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1. Removed some variables that were obsolete, in a desperate attempt …
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…to speed up the runs.

2. Decreased the number of variables to 1100, which is closer to the actual number of 
   variables.
3. Changed the buffer creation/extraction slightly, and added some sanity checks to make 
   sure 4-D variables weren't messed up.  Still checking it, though...
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Marcos Longo committed Mar 21, 2012
1 parent 9291361 commit eb4c96e
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Showing 37 changed files with 472 additions and 1,383 deletions.
23 changes: 11 additions & 12 deletions BRAMS/build/bin/dependency.mk
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Expand Up @@ -562,8 +562,8 @@ phenology_startup.o: grid_coms.mod phenology_aux.mod phenology_coms.mod
average_utils.o: allometry.mod canopy_radiation_coms.mod consts_coms.mod
average_utils.o: ed_max_dims.mod ed_misc_coms.mod ed_state_vars.mod
average_utils.o: grid_coms.mod pft_coms.mod therm_lib.mod
ed_init_full_history.o: allometry.mod c34constants.mod ed_max_dims.mod
ed_init_full_history.o: ed_misc_coms.mod ed_node_coms.mod ed_state_vars.mod
ed_init_full_history.o: allometry.mod ed_max_dims.mod ed_misc_coms.mod
ed_init_full_history.o: ed_node_coms.mod ed_state_vars.mod
ed_init_full_history.o: fusion_fission_coms.mod grid_coms.mod
ed_init_full_history.o: hdf5_coms.mod phenology_startup.mod soil_coms.mod
ed_load_namelist.o: canopy_air_coms.mod canopy_layer_coms.mod
Expand Down Expand Up @@ -593,12 +593,11 @@ ed_xml_config.o: ed_max_dims.mod ed_misc_coms.mod fusion_fission_coms.mod
ed_xml_config.o: grid_coms.mod hydrology_coms.mod met_driver_coms.mod
ed_xml_config.o: pft_coms.mod phenology_coms.mod physiology_coms.mod
ed_xml_config.o: rk4_coms.mod soil_coms.mod
edio.o: c34constants.mod consts_coms.mod ed_max_dims.mod ed_misc_coms.mod
edio.o: ed_node_coms.mod ed_state_vars.mod grid_coms.mod pft_coms.mod
edio.o: soil_coms.mod therm_lib.mod
h5_output.o: an_header.mod c34constants.mod ed_max_dims.mod ed_misc_coms.mod
h5_output.o: ed_node_coms.mod ed_state_vars.mod ed_var_tables.mod
h5_output.o: fusion_fission_coms.mod grid_coms.mod hdf5_coms.mod
edio.o: consts_coms.mod ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod
edio.o: ed_state_vars.mod grid_coms.mod pft_coms.mod soil_coms.mod therm_lib.mod
h5_output.o: an_header.mod ed_max_dims.mod ed_misc_coms.mod ed_node_coms.mod
h5_output.o: ed_state_vars.mod ed_var_tables.mod fusion_fission_coms.mod
h5_output.o: grid_coms.mod hdf5_coms.mod
leaf_database.o: grid_coms.mod hdf5_utils.mod soil_coms.mod
canopy_air_coms.o: consts_coms.mod therm_lib.mod therm_lib8.mod
canopy_radiation_coms.o: ed_max_dims.mod
Expand All @@ -610,10 +609,10 @@ ed_mem_alloc.o: ed_max_dims.mod ed_mem_grid_dim_defs.mod ed_node_coms.mod
ed_mem_alloc.o: ed_state_vars.mod ed_work_vars.mod grid_coms.mod
ed_mem_alloc.o: mem_polygons.mod
ed_misc_coms.o: ed_max_dims.mod
ed_state_vars.o: c34constants.mod disturb_coms.mod ed_max_dims.mod
ed_state_vars.o: ed_misc_coms.mod ed_node_coms.mod ed_var_tables.mod
ed_state_vars.o: fusion_fission_coms.mod grid_coms.mod met_driver_coms.mod
ed_state_vars.o: phenology_coms.mod soil_coms.mod
ed_state_vars.o: disturb_coms.mod ed_max_dims.mod ed_misc_coms.mod
ed_state_vars.o: ed_node_coms.mod ed_var_tables.mod fusion_fission_coms.mod
ed_state_vars.o: grid_coms.mod met_driver_coms.mod phenology_coms.mod
ed_state_vars.o: soil_coms.mod
ed_var_tables.o: ed_max_dims.mod
ed_work_vars.o: ed_max_dims.mod
ename_coms.o: ed_max_dims.mod
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213 changes: 161 additions & 52 deletions BRAMS/src/mpi/mpass_full.f90
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20 changes: 10 additions & 10 deletions BRAMS/src/mpi/mpass_init.f90
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Expand Up @@ -1432,16 +1432,16 @@ subroutine nodeget_grid_dimens()

!----- Assigning the node_mod shortcuts with the appropiate values. --------------------!
do ng=1,ngrids
mmxp(ng)=nodemxp(mynum,ng)
mmyp(ng)=nodemyp(mynum,ng)
mmzp(ng)=nodemzp(mynum,ng)
mia(ng)=nodeia(mynum,ng)
miz(ng)=nodeiz(mynum,ng)
mja(ng)=nodeja(mynum,ng)
mjz(ng)=nodejz(mynum,ng)
mi0(ng)=nodei0(mynum,ng)
mj0(ng)=nodej0(mynum,ng)
mibcon(ng)=nodeibcon(mynum,ng)
mmxp(ng) = nodemxp(mynum,ng)
mmyp(ng) = nodemyp(mynum,ng)
mmzp(ng) = nodemzp(mynum,ng)
mia(ng) = nodeia(mynum,ng)
miz(ng) = nodeiz(mynum,ng)
mja(ng) = nodeja(mynum,ng)
mjz(ng) = nodejz(mynum,ng)
mi0(ng) = nodei0(mynum,ng)
mj0(ng) = nodej0(mynum,ng)
mibcon(ng) = nodeibcon(mynum,ng)
end do
write (unit=*,fmt='(a)') '---------------------------------------------------------'
write (unit=*,fmt='(a,1x,i5)') 'In nodeget_grid_dimens, mynum=',mynum
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10 changes: 6 additions & 4 deletions BRAMS/src/mpi/paral.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -248,12 +248,14 @@ subroutine master_getanl(vtype)
select case (trim(vtype))
!----- Instantaneous variables, use var_p pointer --------------------------------!
case ('LITE')
call ex_full_buff(vtab_r(nv,ng)%var_p,scratch%scr1,fdzp,nnxp(ng),nnyp(ng) &
,fdep,mlon,mlat,ioff,joff)
call ex_full_buff(vtab_r(nv,ng)%var_p,scratch%scr1,npts,fdzp,nnxp(ng) &
,nnyp(ng),fdep,mlon,mlat,ioff,joff,iwest,ieast &
,jsouth,jnorth)
!----- Averaged variables, use var_m pointer -------------------------------------!
case ('MEAN','BOTH')
call ex_full_buff(vtab_r(nv,ng)%var_m,scratch%scr1,fdzp,nnxp(ng),nnyp(ng) &
,fdep,mlon,mlat,ioff,joff)
call ex_full_buff(vtab_r(nv,ng)%var_m,scratch%scr1,npts,fdzp,nnxp(ng) &
,nnyp(ng),fdep,mlon,mlat,ioff,joff,iwest,ieast &
,jsouth,jnorth)
end select
end do varloop
end do machloop
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107 changes: 54 additions & 53 deletions ED/Template/Template/plot_daily.r
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Original file line number Diff line number Diff line change
Expand Up @@ -58,16 +58,16 @@ tsplot04 = list(vnam="mcopft" ,desc="Maintenance costs" ,unit="kgC/m2/

#----- Size (DBH) and age structure of cohort level variables. ----------------------------#
npsas = 10
psas01 = list(vnam="beamextco",desc="Downward direct light" ,unit="--" , plt=T)
psas02 = list(vnam="gppco" ,desc="Gross primary productivity",unit="kgC/plant/yr", plt=T)
psas03 = list(vnam="respco" ,desc="Total plant respiration" ,unit="kgC/plant/yr", plt=T)
psas04 = list(vnam="nppco" ,desc="Net primary productivity" ,unit="kgC/plant/yr", plt=T)
psas05 = list(vnam="mcostco" ,desc="Maintenance costs" ,unit="kgC/plant/yr", plt=T)
psas06 = list(vnam="ncbmortco",desc="Mortality due to Neg. CB" ,unit="1/yr" , plt=T)
psas07 = list(vnam="agbco" ,desc="Above-ground biomass" ,unit="kgC/plant" , plt=T)
psas08 = list(vnam="fsoco" ,desc="Fraction of open stomata" ,unit="--" , plt=T)
psas09 = list(vnam="nplantco" ,desc="Plant density" ,unit="plant/m2" , plt=T)
psas10 = list(vnam="laico" ,desc="Leaf area index" ,unit="m2/m2" , plt=T)
psas01 = list(vnam="lightbeamco",desc="Downward direct light" ,unit="--" , plt=T)
psas02 = list(vnam="gppco" ,desc="Gross primary product." ,unit="kgC/plant/yr", plt=T)
psas03 = list(vnam="respco" ,desc="Total plant respiration" ,unit="kgC/plant/yr", plt=T)
psas04 = list(vnam="nppco" ,desc="Net primary productivity",unit="kgC/plant/yr", plt=T)
psas05 = list(vnam="mcostco" ,desc="Maintenance costs" ,unit="kgC/plant/yr", plt=T)
psas06 = list(vnam="ncbmortco" ,desc="Mortality due to Neg. CB",unit="1/yr" , plt=T)
psas07 = list(vnam="agbco" ,desc="Above-ground biomass" ,unit="kgC/plant" , plt=T)
psas08 = list(vnam="fsoco" ,desc="Fraction of open stomata",unit="--" , plt=T)
psas09 = list(vnam="nplantco" ,desc="Plant density" ,unit="plant/m2" , plt=T)
psas10 = list(vnam="laico" ,desc="Leaf area index" ,unit="m2/m2" , plt=T)
#----- Similar to Hovmoller diagrams. -----------------------------------------------------#
nhov = 4
hovdi01 = list(vnam = c("gpp","plresp","hetresp","nep")
Expand Down Expand Up @@ -297,7 +297,7 @@ for (ipy in 1:nplaces){
p$soil.temp = NULL
p$soil.moist = NULL
#----- Cohort level lists. -------------------------------------------------------------#
p$beamextco = list()
p$lightbeamco = list()
p$gppco = list()
p$respco = list()
p$nppco = list()
Expand Down Expand Up @@ -466,23 +466,24 @@ for (year in yeara:yearz){
hetresppanow = myday$DMEAN.RH.PA[apa:zpa]

#----- Load the other cohort-level variables. --------------------------------#
pftconow = myday$PFT[aco:zco]
nplantconow = myday$NPLANT[aco:zco]
agbconow = myday$AGB.CO[aco:zco]
laiconow = myday$LAI.CO[aco:zco]
gppconow = myday$DMEAN.GPP.CO[aco:zco]
respconow = myday$DMEAN.LEAF.RESP.CO [aco:zco] +
myday$DMEAN.ROOT.RESP.CO [aco:zco] +
growth.resp.fac[myday$PFT[aco:zco]] *
( myday$DMEAN.GPP.CO [aco:zco] -
myday$DMEAN.LEAF.RESP.CO[aco:zco] -
myday$DMEAN.ROOT.RESP.CO[aco:zco] )
nppconow = gppconow-respconow
mcostconow = myday$LEAF.MAINTENANCE [aco:zco] +
myday$ROOT.MAINTENANCE [aco:zco]
ncbmortconow = myday$MORT.RATE.CO[aco:zco,2]
fsoconow = myday$DMEAN.FS.OPEN.CO[aco:zco]
beamextconow = myday$DMEAN.BEAMEXT.LEVEL[aco:zco]
pftconow = myday$PFT[aco:zco]
nplantconow = myday$NPLANT[aco:zco]
agbconow = myday$AGB.CO[aco:zco]
laiconow = myday$LAI.CO[aco:zco]
gppconow = myday$DMEAN.GPP.CO[aco:zco]
respconow = ( myday$DMEAN.LEAF.RESP.CO [aco:zco]
+ myday$DMEAN.ROOT.RESP.CO [aco:zco]
+ growth.resp.fac[myday$PFT[aco:zco]]
* ( myday$DMEAN.GPP.CO [aco:zco]
- myday$DMEAN.LEAF.RESP.CO[aco:zco]
- myday$DMEAN.ROOT.RESP.CO[aco:zco] )
)
nppconow = gppconow-respconow
mcostconow = myday$LEAF.MAINTENANCE [aco:zco] +
myday$ROOT.MAINTENANCE [aco:zco]
ncbmortconow = myday$MORT.RATE.CO[aco:zco,2]
fsoconow = myday$DMEAN.FS.OPEN.CO[aco:zco]
lightbeamconow = myday$DMEAN.LIGHTBEAM.LEVEL[aco:zco]
#-----------------------------------------------------------------------------#


Expand Down Expand Up @@ -540,33 +541,33 @@ for (year in yeara:yearz){
monyear = paste("m",cmonth,"y",year,sep="")
if (day == firstday){
#----- Binding the current cohorts. ---------------------------------------#
p$beamextco[[monyear]] = beamextconow * ndaysi
p$gppco[[monyear]] = gppconow * ndaysi
p$respco[[monyear]] = respconow * ndaysi
p$nppco[[monyear]] = nppconow * ndaysi
p$mcostco[[monyear]] = mcostconow * ndaysi
p$ncbmortco[[monyear]] = ncbmortconow * ndaysi
p$agbco[[monyear]] = agbconow * ndaysi
p$fsoco[[monyear]] = fsoconow * ndaysi
p$nplantco[[monyear]] = nplantconow * ndaysi
p$dbhco[[monyear]] = dbhconow * ndaysi
p$laico[[monyear]] = laiconow * ndaysi
p$lightbeamco[[monyear]] = lightbeamconow * ndaysi
p$gppco [[monyear]] = gppconow * ndaysi
p$respco [[monyear]] = respconow * ndaysi
p$nppco [[monyear]] = nppconow * ndaysi
p$mcostco [[monyear]] = mcostconow * ndaysi
p$ncbmortco [[monyear]] = ncbmortconow * ndaysi
p$agbco [[monyear]] = agbconow * ndaysi
p$fsoco [[monyear]] = fsoconow * ndaysi
p$nplantco [[monyear]] = nplantconow * ndaysi
p$dbhco [[monyear]] = dbhconow * ndaysi
p$laico [[monyear]] = laiconow * ndaysi
#----- The following variables are not averaged. --------------------------#
p$pftco[[monyear]] = pftconow
p$ageco[[monyear]] = ageconow
p$areaco[[monyear]] = areaconow
p$pftco [[monyear]] = pftconow
p$ageco [[monyear]] = ageconow
p$areaco [[monyear]] = areaconow
}else{
p$beamextco[[monyear]] = p$beamextco[[monyear]] + beamextconow * ndaysi
p$gppco[[monyear]] = p$gppco[[monyear]] + gppconow * ndaysi
p$respco[[monyear]] = p$respco[[monyear]] + respconow * ndaysi
p$nppco[[monyear]] = p$nppco[[monyear]] + nppconow * ndaysi
p$mcostco[[monyear]] = p$mcostco[[monyear]] + mcostconow * ndaysi
p$ncbmortco[[monyear]] = p$ncbmortco[[monyear]] + ncbmortconow * ndaysi
p$agbco[[monyear]] = p$agbco[[monyear]] + agbconow * ndaysi
p$fsoco[[monyear]] = p$fsoco[[monyear]] + fsoconow * ndaysi
p$nplantco[[monyear]] = p$nplantco[[monyear]] + nplantconow * ndaysi
p$dbhco[[monyear]] = p$dbhco[[monyear]] + dbhconow * ndaysi
p$laico[[monyear]] = p$laico[[monyear]] + laiconow * ndaysi
p$lightbeamco[[monyear]] = p$lightbeamco[[monyear]] + lightbeamconow*ndaysi
p$gppco [[monyear]] = p$gppco [[monyear]] + gppconow *ndaysi
p$respco [[monyear]] = p$respco [[monyear]] + respconow *ndaysi
p$nppco [[monyear]] = p$nppco [[monyear]] + nppconow *ndaysi
p$mcostco [[monyear]] = p$mcostco [[monyear]] + mcostconow *ndaysi
p$ncbmortco [[monyear]] = p$ncbmortco [[monyear]] + ncbmortconow *ndaysi
p$agbco [[monyear]] = p$agbco [[monyear]] + agbconow *ndaysi
p$fsoco [[monyear]] = p$fsoco [[monyear]] + fsoconow *ndaysi
p$nplantco [[monyear]] = p$nplantco [[monyear]] + nplantconow *ndaysi
p$dbhco [[monyear]] = p$dbhco [[monyear]] + dbhconow *ndaysi
p$laico [[monyear]] = p$laico [[monyear]] + laiconow *ndaysi
} #end if month=sasmonth
#-----------------------------------------------------------------------------#

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80 changes: 38 additions & 42 deletions ED/Template/Template/plot_monthly.r
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Original file line number Diff line number Diff line change
Expand Up @@ -294,10 +294,9 @@ for (place in myplaces){

#----- Cohort level lists. -------------------------------------------------------------#
lightco = list()
beamextco = list()
diffextco = list()
lightbeamco = list()
lightdiffco = list()
parlco = list()
lambdaco = list()
gppco = list()
gpplco = list()
respco = list()
Expand Down Expand Up @@ -781,9 +780,8 @@ for (place in myplaces){
ncbmortconow = mymont$MMEAN.MORT.RATE[,2]
fsoconow = mymont$MMEAN.FS.OPEN.CO
lightconow = mymont$MMEAN.LIGHT.LEVEL
lambdaconow = mymont$MMEAN.LAMBDA.LIGHT.CO
beamextconow = mymont$MMEAN.BEAMEXT.LEVEL
diffextconow = mymont$MMEAN.BEAMEXT.LEVEL
lightbeamconow = mymont$MMEAN.LIGHT.LEVEL.BEAM
lightdiffconow = mymont$MMEAN.LIGHT.LEVEL.DIFF
parlconow = mymont$MMEAN.PAR.L

baliveconow = mymont$BALIVE
Expand Down Expand Up @@ -842,9 +840,8 @@ for (place in myplaces){
ncbmortconow = NA
fsoconow = NA
lightconow = NA
lambdaconow = NA
beamextconow = NA
diffextconow = NA
lightbeamconow = NA
lightdiffconow = NA
parlconow = NA
demandconow = NA
supplyconow = NA
Expand Down Expand Up @@ -1130,39 +1127,38 @@ for (place in myplaces){
cmonth = substring(100+month,2,3)
labwhen = paste("y",cyear,"m",cmonth,sep="")
#----- Binding the current cohorts. ------------------------------------------#
lightco [[labwhen]] = lightconow
beamextco[[labwhen]] = beamextconow
diffextco[[labwhen]] = diffextconow
parlco [[labwhen]] = parlconow
lambdaco [[labwhen]] = lambdaconow
gppco [[labwhen]] = gppconow
gpplco [[labwhen]] = gpplconow
respco [[labwhen]] = respconow
nppco [[labwhen]] = nppconow
cbrbarco [[labwhen]] = cbrbarconow
cbalco [[labwhen]] = cbalconow
mcostco [[labwhen]] = mcostconow
ncbmortco[[labwhen]] = ncbmortconow
agbco [[labwhen]] = agbconow
fsoco [[labwhen]] = fsoconow
nplantco [[labwhen]] = nplantconow * areaconow
heightco [[labwhen]] = heightconow
baco [[labwhen]] = nplantconow * baconow * areaconow
pftco [[labwhen]] = pftconow
dbhco [[labwhen]] = dbhconow
laico [[labwhen]] = laiconow
waico [[labwhen]] = waiconow
taico [[labwhen]] = taiconow
ageco [[labwhen]] = ageconow
areaco [[labwhen]] = areaconow
demandco [[labwhen]] = demandconow
supplyco [[labwhen]] = supplyconow
baliveco [[labwhen]] = baliveconow
bdeadco [[labwhen]] = bdeadconow
bleafco [[labwhen]] = bleafconow
brootco [[labwhen]] = brootconow
bswoodco [[labwhen]] = bswoodconow
bstoreco [[labwhen]] = bstoreconow
lightco [[labwhen]] = lightconow
lightbeamco [[labwhen]] = lightbeamconow
lightdiffco [[labwhen]] = lightdiffconow
parlco [[labwhen]] = parlconow
gppco [[labwhen]] = gppconow
gpplco [[labwhen]] = gpplconow
respco [[labwhen]] = respconow
nppco [[labwhen]] = nppconow
cbrbarco [[labwhen]] = cbrbarconow
cbalco [[labwhen]] = cbalconow
mcostco [[labwhen]] = mcostconow
ncbmortco [[labwhen]] = ncbmortconow
agbco [[labwhen]] = agbconow
fsoco [[labwhen]] = fsoconow
nplantco [[labwhen]] = nplantconow * areaconow
heightco [[labwhen]] = heightconow
baco [[labwhen]] = nplantconow * baconow * areaconow
pftco [[labwhen]] = pftconow
dbhco [[labwhen]] = dbhconow
laico [[labwhen]] = laiconow
waico [[labwhen]] = waiconow
taico [[labwhen]] = taiconow
ageco [[labwhen]] = ageconow
areaco [[labwhen]] = areaconow
demandco [[labwhen]] = demandconow
supplyco [[labwhen]] = supplyconow
baliveco [[labwhen]] = baliveconow
bdeadco [[labwhen]] = bdeadconow
bleafco [[labwhen]] = bleafconow
brootco [[labwhen]] = brootconow
bswoodco [[labwhen]] = bswoodconow
bstoreco [[labwhen]] = bstoreconow
} #end if month=sasmonth
#--------------------------------------------------------------------------------#

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