! source file: /gxfs_work/geomar/smomw113/UVic_ESCM/2.9_dk_0814/updates/11_valley/source/mom/tracer.F subroutine tracer (joff, js, je, is, ie) !======================================================================= ! compute tracers at "tau+1" for rows js through je in the MW. ! input: ! joff = offset relating "j" in the MW to latitude "jrow" ! js = starting row in the MW ! je = ending row in the MW ! is = starting longitude index in the MW ! ie = ending longitude index in the MW !======================================================================= implicit none character(120) :: fname, new_file_name integer istrt, iend, i, k, j, ip, kr, jq, n, jp, jrow, iou, js integer je, limit, joff, is, ie, kmx, m, kb, idiag, index integer it(10), iu(10), ib(10), ic(10), nfnpzd, mfnpzd, mxfnpzd integer id_time, id_xt, id_yt, id_zt integer fe_jlo, fe_m, fe_k, fe_n parameter (fe_n = 14) logical inqvardef, exists real rctheta, declin, gl, impo, expo, npp, time real remi, excr, graz, morp, morpt, morz, temp, swr, dayfrac real graz_Det, graz_Z, avej, avej_D, gmax, no3P, po4P, po4_D real phin, dz, prca, dprca, nud, bct, tap, fo2, so2, ai, hi, hs real npp_D, graz_D, morp_D, no3flag, deni, nfix, felimit real t_i, t_j, dz_t2r, dz_tr, dz_wtr, dx_t2r, dx_tr, dy_t2r real dy_tr, adv_tx, adv_ty, adv_tz, adv_txiso, adv_tyiso real adv_tziso, diff_tx, diff_ty, diff_tz, zmax, cont, drho real drhom1, wt, ahbi_cstr, ahbi_csu_dyur, gamma, rrstd, fy, fyz real bctz, felimit_D real Paulmier_a, Paulmier_z, Paulmier_R0, o2thresh, no3thresh real fe_dy, fe_conc0,fe_conc, fe_x(fe_n), fe_y(fe_n) real sss,sst,t_in,s_in,sit_in,pt_in,atmpres,co2_in,dicsat &, ta_in, dic_in, depth, phlo, phhi logical co2calc_debug include "size.h" include "param.h" include "pconst.h" include "stdunits.h" include "accel.h" include "coord.h" include "cregin.h" include "csbc.h" include "emode.h" include "grdvar.h" include "hmixc.h" include "levind.h" include "mw.h" include "scalar.h" include "switch.h" include "timeavgs.h" include "tmngr.h" include "vmixc.h" include "diaga.h" include "ice.h" include "atm.h" include "npzd.h" parameter (istrt=2, iend=imt-1) real twodt(km) real snpzd(ntnpzd), tnpzd(ntnpzd) real src(imt,km,jsmw:jemw,nsrc) include "isopyc.h" include "fdift.h" !cwk next !_bailout ! o2thresh = threshold for oxic metabolism, mmol/m3 ! This is used with fo2 to limit oxygen consumption below concentrations of 5umol/kg as recommended in OCMIP. ! With _no_sulphidic, I now compute fo2 also before npzd_src. o2thresh = 5. !----------------------------------------------------------------------- ! bail out if starting row exceeds ending row !----------------------------------------------------------------------- if (js .gt. je) return !----------------------------------------------------------------------- ! limit the longitude indices based on those from the argument list ! Note: this is currently bypassed. istrt and iend are set as ! parameters to optimize performance !----------------------------------------------------------------------- ! istrt = max(2,is) ! iend = min(imt-1,ie) !----------------------------------------------------------------------- ! build coefficients to minimize advection and diffusion computation !----------------------------------------------------------------------- limit = min(je+1+joff,jmt) - joff do j=js,limit jrow = j + joff do i=istrt-1,iend cstdxtr(i,j) = cstr(jrow)*dxtr(i) cstdxt2r(i,j) = cstr(jrow)*dxtr(i)*p5 cstdxur(i,j) = cstr(jrow)*dxur(i) ah_cstdxur(i,j) = diff_cet*cstr(jrow)*dxur(i) enddo enddo !----------------------------------------------------------------------- ! calculation of biological interactions !----------------------------------------------------------------------- declin = sin((mod(relyr,1.) - 0.22)*2.*pi)*0.4 ! declination do k=1,km twodt(k) = c2dtts*dtxcel(k) nbio(k) = twodt(k)/dtnpzd dtbio(k) = twodt(k)/nbio(k) rdtts(k) = 1./twodt(k) rnbio(k) = 1./nbio(k) enddo tap = 2.*alpha*par if (joff.gt.0) then write(20,*) 'stopping in tracer.f, line 409, or so' stop endif do j=js,je jrow = j + joff do i=is,ie if (kmt(i,jrow) .gt. 0) then ai = aice(i,jrow,2) hi = hice(i,jrow,2) hs = hsno(i,jrow,2) ! calculate day fraction and incoming solar ! angle of incidence = lat - declin, refraction index = 1.33 rctheta = max(-1.5, min(1.5, tlat(i,jrow)/radian - declin)) rctheta = kw/sqrt(1. - (1. - cos(rctheta)**2.)/1.33**2.) dayfrac = min( 1., -tan(tlat(i,jrow)/radian)*tan(declin)) dayfrac = max(1e-12, acos(max(-1., dayfrac))/pi) swr = dnswr(i,jrow)*1e-3*(1. + ai*(exp(-ki*(hi + hs)) - 1.)) expo = 0.0 impo = 0.0 phin = 0.0 ! integrated phytoplankton prca = 0.0 ! integrated production of calcite !cwk next !_bailout kmx = min(kmt(i,jrow), kpzd) do k=1,kmx !----------------------------------------------------------------------- ! limit tracers to positive values !----------------------------------------------------------------------- ! { cwk 29.03.22 ! UVic version differ about the best approach where to limit tracers to ! positive values. In other UVic version this is not done here, but within ! npzd_src.F. This is related to the two (or more, parameter dependent) ! bio-loops in npzd_src.f. I stick to David's original / my version for ! long term consistency of model output. ! cwk 29.03.22 } tnpzd(1) = max(t(i,k,j,ipo4,taum1), trcmin) tnpzd(2) = max(t(i,k,j,iphyt,taum1), trcmin) tnpzd(3) = max(t(i,k,j,izoop,taum1), trcmin) tnpzd(4) = max(t(i,k,j,idetr,taum1), trcmin) tnpzd(5) = max(t(i,k,j,ino3,taum1), trcmin) tnpzd(6) = max(t(i,k,j,idiaz,taum1), trcmin) swr = swr*exp(-kc*phin) phin = (tnpzd(6) + tnpzd(2))*dzt(k) gl = tap*swr*exp(ztt(k)*rctheta) impo = expo*dztr(k) bct = bbio**(cbio*t(i,k,j,itemp,taum1)) if (t(i,k,j,itemp,taum1).gt.20) then bctz = (0.5*(tanh(t(i,k,j,io2,taum1)*1000. - 8.)+1)) & *bbio**(cbio*20) else bctz = (0.5*(tanh(t(i,k,j,io2,taum1)*1000. - 8.)+1)) & *bct endif !----------------------------------------------------------------------- ! Fe-mask model !----------------------------------------------------------------------- cwk what follows is the normal (non-pipe) iron code from Dave if (k.le.3) then ! create x (time) and y (data) arrays for fe interpolation ! first zero them out just in case fe_y(:) = 0 fe_x(:) = 0 ! write in values for days 0 and 365 for interp. bounds fe_y(1) = fe_dissolved(i,j,k,1) fe_x(1) = 0 fe_y(14) = fe_dissolved(i,j,k,12) fe_x(14) = 365 ! now create the rest of the array based on the BLING ! data which is from day 16 of each month do m=2,13 fe_y(m) = fe_dissolved(i,j,k,m-1) if (m.eq.2) then fe_x(2) = 16 else if (m.eq.3) then fe_x(3) = 47 else if (m.eq.4) then fe_x(4) = 75 else if (m.eq.5) then fe_x(5) = 106 else if (m.eq.6) then fe_x(6) = 136 else if (m.eq.7) then fe_x(7) = 167 else if (m.eq.8) then fe_x(8) = 197 else if (m.eq.9) then fe_x(9) = 228 else if (m.eq.10) then fe_x(10) = 259 else if (m.eq.11) then fe_x(11) = 289 else if (m.eq.12) then fe_x(12) = 320 else if (m.eq.13) then fe_x(13) = 350 endif enddo fe_jlo = 2 fe_m = 4 ! find fe data day index call hunt (fe_x,fe_n,dayoyr,fe_jlo) ! initialize the fe data array at the right day fe_k = min(max(fe_jlo-(fe_m-1)/2,1),fe_n+1-fe_m) ! interpolate the fe data, note this does not use the whole array call polint (fe_x(fe_k),fe_y(fe_k) &, fe_m,dayoyr,fe_conc,fe_dy) ! calculate the fe limitation term felimit = fe_conc/(kfe + fe_conc) felimit_D = fe_conc/(kfe_D + fe_conc) else felimit = 1 felimit_D = 1 endif ! decrease remineralisation rate in oxygen minimum zone nud = nud0*(0.65+0.35*tanh(t(i,k,j,io2,taum1)*1000.-6.)) !----------------------------------------------------------------------- ! call the npzd model !----------------------------------------------------------------------- call npzd_src (tnpzd, nbio(k), dtbio(k), gl, bct, impo &, dzt(k), dayfrac, wd(k), rkwz(k), nud &, snpzd, expo, graz, morp, morz &, graz_Det, graz_Z &, npp, morpt, remi, excr &, npp_D, graz_D, morp_D, nfix &, felimit, felimit_D &, bctz & ) ! These are source/sink terms snpzd(1:4) = snpzd(1:4)*rdtts(k) snpzd(5:6) = snpzd(5:6)*rdtts(k) expo = expo*rnbio(k) rexpo(i,k,j) = expo rgraz(i,k,j) = graz*rnbio(k) rgraz_Det(i,k,j) = graz_Det*rnbio(k) rgraz_Z(i,k,j) = graz_Z*rnbio(k) rmorp(i,k,j) = morp*rnbio(k) rmorz(i,k,j) = morz*rnbio(k) rnpp(i,k,j) = npp*rnbio(k) rmorpt(i,k,j) = morpt*rnbio(k) rremi(i,k,j) = remi*rnbio(k) rexcr(i,k,j) = excr*rnbio(k) rnpp_D(i,k,j) = npp_D*rnbio(k) rgraz_D(i,k,j) = graz_D*rnbio(k) rmorp_D(i,k,j) = morp_D*rnbio(k) rnfix(i,k,j) = nfix*rnbio(k) ta_wd(k)=wd(k)*dzt(k)*86400./100. !----------------------------------------------------------------------- ! calculate detritus at the bottom and remineralize !----------------------------------------------------------------------- if (k .eq. kmt(i,jrow)) then rremi(i,k,j) = rremi(i,k,j) + expo snpzd(1) = snpzd(1) + redptn*expo snpzd(5) = snpzd(5) + expo endif !----------------------------------------------------------------------- ! set major source/sink terms !----------------------------------------------------------------------- src(i,k,j,ispo4) = snpzd(1) src(i,k,j,isphyt) = snpzd(2) src(i,k,j,iszoop) = snpzd(3) src(i,k,j,isdetr) = snpzd(4) src(i,k,j,isno3) = snpzd(5) src(i,k,j,isdiaz) = snpzd(6) if (k.gt.1) then src(i,k,j,ispo4r) = src(i,k,j,ispo4) src(i,k,j,isno3r) = src(i,k,j,isno3) endif ! production of calcite dprca = (morp+morz+(graz+graz_Z)*(1.-gamma1)) & *capr & *redctn*rnbio(k) prca = prca + dprca*dzt(k) src(i,k,j,isdic) = ( & snpzd(1)*redctp & - dprca) if (k.gt.1) & src(i,k,j,isdicr) = & (snpzd(1)*redctp) src(i,k,j,isalk) = ( & -snpzd(1)*redntp*1.e-3 & - 2.*dprca) if (k.gt.1) & src(i,k,j,isalkr) = & (-1)*snpzd(1)*redntp*1.e-3 !----------------------------------------------------------------------- ! accumulate time averages !----------------------------------------------------------------------- if (timavgperts .and. .not. euler2) then ta_rnpp(i,k,jrow) = ta_rnpp(i,k,jrow) + rnpp(i,k,j) ta_rgraz(i,k,jrow) = ta_rgraz(i,k,jrow) + rgraz(i,k,j) ta_rgraz_Z(i,k,jrow) = ta_rgraz_Z(i,k,jrow) & + rgraz_Z(i,k,j) ta_rgraz_Det(i,k,jrow) = ta_rgraz_Det(i,k,jrow) & + rgraz_Det(i,k,j) ta_rmorp(i,k,jrow) = ta_rmorp(i,k,jrow) + rmorp(i,k,j) ta_rmorpt(i,k,jrow)= ta_rmorpt(i,k,jrow) + rmorpt(i,k,j) ta_rmorz(i,k,jrow) = ta_rmorz(i,k,jrow) + rmorz(i,k,j) ta_rexcr(i,k,jrow) = ta_rexcr(i,k,jrow) + rexcr(i,k,j) ta_rnpp_D(i,k,jrow) = ta_rnpp_D(i,k,jrow) & + rnpp_D(i,k,j) ta_rgraz_D(i,k,jrow) = ta_rgraz_D(i,k,jrow) & + rgraz_D(i,k,j) ta_rmorp_D(i,k,jrow) = ta_rmorp_D(i,k,jrow) & + rmorp_D(i,k,j) ta_rnfix(i,k,jrow) = ta_rnfix(i,k,jrow) + rnfix(i,k,j) endif ! calculate total export to get total import for next layer expo = expo*dzt(k) enddo ! k-loop which started in 420 !----------------------------------------------------------------------- ! set o2 sinks-minus-sources !----------------------------------------------------------------------- kmx = kmt(i,jrow) do k=1,kmx fo2 = 0.5*tanh(t(i,k,j,io2,taum1)*1000. - o2thresh) ! sink of oxygen (so2) ! O2 is needed to generate the equivalent of NO3 from N2 during N2 fixation ! 0.5 H2O + 0.5 N2+1.25O2 -> HNO3 ! note that so2 is -dO2/dt so2 = src(i,k,j,ispo4)*redotp & + rnfix(i,k,j)*1.25e-3 src(i,k,j,iso2) = -so2*(0.5 + fo2) ! last endif: of _respi_data & _respi_data_transient (l 749) ! last endif: of defined _respi_data & defined _respi_data_repyr ! ... accumulated diagnostics ! (Note, runs prior to 28.02.2018 have wrong o_o2sms output) if (timavgperts .and. .not. euler2) then ta_respi_data(i,k,j) = ta_respi_data(i,k,j) & + src(i,k,j,iso2) ta_dicr_sms_data(i,k,j) = ta_dicr_sms_data(i,k,j) & + src(i,k,j,isdicr) ta_alkr_sms_data(i,k,j) = ta_alkr_sms_data(i,k,j) & + src(i,k,j,isalkr) endif if (k.gt.1) & src(i,k,j,iso2r) = src(i,k,j,iso2) !----------------------------------------------------------------------- ! calculate denitrification, its effect on alkalinity and ideal. tracers !----------------------------------------------------------------------- ! add denitrification as source term for NO3 no3flag = 0.5+sign(0.5,t(i,k,j,ino3,taum1)-trcmin) ! 800 = 0.8*1000 = (elec/mol O2)/(elec/mol NO3)*(mmol/mol) deni = max(0., 800.*no3flag*so2*(0.5 - fo2)) src(i,k,j,isno3) = src(i,k,j,isno3) - deni rdeni(i,k,jrow) = deni if (k.gt.1) & src(i,k,j,isno3d) = (-1.) * deni !----------------------------------------------------------------------- ! alkalinity corrections: denitrification, n2-fixation, sulphate reduction, etc !----------------------------------------------------------------------- ! Correct the alkalinty effect of denitrification based on the stoichiometric model ! formulated in Paulmier et al. 2009 BG cwk In the following I added more comments in order to better understand what is done here. cwk In particularly, it was confusing that the code deviates from equation given in Paulmier. cwk However, the computed R0 values nevertheless agree! This is documented below. cwk For some unexplained reason the term Paulmier_a is here the C:N ratio instead of the C:P ratio Paulmier_a = 1.e3*redctn cwk Excess hydrogen, z, for complete respiration with NO3 as N-endproduct; Eq 27 in Paulmier cwk z = 4 * rO2:P - 4a -8d, with rO2:P = R0 + 2d; a is the C:P ratio of organic matter, d is the N:P ratio cwk For some unexplained reason Paulmier_z uses the C:N ratio instead of the C:P ratio?? Paulmier_z = 4*1.e3*redotp - 4.*Paulmier_a - 8.*redntp cwk Compute R0 in the absence of knowing the hydrogen and oxygen contend of organic matter, using cwk equation 26 of Paulmier cwk Given typical UVic parameters, redctn=6.625, redctp=106, redntp =16, redotp=160 cwk equation 27 gives z=640 - 424 - 128 = 88 cwk equation Paulmier_z = 640 - 26.5 - 128 = 485.5 Paulmier_R0 = Paulmier_a + 0.25*Paulmier_z cwk R0 based on z from equ 27 gives: 106 + 22 = 128 cwk R0 based on Paulmier_z = 6.625 + 121.375 = 128 src(i,k,j,isalk) = src(i,k,j,isalk) & + no3flag*src(i,k,j,ispo4)*(0.5-fo2) cwk Paulmier et al equation from their table 1 is: 4/5 R0 + 3/5d -1 cwk The term -1 reflects the alkalinity effect of P (which is ignored in Uvic) cwk The term (3/5+1)d instead of 3/5d backcorrects the already considers nitrate effect on alk cwk (src(i,k,j,isalk) = -snpzd(1)*redntp*1.e-3), see above & *(4./5.*Paulmier_R0 + (3./5. +1.)*redntp) * 1.e-3 cwk gives 0.8*128 + (0.6+1)*16 = 102.4 + 25.6 = 128 ! Now account for N2 fixation (ALK production is tied to PO4 change and ! thus in the case of N2 fixation was not correct without this fix). src(i,k,j,isalk) = src(i,k,j,isalk) & - rnfix(i,k,j)*1.e-3 if (k.gt.1) & src(i,k,j,isalkr) = src(i,k,j,isalkr) ! next two lines include the effect of denitrification & + no3flag*src(i,k,j,ispo4)*(0.5-fo2) & *(4./5.*Paulmier_R0 + (3./5. +1.)*redntp) * 1.e-3 ! next line corrects for the effect of N2-fix (hardly important for k.gt.1 & - rnfix(i,k,j)*1.e-3 ! last endif: of _n2o (line 1345) ! last endif: of _npzd_nitrogen (l 875) enddo ! of do over k (line 725), beginning of block: set o2 sinks-minus-sources ! last endif: of _npzd_o2 (l 725) !----------------------------------------------------------------------- ! remineralize calcite !----------------------------------------------------------------------- kmx = kmt(i,jrow) do k=1,kmx-1 src(i,k,j,isdic) = src(i,k,j,isdic) & + prca*rcak(k) src(i,k,j,isalk) = src(i,k,j,isalk) & + 2.*prca*rcak(k) if (k.eq.1) & src(i,k,j,isalks) = 0. if (k.gt.1) & src(i,k,j,isalks) = & 2.*prca*rcak(k) enddo src(i,kmx,j,isdic) = src(i,kmx,j,isdic) & + prca*rcab(kmx) src(i,kmx,j,isalk) = src(i,kmx,j,isalk) & + 2.*prca*rcab(kmx) if (kmx.gt.1) & src(i,kmx,j,isalks) = 0. & + 2.*prca*rcab(kmx) ! wk, 20.11.19, bottom water calcite degradation error corrected ! wk, 08.01.20, additional issue with bottom water calcite dissolution corrected ! The following line numbers are outdated due to new code additions. ! Also with all the assimilation code there are several instances where the respective ! variables are modified. This always needs a close inspection by checking code/tracer.f ! for src(i,k,j,iso2r) see code in line 1218ff ! for src(i,k,j,ispo4r) see code in line 879ff ! for src(i,k,j,isno3r) see code in line 880ff ! for src(i,k,j,isdicr) see code in line 907, 1101, 1131, 1169 ! for src(i,k,j,isalkr) see code in line 926, 1105, 1135, 1172, 1334 ! for src(i,k,j,isalks) see code below in line 656ff ! for src(i,k,j,isno3d) see code in line 614ff !----------------------------------------------------------------------- ! accumulate time averages for full depth variables !----------------------------------------------------------------------- if (timavgperts .and. .not. euler2) then kmx = kmt(i,jrow) expo = prca ta_rprocal(i,jrow) = ta_rprocal(i,jrow) + prca do k=1,kmx expo = expo*dztr(k) ta_rremi(i,k,jrow) = ta_rremi(i,k,jrow) + rremi(i,k,j) ta_rexpo(i,k,jrow) = ta_rexpo(i,k,jrow) + rexpo(i,k,j) cwk 14.07.22 next two lines be aware that below the variable expo is reasigned (i.e. f. CaCO3 export) cwk this is very old ('dirty', I think) code expo = expo - prca*rcak(k) ta_rexpocal(i,k,jrow) = ta_rexpocal(i,k,jrow) + expo expo = expo*dzt(k) ta_rdeni(i,k,jrow) = ta_rdeni(i,k,jrow) + rdeni(i,k,j) enddo endif ! last endif: of _time_averages && _save_npzd (line 1175) endif enddo enddo ! last endif: of _npzd (line 404 ! last endif: of _carbon_fnpzd (line 1225) cwk 4.01.19 I moved the code for age change of the ideal age tracer to here cwk i.e. outside 1 cwk 12.03.19, however, I did not include the two outer do j, do i loops! cwk added now !----------------------------------------------------------------------- ! increment ideal age !----------------------------------------------------------------------- do j=js,je jrow = j + joff do i=is,ie if (kmt(i,jrow) .gt. 0) then kmx = kmt(i,jrow) do k=1,kmx src(i,k,j,isidealage) = 1.0 / 3.6e3 /24. enddo endif enddo enddo !----------------------------------------------------------------------- cwk 4.01.09 BGC sms are done by now, compute the transport terms: !----------------------------------------------------------------------- !----------------------------------------------------------------------- ! solve for one tracer at a time ! n = 1 => temperature ! n = 2 => salinity ! n > 2 => other tracers (if applicable) !----------------------------------------------------------------------- do n=1,nt !----------------------------------------------------------------------- ! calculate advective tracer flux !----------------------------------------------------------------------- call adv_flux (joff, js, je, is, ie, n) !----------------------------------------------------------------------- ! calculate diffusive flux across eastern and northern faces ! of "T" cells due to various parameterizations for diffusion. !----------------------------------------------------------------------- ! diffusive flux on eastern face of "T" cells do j=js,je do k=1,km do i=istrt-1,iend diff_fe(i,k,j) = & ah_cstdxur(i,j)* & (t(i+1,k,j,n,taum1) - t(i,k,j,n,taum1)) enddo enddo enddo ! diffusive flux on northern face of "T" cells ! (background for isopycnal mixing) do j=js-1,je jrow = j + joff do k=1,km do i=istrt,iend diff_fn(i,k,j) = & diff_cnt* & csu_dyur(jrow)*(t(i,k,j+1,n,taum1) - t(i,k,j,n,taum1)) enddo enddo enddo ! last endif: of _isopycmix ! last endif: of !_biharmonic || _bryan_lewis_horizontal ! lase endif of _consthmix !----------------------------------------------------------------------- ! calculate diffusive flux across bottom face of "T" cells !----------------------------------------------------------------------- do j=js,je do k=1,km-1 do i=istrt,iend diff_fb(i,k,j) = diff_cbt(i,k,j)*dzwr(k)* & (t(i,k,j,n,taum1) - t(i,k+1,j,n,taum1)) enddo enddo enddo !----------------------------------------------------------------------- ! compute isopycnal diffusive flux through east, north, ! and bottom faces of T cells. !----------------------------------------------------------------------- call isoflux (joff, js, je, is, ie, n) !----------------------------------------------------------------------- ! set surface and bottom vert b.c. on "T" cells for diffusion ! and advection. for isopycnal diffusion, set adiabatic boundary ! conditions. ! note: the b.c. at adv_fb(i,k=bottom,j) is set by the above code. ! However, it is not set when k=km so it is set below. ! adv_fb(i,km,j) is always zero (to within roundoff). !----------------------------------------------------------------------- do j=js,je jrow = j + joff do i=istrt,iend kb = kmt(i,jrow) diff_fb(i,0,j) = stf(i,j,n) diff_fb(i,kb,j) = btf(i,j,n) adv_fb(i,0,j) = adv_vbt(i,0,j)*(t(i,1,j,n,tau) + & t(i,1,j,n,tau)) adv_fb(i,km,j) = adv_vbt(i,km,j)*t(i,km,j,n,tau) enddo enddo !----------------------------------------------------------------------- ! set source term for "T" cells !----------------------------------------------------------------------- source(:,:,:) = c0 if (itrc(n) .ne. 0) then do j=js,je do k=1,km do i=istrt,iend source(i,k,j) = src(i,k,j,itrc(n)) enddo enddo enddo endif !----------------------------------------------------------------------- ! solve for "tau+1" tracer using statement functions to represent ! each component of the calculation !----------------------------------------------------------------------- ! 1st: solve using all components which are treated explicitly do j=js,je jrow = j + joff do k=1,km twodt(k) = c2dtts*dtxcel(k) do i=istrt,iend t(i,k,j,n,taup1) = t(i,k,j,n,taum1) + twodt(k)*( & DIFF_Tx(i,k,j) + DIFF_Ty(i,k,j,jrow,n) + DIFF_Tz(i,k,j) & - ADV_Tx(i,k,j) - ADV_Ty(i,k,j,jrow,n) - ADV_Tz(i,k,j) & + source(i,k,j) & )*tmask(i,k,j) enddo enddo enddo ! 2nd: add in portion of vertical diffusion handled implicitly call ivdift (joff, js, je, istrt, iend, n, twodt) do j=js,je call setbcx (t(1,1,j,n,taup1), imt, km) enddo !----------------------------------------------------------------------- ! construct diagnostics associated with tracer "n" !----------------------------------------------------------------------- call diagt1 (joff, js, je, istrt, iend, n, twodt) !----------------------------------------------------------------------- ! end of tracer component "n" loop !----------------------------------------------------------------------- enddo ! of do n=1,nt (line 1400), i.e. 'solve for one tracer at a time' !----------------------------------------------------------------------- cwk !----------------------------------------------------------------------- !----------------------------------------------------------------------- ! explicit convection: adjust column if gravitationally unstable !----------------------------------------------------------------------- call convct2 (t(1,1,1,1,taup1), joff, js, je, is, ie, kmt) do j=js,je do n=1,nt call setbcx (t(1,1,j,n,taup1), imt, km) enddo enddo if (timavgperts .and. eots) then if (joff .eq. 0) nta_conv = nta_conv + 1 do j=js,je jrow = j + joff do i=istrt,iend ta_totalk(i,jrow) = ta_totalk(i,jrow) + totalk(i,j) ta_vdepth(i,jrow) = ta_vdepth(i,jrow) + vdepth(i,j) ta_pe(i,jrow) = ta_pe(i,jrow) + pe(i,j) enddo enddo endif !----------------------------------------------------------------------- ! construct diagnostics after convection !----------------------------------------------------------------------- idiag = 10 call diagt2 (joff, js, je, istrt, iend, idiag) !----------------------------------------------------------------------- ! filter tracers at high latitudes !----------------------------------------------------------------------- if (istrt .eq. 2 .and. iend .eq. imt-1) then call filt (joff, js, je) else write (stdout,'(a)') & 'Error: filtering requires is=2 and ie=imt-1 in tracer' stop '=>tracer' endif do n=1,nt do j=js,je call setbcx (t(1,1,j,n,taup1), imt, km) enddo enddo !----------------------------------------------------------------------- ! construct diagnostics after filtering (for total dT/dt) !----------------------------------------------------------------------- idiag = 1 call diagt2 (joff, js, je, istrt, iend, idiag) ! ---------------------------------------------------------------------- ! restore t(iidealage,taup1) to 0.0 in the surface layer ! ! ---------------------------------------------------------------------- do j=js,je ! I dont really use the next line ..... but the output looks fine jrow = j + joff do i=istrt,iend t(i,1,j,iidealage,taup1)= 0.0 enddo enddo ! ---------------------------------------------------------------------- ! restore the remineralised tracer in the surface layer to zero ! ! ---------------------------------------------------------------------- do j=js,je do i=istrt,iend t(i,1,j,io2r,taup1) = 0.0 t(i,1,j,ipo4r,taup1) = 0.0 t(i,1,j,ino3r,taup1) = 0.0 t(i,1,j,idicr,taup1) = 0.0 t(i,1,j,ialkr,taup1) = 0.0 t(i,1,j,ialks,taup1) = 0.0 t(i,1,j,ino3d,taup1) = 0.0 enddo enddo ! next pc endif is of _tou (line 3371 / 010923) ! bailed out code moved to dye_tracer.F, starting here ! bailed out code moved to dye_tracer.F, ending here here ! ---------------------------------------------------------------------- ! restore preformed tracers in the surface layer to the concentration ! of the respective reference tracer ! ---------------------------------------------------------------------- do j=js,je do i=istrt,iend t(i,1,j,ipreo2,taup1)= t(i,1,j,io2,taup1) t(i,1,j,iprepo4,taup1)= t(i,1,j,ipo4,taup1) t(i,1,j,ipreno3,taup1)= t(i,1,j,ino3,taup1) t(i,1,j,ipredic,taup1)= t(i,1,j,idic,taup1) t(i,1,j,iprealk,taup1)= t(i,1,j,ialk,taup1) enddo enddo cwk / draft July 2020, corrected Feb 2023 ! ---------------------------------------------------------------------- ! compute saturated DIC value for the surface ocean (k=1) ! at model run time (from pCO2atm and TA) ! ---------------------------------------------------------------------- do j=js,je do i=istrt,iend if (tmsk(i,j) .ge. 0.5) then sss = 1000.0*sbc(i,j,isss) + 35.0 sst = t(i,1,j,itemp,taum1) sst = min(35.,max(sst,-2.)) sss = min(45.,max(sss,0.)) t_in = sst s_in = sss sit_in = 7.6875e-03 !mol/m^3 pt_in = 0.5125e-3 !mol/m^3 atmpres = 1.0 !atm ta_in = t(i,1,j,ialk,taum1) phlo=6. phhi=10. depth = 0. co2calc_debug=.FALSE. call get_co2ccn(co2_in) ! get current atmospheric pCO2 if (co2calc_debug) write(20,*) 'pCO2atm:', co2_in call co2calc_TAfCO2 (t_in, s_in, ta_in, co2_in, pt_in &, sit_in, atmpres, depth, phlo, phhi &, co2calc_debug, dicsat) t(i,1,j,iDICsat1,taup1) = dicsat endif enddo enddo cwk / !----------------------------------------------------------------------- ! if needed, construct the Atmos S.B.C.(surface boundary conditions) ! averaged over this segment ! eg: SST and possibly SSS !----------------------------------------------------------------------- call asbct (joff, js, je, istrt, iend, isst, itemp) call asbct (joff, js, je, istrt, iend, isss, isalt) call asbct (joff, js, je, istrt, iend, issdic, idic) call asbct (joff, js, je, istrt, iend, issalk, ialk) call asbct (joff, js, je, istrt, iend, isso2, io2) call asbct (joff, js, je, istrt, iend, isso2abiot &, io2abiot) call asbct (joff, js, je, istrt, iend, issDICsat1 &, iDICsat1) call asbct (joff, js, je, istrt, iend, issDICsat2 &, iDICsat2) call asbct (joff, js, je, istrt, iend, isspo4, ipo4) call asbct (joff, js, je, istrt, iend, issno3, ino3) return end subroutine get_co2ccn(co2ccn_out) ! output: ! co2ccn_out = current atmospheric pCO2 implicit none real co2ccn_out include "cembm.h" co2ccn_out=co2ccn return end subroutine diagt1 (joff, js, je, is, ie, n, twodt) !----------------------------------------------------------------------- ! construct diagnostics associated with tracer component "n" ! input: ! joff = offset relating "j" in the MW to latitude "jrow" ! js = starting row in the MW ! je = ending row in the MW ! is = starting longitude index in the MW ! ie = ending longitude index in the MW ! n = (1,2) = (u,v) velocity component ! twodt = (2*dtts,dtts) on (leapfrog,mixing) time steps !----------------------------------------------------------------------- implicit none integer i, k, j, ip, kr, jq, n, jp, jrow, js, je, joff, is, ie integer mask, m real t_i, t_j, dz_t2r, dz_tr, dz_wtr, dx_t2r, dx_tr, dy_t2r real dy_tr, adv_tx, adv_ty, adv_tz, adv_txiso, adv_tyiso real adv_tziso, diff_tx, diff_ty, diff_tz, dtdx, dtdy, dtdz real r2dt, cosdyt, fx, darea, boxar, rtwodt, sumdx, delx real sumdxr, dxdy, dxdydz include "size.h" include "param.h" include "pconst.h" include "stdunits.h" include "accel.h" include "coord.h" include "cregin.h" include "csbc.h" include "ctavg.h" include "diag.h" include "diaga.h" include "emode.h" include "grdvar.h" include "hmixc.h" include "levind.h" include "mw.h" include "scalar.h" include "switch.h" include "vmixc.h" real temp1(imt,km), temp2(imt,km), temp3(imt,km) real twodt(km) include "isopyc.h" include "fdift.h" !----------------------------------------------------------------------- ! diagnostic: integrate |d(tracer)/dt| and tracer variance on "tau" ! globally !----------------------------------------------------------------------- if (tsiperts .and. eots) then do j=js,je jrow = j + joff r2dt = c1/c2dtts cosdyt = cst(jrow)*dyt(jrow) do k=1,km fx = r2dt/dtxcel(k) do i=is,ie darea = dzt(k)*dxt(i)*cosdyt*tmask(i,k,j) temp3(i,k) = t(i,k,j,n,tau)*darea temp1(i,k) = t(i,k,j,n,tau)**2*darea temp2(i,k) = abs(t(i,k,j,n,taup1)-t(i,k,j,n,taum1))* & darea*fx enddo do i=is,ie tbar(k,n,jrow) = tbar(k,n,jrow) + temp3(i,k) travar(k,n,jrow) = travar(k,n,jrow) + temp1(i,k) dtabs(k,n,jrow) = dtabs(k,n,jrow) + temp2(i,k) enddo enddo enddo endif !----------------------------------------------------------------------- ! diagnostic: accumulate tracers for averages under horizontal ! regions (use units of meters, rather than cm) !----------------------------------------------------------------------- if (tavgts .and. eots) then do j=js,je jrow = j + joff do i=is,ie mask = mskhr(i,jrow) if (mask .ne. 0) then boxar = cst(jrow)*dxt(i)*dyt(jrow)*tmask(i,1,j)*0.0001 sumbf(mask,n) = sumbf(mask,n) + stf(i,j,n)*boxar do k=1,km sumbk(mask,k,n) = sumbk(mask,k,n) + t(i,k,j,n,tau) & *boxar*dzt(k)*tmask(i,k,j)*0.01 enddo endif enddo enddo endif !----------------------------------------------------------------------- ! diagnostic: compute the northward transport components of ! each tracer !----------------------------------------------------------------------- if (gyrets .and. eots) call gyre (joff, js, je, is, ie, n) !----------------------------------------------------------------------- ! diagnostic: integrate r.h.s. terms in the tracer equations ! over specified regional volumes. !----------------------------------------------------------------------- if (trmbts .and. eots) call ttb1 (joff, js, je, is, ie, n) return end subroutine diagt2 (joff, js, je, is, ie, idiag) !----------------------------------------------------------------------- ! construct d(tracer)/dt diagnostics ! input: ! joff = offset relating "j" in the MW to latitude "jrow" ! js = starting row in the MW ! je = ending row in the MW ! is = starting longitude index in the MW ! ie = ending longitude index in the MW ! idiag = 1 => total tracer change ! idiag = 10 => change of tracer due to filtering(also convection) !----------------------------------------------------------------------- implicit none integer idiag, j, js, je, k, i, joff, iocv, jrow, is, ie real rdt, reltim, period include "size.h" include "param.h" include "pconst.h" include "stdunits.h" include "coord.h" include "diaga.h" include "iounit.h" include "mw.h" include "scalar.h" include "switch.h" include "tmngr.h" include "timeavgs.h" !----------------------------------------------------------------------- ! diagnostic: integrate d/dt(tracer) over specified regional volumes ! after convection and filtering !----------------------------------------------------------------------- if (trmbts .and. eots) call ttb2 (joff, js, je, is, ie, idiag) return end subroutine asbct (joff, js, je, is, ie, isbc, itr) !----------------------------------------------------------------------- ! construct the Atmos S.B.C. (surface boundary conditions) ! input: ! joff = offset relating "j" in the MW to latitude "jrow" ! js = starting row in the MW ! je = ending row in the MW ! is = starting longitude index in the MW ! ie = ending longitude index in the MW ! isbc = index for sbc ! itr = index for tracer !----------------------------------------------------------------------- implicit none integer isbc, itr, j, js, je, jrow, joff, i, is, ie real rts include "size.h" include "param.h" include "pconst.h" include "stdunits.h" include "csbc.h" include "levind.h" include "mw.h" include "scalar.h" include "switch.h" ! initialize the Atmos S.B.C. at the start of each ocean segment ! (do not alter values in land) if (isbc .le. 0 .or. itr .le. 0) return if (eots .and. osegs) then do j=js,je jrow = j + joff do i=is,ie if (kmt(i,jrow) .ne. 0) sbc(i,jrow,isbc) = c0 enddo enddo endif ! accumulate surface tracers for the Atmos S.B.C. every time step if (eots) then do j=js,je jrow = j + joff do i=is,ie sbc(i,jrow,isbc) = sbc(i,jrow,isbc)+t(i,1,j,itr,taup1) enddo enddo endif ! average the surface tracers for the Atmos S.B.C. at the end of ! each ocean segment. (do not alter values in land) if (eots .and. osege) then rts = c1/ntspos do j=js,je jrow = j + joff do i=is,ie if (kmt(i,jrow) .ne. 0) & sbc(i,jrow,isbc) = rts*sbc(i,jrow,isbc) enddo enddo endif return end subroutine ivdift (joff, js, je, is, ie, n, twodt) !----------------------------------------------------------------------- ! solve vertical diffusion of tracers implicitly ! input: ! joff = offset relating "j" in the MW to latitude "jrow" ! js = starting row in the MW ! je = ending row in the MW ! is = starting longitude index in the MW ! ie = ending longitude index in the MW ! n = tracer component ! twodt = (2*dtts, dtts) on (leapfrog, mixing) time steps !----------------------------------------------------------------------- implicit none integer j, js, je, k, i, is, ie, n, joff real rc2dt include "size.h" include "param.h" include "pconst.h" include "stdunits.h" include "levind.h" include "mw.h" include "switch.h" include "vmixc.h" real twodt(km) ! store terms to compute implicit vertical mixing on ! diagnostic time steps if (trmbts .and. eots) then do j=js,je do k=1,km do i=is,ie zzi(i,k,j) = t(i,k,j,n,taup1) enddo enddo enddo endif call invtri (t(1,1,1,n,taup1), stf(1,1,n), btf(1,1,n) &, diff_cbt(1,1,jsmw), twodt, kmt, tmask(1,1,1), is, ie &, joff, js, je) ! compute residual implicit vertical mixing if (trmbts .and. eots) then do j=js,je do k=1,km rc2dt = c1/twodt(k) do i=is,ie zzi(i,k,j) = rc2dt*(t(i,k,j,n,taup1) - zzi(i,k,j)) enddo enddo enddo endif return end subroutine swflux0 (joff, js, je, is, ie, source) ! next endif is the one related to _mom in line 3 of tracer.F return end ! subroutine polint (xa,ya,n,x,y,dy) ! implicit none ! integer n,i,m,ns, nmax parameter (nmax = 10) ! largest anticipated value of n real dy,x,y,xa(n),ya(n) real den,dif,dift,ho,hp,w,c(nmax),d(nmax) ! ! Given arrays xa and ya, each of length n, and a given value x, this routine ! returns a value y, and an error estimate dy. If P(x) is the polynomial of ! degree N-1 such that P(xai) = yai, i=1,....,n then the returned value y=P(x) ! ! ns=1 dif=abs(x-xa(1)) ! do i=1,n dift = abs(x-xa(i)) IF (dift.lt.dif) THEN ns = i dif = dift END IF ! c(i) = ya(i) d(i) = ya(i) ! enddo ! y = ya (ns) ! this is the initial approximation to y ns = ns-1 ! do m=1,n-1 do i=1,n-m ho = xa(i) - x hp = xa (i+m) -x w = c(i+1) - d(i) den = ho - hp IF (den.eq.0.) PAUSE 'failure in polint' den = w/den d(i) = hp*den c(i) = ho*den enddo IF (2*ns.lt.n-m) THEN dy = c(ns+1) ELSE dy = d(ns) ns = ns - 1 END IF y = y + dy enddo return end ! subroutine hunt (xa,n,x,jlo) ! integer jlo,n,inc,jhi,jm real x, xa(n) logical ascnd ! ! Given an array xa(1:n), and given a value x, returns a value jlo ! such that x is between xa(jlo) and xa(jlo +1). xa(1:n) must be ! monotonic, either increasing or decreasing. jlo=0 or jlo=n is ! returned to indicate that x is out of range. jlo on input is taken ! as the initial guess for jlo on output ! ascnd = xa(n).ge.xa(1) ! True if ascending order of table, false otherwise IF (jlo.le.0.or.jlo.gt.n) THEN ! Input guess not useful. Go to bisection jlo = 0 jhi = n+1 goto 3 END IF inc = 1 ! Set the hunting increment IF (x.ge.xa(jlo).eqv.ascnd) THEN ! Hunting up: 1 jhi = jlo + inc IF (jhi.gt.n) THEN ! Done hunting, since off end of table jhi = n + 1 ELSE IF (x.ge.xa(jhi).eqv.ascnd) THEN ! Not done hunting jlo = jhi inc = inc + inc ! so double the increment goto 1 ! and try again END IF ! Done hunting, value bracketed. ELSE ! Hunt down: jhi = jlo 2 jlo = jhi-inc IF (jlo.lt.1) THEN !Done hunting, since off end of table jlo = 0 ELSE IF (x.lt.xa(jlo).eqv.ascnd) THEN ! Not done hunting jhi = jlo inc = inc + inc ! so double the increment goto 2 ! and try again END IF ! Done hunting, value bracketed END IF ! Hunt is done, so begin the final bisection phase: ! 3 IF (jhi-jlo.eq.1) THEN IF (x.eq.xa(n)) jlo = n-1 IF (x.eq.xa(1)) jlo = 1 RETURN END IF jm = (jhi + jlo)/2 IF (x.ge.xa(jm).eqv.ascnd) THEN jlo = jm ELSE jhi = jm END IF ! GOTO 3 ! end