minor updates for demo

Author: nicolecx122

cmake/SCHISM.local.build

@@ -31,7 +31,7 @@ set( USE_ICE OFF CACHE BOOLEAN "Use ICE module")
 set( USE_GEN OFF CACHE BOOLEAN "Use generic tracer module")
 set( USE_AGE OFF CACHE BOOLEAN "Use age module")
 set( USE_ECO OFF   CACHE BOOLEAN "Use ECO-SIM module")
-set( USE_ICM ON  CACHE BOOLEAN "Use ICM module")
+set( USE_ICM OFF  CACHE BOOLEAN "Use ICM module")
 ##pH model is active only if ICM is on
 set( ICM_PH OFF   CACHE BOOLEAN "Use pH module inside ICM")
 set( USE_COSINE OFF   CACHE BOOLEAN "Use CoSiNE module")

src/ICM/icm.F90

@@ -3256,10 +3256,10 @@ subroutine calkwq(id,nv,ure,it)
       do j=1,3
         if(tdep-hcanveg(id,j)>1.e-5) then
           if(idry_e(id)==1) then
-            rtmp=rtmp+aocrveg(j)*plfveg(id,j)*tlfveg(id,j)/max(1.e-5,hcanveg(id,j))
+            rtmp=rtmp+aocrveg(j)*plfveg(id,j)*(1-famveg(j))*tlfveg(id,j)/max(1.e-5,hcanveg(id,j))
           else
             if(ze(klev-1,id)<hcanveg(id,j)+ze(kbe(id),id)) then
-              rtmp=rtmp+aocrveg(j)*plfveg(id,j)*tlfveg(id,j)/max(1.e-5,hcanveg(id,j))
+              rtmp=rtmp+aocrveg(j)*plfveg(id,j)*(1-famveg(j))*tlfveg(id,j)/max(1.e-5,hcanveg(id,j))
             endif !ze
           endif !idry_e
         endif !submerged
@@ -3612,16 +3612,20 @@ subroutine calkwq(id,nv,ure,it)
 
       !recycling of nutrients unit: g/m^2/day
       rtmp=(bmlfveg(j)+plfveg(id,j)*famveg(j))*tlfveg(id,j)+bmstveg(j)*tstveg(id,j)
-      !immediate release to add on to benthic fluxes
+      !immediate release to add on to benthic fluxes, fniveg and fpiveg are mostly by default to be 0 
       tNH4veg(id,j)=ancveg(j)*fniveg(j)*rtmp
       tPO4veg(id,j)=apcveg(j)*fpiveg(j)*rtmp
+      !release of POM to add on to depostional fluxes
+      tponveg(id,j)=ancveg(j)*(bmrtveg(j)*trtveg(id,j)+(1-fniveg(j))*rtmp)
+      tpopveg(id,j)=apcveg(j)*(bmrtveg(j)*trtveg(id,j)+(1-fpiveg(j))*rtmp)
+
+      !DOC and DO
+      rtmp=bmlfveg(j)*tlfveg(id,j)+bmstveg(j)*tstveg(id,j)
       tDOveg(id,j)=(1-khrveg(i)/(khrveg(i)+DOO(nv,1)))*aocrveg(j)*fdoveg(j)*rtmp
       tDOCveg(id,j)=(khrveg(i)/(khrveg(i)+DOO(nv,1)))*fdoveg(j)*rtmp
       trtdoveg(id,j)=aocrveg(j)*frtdoveg(j)*bmrtveg(j)*trtveg(id,j)
       !release of POM to add on to depostional fluxes
       tpocveg(id,j)=(1-frtdoveg(j))*bmrtveg(j)*trtveg(id,j)+(1-fdoveg(j))*rtmp
-      tponveg(id,j)=ancveg(j)*(bmrtveg(j)*trtveg(id,j)+(1-fniveg(j))*rtmp)
-      tpopveg(id,j)=apcveg(j)*(bmrtveg(j)*trtveg(id,j)+(1-fpiveg(j))*rtmp)
 
  !     if(isrecnveg==0)then !recycled nutrients go to sediment directly
  !       trtponveg(id,j)=trtponveg(id,j)+ancveg(j)*(1-fniveg(j))* &

src/ICM/icm_sed_flux.F90

@@ -95,7 +95,7 @@ function sed_zbrent(id,ierr)
   integer, intent(out) :: ierr !0: normal; /=0: error
   integer, parameter :: nloop=100
 !Error: tweak single
-  real(kind=iwp), parameter :: eps=3.0e-8_iwp, tol=1.e-5_iwp,sodmin=1.e-8_iwp,sodmax=100._iwp
+  real(kind=iwp), parameter :: eps=3.0e-8_iwp, tol=1.e-5_iwp,sodmin=1.e-10_iwp,sodmax=100._iwp
   !real(kind=iwp),intent(out) :: fout
 !  real(kind=iwp), external :: sedf
   real(kind=iwp) :: sed_zbrent
@@ -126,17 +126,25 @@ function sed_zbrent(id,ierr)
   !call sedf(fb,b)
 
   !root must be bracketed in brent 
-  if(abs(fa)<2.e-6) then
+  if(abs(fa)<1.e-3) then
     sed_zbrent=a
     return
   endif !fa
 
+  if(SOD<1.e-3) then
+    sed_zbrent=SOD
+    return
+  endif 
+
   if(fa*fb>0.0) then
     if(O20<0.02)then
       sed_zbrent=a
       return
+    elseif(SOD<1.e-1)then
+      sed_zbrent=SOD
+      return
     else
-      ierr=1
+      !ierr=1
       write(12,*)'sed_zbrent: sod=',fa,fb,myrank
       return
     endif !water column hypoxia