PlantsConfig Subroutine

SUBROUTINE  PlantsConfig &
!
(iniFile, mask, begin, end)


IMPLICIT NONE

! Arguments with intent(in):
CHARACTER (LEN = 300), INTENT(IN) :: iniFile !!configuration file 
TYPE (grid_integer), INTENT(IN) :: mask  !!mask of simulation domain
TYPE (DateTime), INTENT (IN) :: begin !!simulation starting date
TYPE (DateTime), INTENT(IN) :: end !!simulation ending date


!local declarations:
TYPE(IniList) :: iniDB !!store configuration info
INTEGER (KIND = short) :: i, j, k
CHARACTER (LEN = 300) :: species_file
CHARACTER (LEN = 300) :: ICfile
CHARACTER (LEN = 300) :: PMfile
REAL (KIND = float)   :: scalar


!------------end of declaration------------------------------------------------    

CALL IniOpen (iniFile, iniDB)

!need plants dynamic simulation?
simulatePlants = IniReadInt ('plants-simulation', iniDB)

IF ( simulatePlants == 1) THEN !plants dynamic is simulated: configure forest model
    !plants mask 
    IF ( SectionIsPresent ( 'plants-mask', iniDB)  ) THEN
        CALL GridByIni (iniDB, plants_mask, section = 'plants-mask')
    
    ELSE
        CALL Catch ('error', 'Plants', 'Mask missing in configuration file')
    END IF
    
    !CO2 modifier
    IF ( SectionIsPresent ( 'use-co2-modifier', iniDB)  ) THEN
        IF ( IniReadInt ('use-co2-modifier', iniDB) == 1 ) THEN
            useCO2modifier = .TRUE.
        ELSE 
            useCO2modifier = .FALSE.
        END IF
    ELSE
       !if key is not found, set it to default false
       useCO2modifier = .FALSE.
    END IF
    
    
    !mortality
    IF ( KeyIsPresent ( 'mortality', iniDB)  ) THEN
        IF ( IniReadInt ('mortality', iniDB) == 1 ) THEN
            mortality = .TRUE.
        ELSE 
            mortality = .FALSE.
        END IF
    ELSE
       !if mortality is not found, assume it is not considered
       mortality = .FALSE.
    END IF
    
    
    !load species
    species_file = IniReadString ('plants-species-file', iniDB)
    CALL ReadSpecies (species_file)
    
    !compute number of stands and allocate 
    count_stands = 0
    DO i = 1, plants_mask % idim
        DO j = 1, plants_mask % jdim
            IF ( plants_mask % mat (i,j) /= plants_mask % nodata ) THEN
               count_stands = count_stands + 1
            END IF
        END DO
    END DO

    ALLOCATE ( forest ( count_stands) )

    !initialize list
    k = 1
    DO i = 1, plants_mask % idim
        DO j = 1, plants_mask % jdim
            IF ( plants_mask % mat (i,j) /= plants_mask % nodata ) THEN
                !initialize the first cohort in the stand
                ALLOCATE ( forest (k) % first)
                NULLIFY ( forest (k) % first % next)
                forest (k) % lenght = 1
                !store position of stand
               forest (k) % i = i
               forest (k) % j = j
               k = k + 1
            END IF
        END DO
    END DO
    
    
    !set initial condition
    ICfile = IniReadString ('plants-ic-file', iniDB)
    CALL SetIC (ICfile)
    
    !set plants management options
    IF (KeyIsPresent ('plants-management-file',iniDB) ) THEN 
        plants_management = .TRUE.
        PMfile = IniReadString ('plants-management-file', iniDB)
        CALL SetPlantsManagement (PMfile, begin, end)
        !set management pratice for each stand
        DO k = 1, count_stands
            CALL SetPractice (  management_map % mat (forest (k) % i, forest (k) % j) , forest (k) % thinning )
        END DO

    ELSE !management is turned off
        plants_management = .FALSE.
    END IF
    
    
    !set interception maps if required
    IF (interceptionParametersByMap == 0 ) THEN
         CALL Catch ('warning', 'Plants', 'interception parameters are set only where plants map is not nodata')
         
         !allocate maps
         CALL NewGrid (laimax, plants_mask)	
         CALL NewGrid (canopymax, plants_mask)	
         
         DO k = 1, count_stands
             i = forest (k) % i
             j = forest (k) % j 
             laimax % mat (i,j) = forest (k) % first % species % laimax
             canopymax % mat (i,j) = forest (k) % first % species % canopymax
         END DO
        
    END IF
    
    
    !allocate grids for state variables
    CALL NewGrid (lai, plants_mask)
    CALL NewGrid (fvcover, plants_mask)
    CALL NewGrid (gpp, plants_mask)
    CALL NewGrid (npp, plants_mask)
    CALL NewGrid (carbonroot, plants_mask)
    CALL NewGrid (carbonstem, plants_mask)
    CALL NewGrid (carbonleaf, plants_mask)
    CALL NewGrid (dbh, plants_mask)
    CALL NewGrid (plantsHeight, plants_mask)
    CALL NewGrid (density, plants_mask)
    CALL NewGrid (stemyield, plants_mask)
    
    !fill in grids
    CALL ForestToGrid (lai, 'lai') 
    CALL ForestToGrid (fvcover, 'fv')
    CALL ForestToGrid (gpp, 'gpp')
    CALL ForestToGrid (npp, 'npp')
    CALL ForestToGrid (carbonroot, 'root')
    CALL ForestToGrid (carbonstem, 'stem')
    CALL ForestToGrid (carbonleaf, 'leaf')
    CALL ForestToGrid (dbh, 'dbh')
    CALL ForestToGrid (plantsHeight, 'height')
    CALL ForestToGrid (density, 'density')
    CALL ForestToGrid (stemyield, 'stemyield')
    
    fvcoverLoaded = .TRUE.
    laiLoaded = .TRUE.
    plantsHeightLoaded = .TRUE.
    
ELSE ! no plants dynamic simulation required: read parameters from files
    
    !leaf area index
    IF ( SectionIsPresent ( 'lai', iniDB)  ) THEN
        IF (KeyIsPresent ('scalar', iniDB, 'lai') ) THEN
             scalar = IniReadReal ('scalar', iniDB, 'lai')
             CALL NewGrid (lai, mask, scalar)
        ELSE
            !check if parameter may change in time
             IF (KeyIsPresent ('format', iniDB, 'lai') ) THEN
                 IF ( IniReadString ('format', iniDB, 'lai') == 'net-cdf' ) THEN
                       updatePlantsParameters = .TRUE.
                 END IF
             END IF
             !read map
             CALL GridByIni (iniDB, lai, section = 'lai')
            
        END IF
        laiLoaded = .TRUE.
    ELSE
        CALL Catch ('warning', 'Plants', 'LAI missing in configuration file')
    END IF

    !fraction of vegetation coverage
    IF ( SectionIsPresent ( 'vegetation-fraction', iniDB)  ) THEN
        IF (KeyIsPresent ('scalar', iniDB, 'vegetation-fraction') ) THEN
             scalar = IniReadReal ('scalar', iniDB, 'vegetation-fraction')
             CALL NewGrid (fvcover, mask, scalar)
        ELSE
             !check if parameter may change in time
             IF (KeyIsPresent ('format', iniDB, 'vegetation-fraction') ) THEN
                 IF ( IniReadString ('format', iniDB, 'vegetation-fraction') == 'net-cdf' ) THEN
                       updatePlantsParameters = .TRUE.
                 END IF
             END IF
             !read map
             CALL GridByIni (iniDB, fvcover, section = 'vegetation-fraction')
        END IF
        fvcoverLoaded = .TRUE.
    ELSE
        CALL Catch ('warning', 'Plants', 'vegetation-fraction is missing')
    END IF
    
    
    !plants height
    IF ( SectionIsPresent ( 'vegetation-height', iniDB)  ) THEN
        IF (KeyIsPresent ('scalar', iniDB, 'vegetation-height') ) THEN
             scalar = IniReadReal ('scalar', iniDB, 'vegetation-height')
             CALL NewGrid (plantsHeight, mask, scalar)
        ELSE
             !check if parameter may change in time
             IF (KeyIsPresent ('format', iniDB, 'vegetation-height') ) THEN
                 IF ( IniReadString ('format', iniDB, 'vegetation-height') == 'net-cdf' ) THEN
                       updatePlantsParameters = .TRUE.
                 END IF
             END IF
             !read map
             CALL GridByIni (iniDB, plantsHeight, section = 'vegetation-height')
        END IF
        plantsHeightLoaded = .TRUE.
    ELSE
        CALL Catch ('warning', 'Plants', 'vegetation-height is missing')
    END IF
    
END IF

!minimum stomatal resistance. this is not computed by forest model and it may be used for computing PET
IF ( SectionIsPresent ( 'min-stomatal-resistance', iniDB)  ) THEN
        IF (KeyIsPresent ('scalar', iniDB, 'min-stomatal-resistance') ) THEN
             scalar = IniReadReal ('scalar', iniDB, 'min-stomatal-resistance')
             CALL NewGrid (rsMin, mask, scalar)
        ELSE
             !check if parameter may change in time
             IF (KeyIsPresent ('format', iniDB, 'min-stomatal-resistance') ) THEN
                 IF ( IniReadString ('format', iniDB, 'min-stomatal-resistance') == 'net-cdf' ) THEN
                       updatePlantsParameters = .TRUE.
                 END IF
             END IF
             !read map
             CALL GridByIni (iniDB, rsMin, section = 'min-stomatal-resistance')
        END IF
        rsMinLoaded = .TRUE.
    ELSE
        CALL Catch ('warning', 'Plants', 'min-stomatal-resistance is missing')
    END IF


CALL IniClose (iniDB)

RETURN
END SUBROUTINE PlantsConfig