change name from iSed in ICM to iSFM

sample_inputs/icm.nml

@@ -129,10 +129,10 @@ imarsh_icm = 0   !0: off;  1: mechanistic model;  2: simple formulation
 nmarsh     = 3   !parameters in marsh module must be consistent with
 
 !-----------------------------------------------------------------------
-!Sediment module switch. iSed=1: Use sediment flux model
+!Sediment module switch. iSFM=1: Use sediment flux model
 !benthic flux provided by sed_flux_model
 !-----------------------------------------------------------------------
-iSed = 1 
+iSFM = 1
 
 !-----------------------------------------------------------------------
 !Benthic Algae

sample_inputs/param.nml

@@ -1032,7 +1032,7 @@
 !  !bThp: consective days of hypoxia (day)
 !  !bTox: consective days of oxic condition after hypoxia (day)
 !  !-------------------------------------------------------------
-!  iof_icm_sed      = 1
+!  iof_icm_sfm      = 1
 !
 !  !Benthic Algae model
 !  iof_icm_ba       = 1 !BA    (g[C].m-2)

src/Core/schism_glbl.F90

@@ -93,7 +93,7 @@ module schism_glbl
                   &inv_atm_bnd,ieos_type,ieos_pres,iupwind_mom,inter_mom,ishapiro,iveg, &
                   &nstep_ice,niter_shap,iunder_deep,flag_fib,ielm_transport,max_subcyc, &
                   &itransport_only,iloadtide,nc_out,nu_sum_mult,iprecip_off_bnd, &
-                  &iof_ugrid,model_type_pahm,iof_icm_sav,iof_icm_marsh,iof_icm_sed,iof_icm_ba,&
+                  &iof_ugrid,model_type_pahm,iof_icm_sav,iof_icm_marsh,iof_icm_sfm,iof_icm_ba,&
                   &iof_icm_clam,nbins_veg_vert,veg_lai,veg_cw
   integer,save :: ntrs(natrm),nnu_pts(natrm),mnu_pts,lev_tr_source(natrm)
   integer,save,dimension(:),allocatable :: iof_hydro,iof_wwm,iof_gen,iof_age,iof_sed,iof_eco, &

src/Hydro/schism_init.F90

@@ -211,7 +211,7 @@ subroutine schism_init(iorder,indir,iths,ntime)
      &veg_vert_z,veg_vert_scale_cd,veg_vert_scale_N,veg_vert_scale_D,veg_lai,veg_cw
 
      namelist /SCHOUT/nc_out,iof_hydro,iof_wwm,iof_gen,iof_age,iof_sed,iof_eco,iof_icm_core, &
-     &iof_icm_silica,iof_icm_zb,iof_icm_ph,iof_icm_srm,iof_icm_sav,iof_icm_marsh,iof_icm_sed, &
+     &iof_icm_silica,iof_icm_zb,iof_icm_ph,iof_icm_srm,iof_icm_sav,iof_icm_marsh,iof_icm_sfm, &
      &iof_icm_ba,iof_icm_clam,iof_cos,iof_fib,iof_sed2d,iof_ice,iof_ana,iof_marsh,iof_dvd, &
      &nhot,nhot_write,iout_sta,nspool_sta,iof_ugrid
 
@@ -509,7 +509,7 @@ subroutine schism_init(iorder,indir,iths,ntime)
       iof_hydro=0; iof_wwm=0; iof_gen=0; iof_age=0; iof_sed=0; iof_eco=0; iof_dvd=0
       iof_hydro(1)=1; iof_hydro(25:26)=1
       iof_icm_core=0; iof_icm_silica=0; iof_icm_zb=0; iof_icm_ph=0; iof_icm_srm=0; iof_icm_sav=0
-      iof_icm_marsh=0; iof_icm_sed=0; iof_icm_ba=0; iof_icm_clam=0; iof_cos=0; iof_fib=0; iof_sed2d=0
+      iof_icm_marsh=0; iof_icm_sfm=0; iof_icm_ba=0; iof_icm_clam=0; iof_cos=0; iof_fib=0; iof_sed2d=0
       iof_ice=0; iof_ana=0; iof_marsh=0; nhot=0; nhot_write=8640; iout_sta=0; nspool_sta=10; iof_ugrid=0
 
       read(15,nml=OPT)

src/ICM/icm.F90

@@ -292,7 +292,7 @@ subroutine ecosystem(it)
       if(iClam==1) call clam_calc(id,kb,dz(kb+1))
 
       !sediment flux module
-      if(iSed==1) call sfm_calc(id,kb,tdep,dz(kb+1),it,isub)
+      if(iSFM==1) call sfm_calc(id,kb,tdep,dz(kb+1),it,isub)
 
       !BA module
       if(iBA==1) call ba_calc(id,kb,dz(kb+1))
@@ -326,7 +326,7 @@ subroutine ecosystem(it)
       endif
 
       !sediment fluxes addition from SFM
-      if(iSed==1) then
+      if(iSFM==1) then
         !pH effect on sediment PO4 release
         if(iPh==1 .and.ppatch(id)/=0) then
           JPO4(id)=max(JPO4(id)*exp(1.3*(PH(kb+1)-8.5)),0.02)

src/ICM/icm_init.F90

@@ -23,7 +23,7 @@ subroutine read_icm_param(imode)
   use schism_glbl, only : rkind,dt,nvrt,ne_global,in_dir,out_dir,len_in_dir,len_out_dir, &
             & ihconsv,nws,nea,npa,ihot,idry_e,ze,kbe,irange_tr,tr_el,tr_nd,nea,npa,iof_icm, &
             & iof_icm_core,iof_icm_silica,iof_icm_zb,iof_icm_ph,iof_icm_srm,iof_icm_sav, &
-            & iof_icm_marsh,iof_icm_sed, iof_icm_ba,iof_icm_clam
+            & iof_icm_marsh,iof_icm_sfm,iof_icm_ba,iof_icm_clam
 
   use schism_msgp, only : myrank,parallel_abort
   use icm_misc, only : read_gr3_prop
@@ -41,7 +41,7 @@ subroutine read_icm_param(imode)
   type(icm_pointer),pointer :: p
 
   !define namelists
-  namelist /MARCO/ nsub,iRad,iKe,iLight,iPR,iLimit,isflux,iSed,iBA,iClam,nclam, &
+  namelist /MARCO/ nsub,iRad,iKe,iLight,iPR,iLimit,isflux,iSFM,iBA,iClam,nclam, &
            & ibflux,iSilica,iZB,iPh,iSRM,isav_icm,imarsh_icm,nmarsh,idry_icm,KeC,KeS,KeSalt, &
            & alpha,Ke0,tss2c,PRR,wqc0,WSP,WSPn,iout_icm,nspool_icm,idbg
   namelist /CORE/ GPM,TGP,KTGP,MTR,MTB,TMT,KTMT,FCP,FNP,FPP,FCM,FNM,FPM,  &
@@ -78,11 +78,11 @@ subroutine read_icm_param(imode)
     !read ICM; compute total # of state variables 
     !------------------------------------------------------------------------------------
     !initilize global switches
-    nsub=1; iRad=0; iKe=0; iLight=0; iPR=0; iLimit=0; isflux=0; iSed=1; iBA=0; ibflux=0; iSilica=0; 
+    nsub=1; iRad=0; iKe=0; iLight=0; iPR=0; iLimit=0; isflux=0; iSFM=1; iBA=0; ibflux=0; iSilica=0;
     iZB=0;  iPh=0; iSRM=0; isav_icm=0; imarsh_icm=0; nmarsh=3; idry_icm=0; KeC=0.26; KeS=0.07; KeSalt=-0.02;
     alpha=5.0; Ke0=0.26; tss2c=6.0; PRR=0; wqc0=0; WSP=0.0; WSPn=0.0; iout_icm=0; nspool_icm=0
     iClam=0; nclam=0; idbg=0
-    jdry=>idry_icm; jsav=>isav_icm; jmarsh=>imarsh_icm; ised_icm=>iSed; iBA_icm=>iBA
+    jdry=>idry_icm; jsav=>isav_icm; jmarsh=>imarsh_icm; iBA_icm=>iBA
 
     !read global switches
     open(31,file=in_dir(1:len_in_dir)//'icm.nml',delim='apostrophe',status='old')
@@ -354,7 +354,7 @@ subroutine read_icm_param(imode)
     endif
 
     !SFM module: 8
-    if(iSed==1) then
+    if(iSFM==1) then
       p=>wqout(nout+1);   p%name='ICM_bPOC1';   p%p1=>bPOC(1,:); p%itype=4
       p=>wqout(nout+2);   p%name='ICM_bPOC2';   p%p1=>bPOC(2,:); p%itype=4
       p=>wqout(nout+3);   p%name='ICM_bPOC3';   p%p1=>bPOC(3,:); p%itype=4
@@ -478,7 +478,7 @@ subroutine read_icm_param(imode)
     if(iSRM==1)     iof_icm(iout(1,5): iout(2,5)) =iof_icm_srm
     if(isav_icm/=0) iof_icm(iout(1,6): iout(2,6)) =iof_icm_sav
     if(imarsh_icm==1) iof_icm(iout(1,7): iout(2,7)) =iof_icm_marsh
-    if(ised_icm==1) iof_icm(iout(1,8): iout(2,8)) =iof_icm_sed
+    if(iSFM==1)     iof_icm(iout(1,8): iout(2,8)) =iof_icm_sfm
     if(iBA_icm==1)  iof_icm(iout(1,9): iout(2,9)) =iof_icm_ba
     if(iClam==1)    iof_icm(iout(1,10):iout(2,10))=iof_icm_clam
     do i=1,nout
@@ -1027,7 +1027,7 @@ subroutine icm_vars_init
     endif
 
     !SFM init
-    if(iSed==1) then
+    if(iSFM==1) then
       bPOC(:,i)=bPOC0(:); bPON(:,i)=bPON0(:); bPOP(:,i)=bPOP0(:)
       bNH4(i)=bNH40;      bNO3(i)=bNO30;      bPO4(i)=bPO40
       bH2S(i)=bH2S0;      bCH4(i)=bCH40;      bstc(i)=bstc0
@@ -1307,7 +1307,7 @@ subroutine check_icm_param()
   if(iSRM/=0.and.iSRM/=1) call parallel_abort('ICM iSRM: 0/1')
   if(jsav/=0.and.jsav/=1.and.jsav/=2) call parallel_abort('ICM isav_icm: 0/1/2')
   if(jmarsh/=0.and.jmarsh/=1.and.jmarsh/=2) call parallel_abort('ICM imarsh_icm: 0/1/2')
-  if(iSed/=0.and.iSed/=1) call parallel_abort('ICM iSed: 0/1')
+  if(iSFM/=0.and.iSFM/=1) call parallel_abort('ICM iSFM: 0/1')
   if(iBA/=0.and.iBA/=1) call parallel_abort('ICM iBA: 0/1')
   if(iRad/=0.and.iRad/=1) call parallel_abort('ICM iRad: 0/1')
   if(isflux/=0.and.isflux/=1) call parallel_abort('ICM isflux: 0/1')

src/ICM/icm_mod.F90

@@ -27,11 +27,11 @@ module icm_mod
   !-------------------------------------------------------------------------------
   !global switch and variables
   !-------------------------------------------------------------------------------
-  integer,save,target :: nsub,iKe,iLight,iPR,iLimit,iSed,iBA,iRad,isflux,ibflux,idbg(10),iout_icm,nspool_icm
+  integer,save,target :: nsub,iKe,iLight,iPR,iLimit,iSFM,iBA,iRad,isflux,ibflux,idbg(10),iout_icm,nspool_icm
   integer,save,target :: iSilica,iZB,iPh,iSRM,isav_icm,imarsh_icm,nmarsh,idry_icm,iClam,nclam
   real(rkind),save,target :: KeC,KeS,KeSalt,Ke0,tss2c,PRR(3),wqc0(29),WSP(29),WSPn(29)
   real(rkind),save,target,dimension(3) :: alpha
-  integer,save,pointer :: jdry,jsav,jmarsh,ised_icm,iBA_icm
+  integer,save,pointer :: jdry,jsav,jmarsh,iBA_icm
 
   integer,save,target :: ntrs_icm,nout,nouts(10),iout(2,10),nout_icm_3d(2),nhot_icm
   integer,save,pointer :: itrs_icm(:,:),elem_in(:,:),nout_icm