bottom velocity direction, as [https://www.myroms.org/forum/viewtopic.php?f=14&t=2531&hilit=limit+bottom+stress#p9477 suggested] by John Warner. For example, for linear bottom stress we now have: {{{ ! ! Set linear bottom stress. ! DO j=Jstr,Jend DO i=IstrU,Iend bustr(i,j)=0.5_r8*(rdrag(i-1,j)+rdrag(i,j))* & & u(i,j,1,nrhs) # ifdef LIMIT_BSTRESS cff1=cff*0.5_r8*(Hz(i-1,j,1)+Hz(i,j,1)) bustr(i,j)=SIGN(1.0_r8, bustr(i,j))* & & MIN(ABS(bustr(i,j)), & & ABS(u(i,j,1,nrhs))*cff1) # endif END DO END DO DO j=JstrV,Jend DO i=Istr,Iend bvstr(i,j)=0.5_r8*(rdrag(i,j-1)+rdrag(i,j))* & & v(i,j,1,nrhs) # ifdef LIMIT_BSTRESS cff1=cff*0.5_r8*(Hz(i,j-1,1)+Hz(i,j,1)) bvstr(i,j)=SIGN(1.0_r8, bvstr(i,j))* & & MIN(ABS(bvstr(i,j)), & & ABS(v(i,j,1,nrhs))*cff1) # endif END DO END DO }}} Similar strategy is used for quadratic and logarithmic formulations. I still need to work out the '''TLM''', '''RPM''', and '''ADM''' transformation for this routine, * Modified '''get_varcoords.F''' to expand the processing of the '''coordinates''' attribute in input NetCDF forcing files: {{{ float my_var(time, lat, lon) ; my_var:long_name = ""my variable long name"" ; my_var:units = ""my variable units"" ; my_var:coordinates = ""lon lat time"" ; my_var:time = ""time"" ; ! ! The following ""coordinates"" attribute is also allowed: ! my_var:coordinates = ""lon lat"" ; }}} This is done for '''CF''' compliance. * Corrected a bug in '''t3dmix4_iso.h''' when multiplying by the diffusion coefficient. This is a bad one! Changes are not required in the '''TLM''', '''RPM''', and '''ADM''' versions of this routine since these codes operate the diffusion coefficient factor at the end of the flux computation. This is done because in the linearized codes the operation needs to be recursive. Therefore, the bug in the '''NLM''' due to the split scheme is not present in the '''TLM''', '''RPM''', and '''ADM''' codes. * Update all the standard input scripts in the '''test''' repository." upgrade closed major Release ROMS/TOMS 3.6 Nonlinear 3.6 Done