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poprhythm
2022-09-12 16:40:28 +00:00
parent 78eb7147d0
commit d713d4f61a
110 changed files with 87672 additions and 1098 deletions
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leafres/testarea/LeafGasPISCAL_single.f
+98 -112
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@@ -15,7 +15,7 @@
program main
implicit none
integer dataunit,spareunit,ierr(2),runvalues(8),ipos1,ipos2,
&ntotfiles,noutputfiles,i,j,k,indexunit(20)
&ntotfiles,noutputfiles,i,j,k,indexunit(20),ic3c4cam
character rundate*8,runtime*10,runzone*5,longchar*5000
character*100 datapath,outpath,storein,storeout,
&ACidata(8000)
@@ -23,11 +23,14 @@
! Set input / output directory
parameter(datapath=
! &'../input/',
&'/home/l2g/jimei/',
! &'/home/l2g/ngeetropics/gamboa/curves/',
! &'/home/l2g/ngeetropics/metropolitano/curves/',
! &'/home/l2g/ngeetropics/fortsherman/curves/',
! &'/home/l2g/ngeetropics/kelsey/curves/',
& '/home/l2g/SingleLeafModel/ACiSimulation/hybrid/',
! & '/home/l2g/SingleLeafModel/ACiSimulation/hybrid/',
! &'/home/l2g/leafres/hybriddata/nicksmith/data/',
! &'/home/l2g/leafres/hybriddata/dwestonpoplus/data3/',
! &'/home/l2g/leafres/hybriddata/cernusak/2014data/',
! &'/home/l2g/leafres/hybriddata/hanjimei/',
@@ -59,6 +62,8 @@
! & '/home/l2g/dataassim/leaf/data/dweston/inputs/',
! & '/home/l2g/GEMSiS/curves/',
& outpath=
! &'../output/fitresult/touser/',
&'/home/l2g/jimei/',
! &'/home/l2g/ngeetropics/gamboa/results/',
! &'/home/l2g/ngeetropics/metropolitano/results/',
! &'/home/l2g/ngeetropics/fortsherman/results/',
@@ -69,7 +74,9 @@
! &'/home/l2g/leafres/hybriddata/hanjimei/',
!
! & '/home/l2g/leafres/hybriddata/Berner/',
& '/home/l2g/SingleLeafModel/ACiSimulation/hybrid/',
! & '/home/l2g/SingleLeafModel/ACiSimulation/hybrid/',
! & '/home/l2g/leafres/hybriddata/nicksmith/results/',
! & '/home/l2g/leafres/hybriddata/huidafeng/',
! &'/home/l2g/leafres/hybriddata/dwestonpoplus/data_Pn_tree_1_195_v2/
! &',
@@ -99,43 +106,28 @@
! &storein='/home/l2g/leafweb/users/curves/',
! &storeout='/home/l2g/leafweb/users/results/',
&storein='/home/l2g/leafres/testdata/',
&storeout='/home/l2g/leafres/testdata/',
! &storein='/home/l2g/junk/',
! &storeout='/home/l2g/junk/',
! &storein='../output/clninput/',
! &storeout='../output/fitresult/nottouser/',
&storein='/home/l2g/jimei/',
&storeout='/home/l2g/jimei/',
! &storein='/home/l2g/dataassim/leaf/data/ellsworth/outputs/',
! &storeout='/home/l2g/dataassim/leaf/data/ellsworth/outputs/',
& AllACiFiles='AllLeafGasFiles')
! & AllACiFiles='../piscal.cfg')
&AllACiFiles='/home/l2g/jimei/piscal.cfg')
!---------------End of variable declaration----------------
ierr(1)=-1
ierr(2)=-1
outputfile(1)='leafgasparameters.csv'
outputfile(2)='leafgascomparison.csv'
outputfile(3)='stomwuecicaparameters.csv'
outputfile(4)='stomcomparison.csv'
outputfile(5)='wuecicacomparison.csv'
outputfile(6)='fluorescencefit.csv'
outputfile(7)='fluoresparameters.csv'
outputfile(8)='aciempfitparameters.csv'
outputfile(9)='alightempfitparameters.csv'
outputfile(10)='warningmessage'
outputfile(11)='errormessage'
noutputfiles=11
do i=1,noutputfiles
indexunit(i)=i+9
enddo
do i=1,noutputfiles-1
open(unit=indexunit(i),file=trim(outpath)//trim(outputfile(i)))
enddo
!read A/Ci curve names stored in AllACiFiles
dataunit=1
spareunit=3
open(unit=dataunit,status='scratch')
open(unit=spareunit,file=trim(datapath)//trim(AllACiFiles))
read(spareunit,fmt=300,err=40,end=40)longchar
open(unit=spareunit,file=trim(AllACiFiles))
read(spareunit,fmt=300,err=90,end=90)longchar
rewind(spareunit)
2 read(spareunit,fmt=300,err=40,end=5)longchar
2 read(spareunit,fmt=300,err=90,end=5)longchar
if(longchar.eq.''.or.longchar.eq.' ')goto 2
3 k=index(longchar,char(13))
if(k.gt.0)then
!DOS text format, convert it to unix format
@@ -147,7 +139,34 @@
5 close(spareunit)
rewind(dataunit)
ntotfiles=1
ic3c4cam=-9999
10 read(dataunit,fmt=300,end=20)longchar
if(ntotfiles.eq.1.and.ic3c4cam.lt.0)then
i=0
if((index(longchar,'_photosynthesis_leafweb')+
&index(longchar,'_Photosynthesis_leafweb')+
&index(longchar,'_Photosynthesis_LeafWeb')).gt.0)then
i=index(longchar,'c3')+index(longchar,'C3')
if(i.gt.0)then
ic3c4cam=1
else
i=index(longchar,'c4')+index(longchar,'C4')
if(i.gt.0)then
ic3c4cam=2
else
i=index(longchar,'cam')+index(longchar,'caM')+
&index(longchar,'cAm')+index(longchar,'cAM')+
&index(longchar,'Cam')+index(longchar,'CaM')+
&index(longchar,'CAm')+index(longchar,'CAM')
if(i.gt.0)ic3c4cam=3
endif
endif
endif
if(i.gt.0)goto 10
!if no indication is provided, c3 photosynthesis is assumed and the first line
!contains the name of the first data file
ic3c4cam=1
endif
i=len(longchar)
j=0
15 j=j+1
@@ -170,83 +189,32 @@
goto 10
20 ntotfiles=ntotfiles-1
close(dataunit)
call ToLeafGasOptimization(ntotfiles,ACidata,dataunit,spareunit,
&datapath,indexunit,ierr)
40 do i=1,noutputfiles-1
outputfile(1)='leafgasparameters.csv'
outputfile(2)='leafgascomparison.csv'
outputfile(3)='stomwuecicaparameters.csv'
outputfile(4)='stomcomparison.csv'
outputfile(5)='wuecicacomparison.csv'
outputfile(6)='fluorescencefit.csv'
outputfile(7)='fluoresparameters.csv'
outputfile(8)='aciempfitparameters.csv'
outputfile(9)='alightempfitparameters.csv'
outputfile(10)='warningmessage'
outputfile(11)='errormessage'
noutputfiles=11
do i=1,noutputfiles
if(ic3c4cam.eq.1)outputfile(i)='C3_'//outputfile(i)
if(ic3c4cam.eq.2)outputfile(i)='C4_'//outputfile(i)
if(ic3c4cam.eq.3)outputfile(i)='CAM_'//outputfile(i)
indexunit(i)=i+9
enddo
do i=1,noutputfiles
open(unit=indexunit(i),file=trim(outpath)//trim(outputfile(i)))
enddo
call ToLeafGasOptimization(ic3c4cam,ntotfiles,ACidata,dataunit,
&spareunit,datapath,indexunit,ierr)
do i=1,noutputfiles
close(indexunit(i))
enddo
if(ierr(1).ne.0)then
i=indexunit(noutputfiles)
open(unit=i,file=trim(outpath)//trim(outputfile(noutputfiles)))
if(ierr(1).eq.-1)then
close(spareunit)
write(i,*)
&'No data files to analyze or incorrect file name format'
else
write(i,*)'Input data error in ',trim(ACidata(ierr(2)))
write(i,*)
&'Please resubmit the data after correcting the following error:'
endif
if(ierr(1).eq.1)then
write(i,*)'Photosynthesis (umol/m2/s) out of range'
endif
if(ierr(1).eq.2)then
write(i,*)'Intercellular CO2(ppm) out of range'
endif
if(ierr(1).eq.3)then
write(i,*)'Leaf temperature (oC) out of range'
endif
if(ierr(1).eq.4)then
write(i,*)'Chamber PAR (umol/m2/s) out of range'
endif
if(ierr(1).eq.5)then
write(i,*)'Atmospheric pressure (Pa) out of range'
endif
if(ierr(1).eq.13)then
write(i,*)'Check line 13 for data entry error'
endif
if(ierr(1).eq.14)then
write(i,*)'Specified chloroplastic CO2 compensation point',
&'(Pa) out of range'
endif
if(ierr(1).eq.15)then
write(i,*)'Specified Michaelis-Menten constant for the',
&'carboxylase (Kc) out of range'
endif
if(ierr(1).eq.16)then
write(i,*)'Specified Michaelis-Menten constant for the',
&'oxygenase (Ko) out of range'
endif
if(ierr(1).eq.17)then
write(i,*)'Specified fraction of nonreturned glycolate',
&'carbon(alpha) out of range 0~1'
endif
if(ierr(1).eq.18)then
write(i,*)'Specified dark respiration rate Rd out of range >0'
endif
if(ierr(1).eq.19)then
write(i,*)'Specified internal (mesophyll) conductance gi out',
&'of range >0'
endif
if(ierr(1).eq.34)then
write(i,*)'Check Column 33 or 34. Mixing area- and mass-based
&measurements is not allowed'
endif
if(ierr(1).eq.36)then
write(i,*)'Check line 16 for data entry error'
endif
if(ierr(1).eq.39)then
write(i,*)
&'Check the main body of data for data entry error, starting from
&line 19'
endif
if(ierr(1).eq.40)then
write(i,*)
&'Data file format cannot be recognized'
endif
close(i)
endif
do j=1,noutputfiles
open(unit=2,file=trim(outpath)//trim(outputfile(j)))
read(2,*,end=70)
@@ -260,29 +228,47 @@
80 enddo
!----------------------------------------------------------
!intercept the data
goto 450
399 call date_and_time(rundate,runtime,runzone,runvalues)
90 if(ierr(1).ne.0)then
if(ierr(1).eq.-1)then
close(spareunit)
open(unit=spareunit,file=trim(outpath)//'errormessage')
write(spareunit,*)'No data files to analyze'
close(spareunit)
goto 450
endif
do i=1,ntotfiles
open(unit=1,file=trim(datapath)//'clean'//trim(ACidata(i)))
close(1,status='delete')
enddo
goto 450
endif
call date_and_time(rundate,runtime,runzone,runvalues)
do i=1,ntotfiles
open(unit=1,file=trim(datapath)//trim(ACidata(i)))
open(unit=1,file=trim(datapath)//'clean'//trim(ACidata(i)))
open(unit=2,file=
&trim(storein)//rundate//runtime(1:6)//trim(ACidata(i)))
&trim(storein)//rundate//runtime(1:6)//'clean'//trim(ACidata(i)))
400 read(1,fmt=300,end=410)longchar
write(2,310)trim(longchar)
goto 400
410 close(1)
410 close(1,status='delete')
close(2)
enddo
do i=1,6
do i=1,noutputfiles
k=0
open(unit=1,file=trim(outpath)//trim(outputfile(i)))
open(unit=2,file=
if(i.ge.3.and.i.le.5)then
open(unit=2,file=
&trim(storeout)//rundate//runtime(1:6)//trim(outputfile(i)))
else
open(unit=2,file=
&trim(outpath)//rundate//runtime(1:6)//trim(outputfile(i)))
endif
420 read(1,fmt=300,end=430)longchar
write(2,310)trim(longchar)
k=1
goto 420
430 if(k.eq.1)then
close(1)
close(1,status='delete')
close(2)
else
close(1,status='delete')