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Merge depo_mass (SED3D work) back to master and close out.
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Special thanks to la Rochelle group (Baptiste M, Xavier B. et al.)
Squashed commit of the following:

commit 6d261ae
Author: Joseph Zhang <yinglong@james.hpc.vims.edu>
Date:   Wed May 6 12:23:03 2020 -0400

    update notes

commit 7f731dc
Author: Joseph Zhang <yjzhang@vims.edu>
Date:   Sat Apr 25 14:32:34 2020 -0400

    remove old info in sflux_input.txt

commit 2687835
Author: Joseph Zhang <yjzhang@vims.edu>
Date:   Sat Apr 25 14:20:29 2020 -0400

    Fixed the issue with NARR linker (not sure why this got clobbered)

commit 80e7392
Author: Joseph Zhang <yjzhang@vims.edu>
Date:   Fri Apr 24 10:05:12 2020 -0400

    Revert to old approach for depositional mass (c/o Baptiste Mengual).
    Testing....
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Joseph Zhang committed May 6, 2020
1 parent 1b42b19 commit e703189
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Showing 4 changed files with 67 additions and 75 deletions.
2 changes: 1 addition & 1 deletion src/Hydro/schism_step.F90
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Expand Up @@ -4585,7 +4585,7 @@ subroutine schism_step(it)
if(itur==5) then !1018:itur==5
bigf1=bigf1+(TDxz(nvrt,isd)-TDxz(kbs(isd)+1,isd)) !/i34(i)
bigf2=bigf2+(TDyz(nvrt,isd)-TDyz(kbs(isd)+1,isd)) !/i34(i)
!Error: Hai, shouldn't there be botf[1,2] also?
!Assume botf1=botf2
endif
#endif /*USE_SED*/

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5 changes: 3 additions & 2 deletions src/Readme.beta_notes
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Expand Up @@ -7,8 +7,8 @@ eb00a00 (Mar 31, 2020): add 12th tracer model (USE_DVD of Klingbeil); if invoked
cd9664a (Mar 16, 2020): [1st PR from Baptiste Mengual] added iof_sed(12:15) for new SED code. In sediment.in:
new options for various parameters and a few new parameters;
sed_morph=1 requires imorphogrid.gr3 (a scale applied to depth change at each node);
7506147 (Mar 1, 2020): add limiter for settling vel to avoid char line out of bnd;
73f7451 (Jan 14, 2020): changed ifltyp=3 to be consistent with '5' (i.e., now the amp/phases should be variable along open bnd);
also morp factors are replaced by a single 'sed_morph_fac' fro all classes;
73f7451 (Jan 14, 2020): changed ifltype=3 to be consistent with '5' (i.e., now the amp/phases should be variable along open bnd);
59741d4 (Jan 9, 2020): added another pre-proc flag 'ipre2' for more diagnostic outputs (can be used with >1 CPU; stops
after outputs);
4e2eb86 (Dec 11, 2019): added optional flags 'iadjust_mass_consv0' to enforce mass conservation for each of (11) tracer models;
Expand Down Expand Up @@ -425,6 +425,7 @@ git versions:
(104) eb00a00 (Mar 31, 2020): added 12th tracer model (USE_DVD of Klingbeil)
(105) aaf1306 (April 4, 2020): added hybrid ELM transport for efficiency (via branch hybrid_ELM);
(106) 40955ab (April 16, 2020): replaced the fatal error in nadv=2 (aptivity trap) with exit
(107) (April 24, 2020): reverted to old simple approach for deposional mass (c/o Baptiste Mengual);

---------------------------------------------------------------
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117 changes: 56 additions & 61 deletions src/Sediment/sediment.F90
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Expand Up @@ -1000,72 +1000,67 @@ subroutine sediment(it,moitn,mxitn,rtol,dave,tot_bedmass)

select case(ised_bc_bot)
case(1) !Warner
!Depositional mass (kg/m/m) in a time step; use
!semi-Lagrangian to calculate depo_mss=\int w_s*c^* dt
cff=ze(nvrt,i)-ze(kbe(i),i) !total depth
cff1=ze(kbe(i)+1,i)-ze(kbe(i),i) !bottom cell thickness

if(cff1.LE.0.d0) then
WRITE(errmsg,*)'SED, wrong bottom layer0:',cff,ze(kbe(i)+1,i),ze(kbe(i),i)
CALL parallel_abort(errmsg)
endif

!Limit ratio between reference depth and bottom depth
!ta=min(0.5d0,relath*cff/cff1) !usually the relath is 0.01; for natural river, it should be even smaller

!aref=ta*we(kbe(i)+1,i) !w-vel. at ref. height
!Estimate the starting pt
cff8=(ze(kbe(i)+1,i)+ze(kbe(i),i))/2 !bottom half cell -starting pt of ELM
cff9=cff8+Wsed(ised)*dt !>cff8; foot of char.
if(cff9<=cff8) call parallel_abort('SED: (9)')
Ksed=nvrt+1 !init. for abnormal case
do k=kbe(i)+2,nvrt
if(cff9<=(ze(k,i)+ze(k-1,i))/2) then
Ksed=k
exit
endif
enddo !k

depo_mss=0 !(min(cff9,cff8)-ze(kbe(i),i))*tr_el(indx,kbe(i)+1,i)
do k=kbe(i)+2,min(nvrt,Ksed)
cff7=(ze(k-2,i)+ze(k-1,i))/2
cff8=(ze(k,i)+ze(k-1,i))/2
if(cff9<cff7) then
WRITE(errmsg,*)'SED, wrong cff9:',cff9,cff7,ielg(i),ised,k
CALL parallel_abort(errmsg)
endif

if(cff9<cff8) then
cff5=(cff9-cff7)/(cff8-cff7) !ratio
if(cff5<0.or.cff5>1) then
WRITE(errmsg,*)'SED, wrong ratio:',cff5,ielg(i),ised,k
CALL parallel_abort(errmsg)
endif
cff6=(1-cff5)*tr_el(indx,k-1,i)+cff5*tr_el(indx,k,i) !conc @upper layer
else
cff6=tr_el(indx,k,i)
endif

depo_mss=depo_mss+(cff6+tr_el(indx,k-1,i))/2*(min(cff9,cff8)-cff7) !>=0
!depo_mss=depo_mss+cff6*(min(cff9,cff8)-cff7) !>=0 (lower depos. flux)
enddo !k

!Deal with above F.S. case
if(Ksed==nvrt+1) then
cff7=(ze(nvrt,i)+ze(nvrt-1,i))/2
depo_mss=depo_mss+(min(ze(nvrt,i),cff9)-cff7)*tr_el(indx,nvrt,i)
endif
!Depositional mass (kg/m/m) in a time step
! cff=ze(nvrt,i)-ze(kbe(i),i) !total depth
! cff1=ze(kbe(i)+1,i)-ze(kbe(i),i) !bottom cell thickness
!
! if(cff1.LE.0.d0) then
! WRITE(errmsg,*)'SED, wrong bottom layer0:',cff,ze(kbe(i)+1,i),ze(kbe(i),i)
! CALL parallel_abort(errmsg)
! endif
!
! !Limit ratio between reference depth and bottom depth
! !ta=min(0.5d0,relath*cff/cff1) !usually the relath is 0.01; for natural river, it should be even smaller
!
! !aref=ta*we(kbe(i)+1,i) !w-vel. at ref. height
! !Estimate the starting pt
! cff8=(ze(kbe(i)+1,i)+ze(kbe(i),i))/2 !bottom half cell -starting pt of ELM
! cff9=cff8+Wsed(ised)*dt !>cff8; foot of char.
! if(cff9<=cff8) call parallel_abort('SED: (9)')
! Ksed=nvrt+1 !init. for abnormal case
! do k=kbe(i)+2,nvrt
! if(cff9<=(ze(k,i)+ze(k-1,i))/2) then
! Ksed=k
! exit
! endif
! enddo !k
!
! depo_mss=0 !(min(cff9,cff8)-ze(kbe(i),i))*tr_el(indx,kbe(i)+1,i)
! do k=kbe(i)+2,min(nvrt,Ksed)
! cff7=(ze(k-2,i)+ze(k-1,i))/2
! cff8=(ze(k,i)+ze(k-1,i))/2
! if(cff9<cff7) then
! WRITE(errmsg,*)'SED, wrong cff9:',cff9,cff7,ielg(i),ised,k
! CALL parallel_abort(errmsg)
! endif
!
! if(cff9<cff8) then
! cff5=(cff9-cff7)/(cff8-cff7) !ratio
! if(cff5<0.or.cff5>1) then
! WRITE(errmsg,*)'SED, wrong ratio:',cff5,ielg(i),ised,k
! CALL parallel_abort(errmsg)
! endif
! cff6=(1-cff5)*tr_el(indx,k-1,i)+cff5*tr_el(indx,k,i) !conc @upper layer
! else
! cff6=tr_el(indx,k,i)
! endif
!
! depo_mss=depo_mss+(cff6+tr_el(indx,k-1,i))/2*(min(cff9,cff8)-cff7) !>=0
! !depo_mss=depo_mss+cff6*(min(cff9,cff8)-cff7) !>=0 (lower depos. flux)
! enddo !k
!
! !Deal with above F.S. case
! if(Ksed==nvrt+1) then
! cff7=(ze(nvrt,i)+ze(nvrt-1,i))/2
! depo_mss=depo_mss+(min(ze(nvrt,i),cff9)-cff7)*tr_el(indx,nvrt,i)
! endif

!BM: Correction of depo_mss, otherwise conservativity
! issues occur
!Error: this will change conservation
!depo_mss=dt*Wsed(ised)*tr_el(indx,kbe(i)+1,i) !s * m/s * kg/m3
depo_mss=dt*Wsed(ised)*tr_el(indx,kbe(i)+1,i) !s * m/s * kg/m3

!BM: output
depflxel(i,ised)=depo_mss/dt ! en kg/m2/s

!Apply a scale to depo_mss
!depo_mss=depo_mss*depo_scale
depflxel(i,ised)=depo_mss/dt ! en kg/m2/s

! - Compute erosion, eros_mss (kg/m/m) following
! (original erosion flux is in kg/m/m/s; note dt below)
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18 changes: 7 additions & 11 deletions src/Utility/Sflux_nc/NARR_util/make_sflux_links.csh
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#### On a new system, change util_bin and data_grandparent below
######## define locations and names for utilities ######################

set util_bin = ~yinglong/SELFE/svn/trunk/src/Utility/Sflux_nc/NARR_util/src/
set util_bin = ~yinglong/git/schism/src/Utility/Sflux_nc/NARR_util/src/
set cjd_util = $util_bin'cjd/cjd'


Expand Down Expand Up @@ -103,8 +103,7 @@ set src_1 = ""
set src_2 = ""
set domain_1 = "."
set domain_2 = "."
#set data_grandparent = '/home/workspace/ccalmr37/sflux_data/'
set data_grandparent = '/home/dogami/'
set data_grandparent = '~yinglong/vims20/'

if ($data_source_code == "1") then
set src_1 = "nam"
Expand Down Expand Up @@ -186,11 +185,6 @@ echo " " $dest_dir$inputs_file

cat > $dest_dir$inputs_file << EOF
&sflux_inputs
start_year = $year_start,
start_month = $month_start,
start_day = $day_start,
start_hour = $start_hour,
utc_start = $utc_start,
/
EOF

Expand Down Expand Up @@ -229,12 +223,14 @@ foreach file_type (air rad prc)
foreach in_file (`ls $src_1'_'$file_type$domain_1$date_string'.nc'`)
set type_counter = `echo \($type_counter + 1\) | bc` >& /dev/null

if ($type_counter >= 100) then
if ($type_counter >= 1000) then
set type_counter_label = $type_counter
else if ($type_counter >= 10) then
else if ($type_counter >= 100) then
set type_counter_label = 0$type_counter
else
else if ($type_counter >= 10) then
set type_counter_label = 00$type_counter
else
set type_counter_label = 000$type_counter
endif

set link_name = sflux_$file_type"_1."$type_counter_label.nc
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