Arabidopsis_ Derived Type

type, public :: Arabidopsis_


Components

Type Visibility Attributes Name Initial
integer(kind=int32), public :: TYPE_STEM = 1
integer(kind=int32), public :: TYPE_LEAF = 2
integer(kind=int32), public :: TYPE_ROOT = 3
type(Mesh_), public :: struct
integer(kind=int32), public, allocatable :: leaf2stem(:,:)
integer(kind=int32), public, allocatable :: stem2stem(:,:)
integer(kind=int32), public, allocatable :: root2stem(:,:)
integer(kind=int32), public, allocatable :: root2root(:,:)
real(kind=real64), public :: mainstem_length
real(kind=real64), public :: mainstem_width
integer(kind=int32), public :: mainstem_node
real(kind=real64), public :: mainroot_length
real(kind=real64), public :: mainroot_width
integer(kind=int32), public :: mainroot_node
integer(kind=int32), public :: num_branch_root
integer(kind=int32), public :: num_branch_root_node
real(kind=real64), public :: ms_angle_ave = 0.0d0
real(kind=real64), public :: ms_angle_sig = 0.0d0
integer(kind=int32), public, allocatable :: Leaf_From(:)
real(kind=real64), public, allocatable :: leaf_curvature(:)
real(kind=real64), public, allocatable :: leaf_thickness_ave(:)
real(kind=real64), public, allocatable :: leaf_thickness_sig(:)
real(kind=real64), public, allocatable :: leaf_angle_ave_x(:)
real(kind=real64), public, allocatable :: leaf_angle_sig_x(:)
real(kind=real64), public, allocatable :: leaf_angle_ave_z(:)
real(kind=real64), public, allocatable :: leaf_angle_sig_z(:)
real(kind=real64), public, allocatable :: leaf_length_ave(:)
real(kind=real64), public, allocatable :: leaf_length_sig(:)
real(kind=real64), public, allocatable :: leaf_width_ave(:)
real(kind=real64), public, allocatable :: leaf_width_sig(:)
integer(kind=int32), public :: num_leaf
integer(kind=int32), public :: num_stem
integer(kind=int32), public :: num_root
type(FEMDomain_), public, allocatable :: leaf_list(:)
type(FEMDomain_), public, allocatable :: stem_list(:)
type(FEMDomain_), public, allocatable :: root_list(:)
character(len=:), public, allocatable :: LeafSurfaceData
type(Leaf_), public, allocatable :: Leaf(:)
type(Stem_), public, allocatable :: Stem(:)
type(Root_), public, allocatable :: Root(:)
integer(kind=int32), public, allocatable :: NodeID_MainStem(:)
type(Arabidopsis_NodeID_Branch_), public, allocatable :: NodeID_Branch(:)
logical, public :: inLoop = .false.
real(kind=real64), public :: hours = 0.0d0
real(kind=real64), public :: FullyExpanded_stem_threshold = 0.10d0
integer(kind=int32), public :: MaxBranchNum = 20
type(Arabidopsis_internode_info_), public, allocatable :: InterNodeInfo(:)
real(kind=real64), public :: default_Leaf_growth_ratio = 1.0d0/3.0d0
real(kind=real64), public :: default_Stem_growth_ratio = 1.0d0/3.0d0
integer(kind=int32), public, allocatable :: MainStem_num_branch(:)
real(kind=real64), public :: apical_dominance_distance = 1.0d0
type(ContactMechanics_), public :: contact
real(kind=real64), public :: Gravity_acceralation = 9.810d0
real(kind=real64), public :: PenaltyParameter = 100000.0d0
logical, public :: GaussPointProjection = .false.
integer(kind=int32), public :: stem_division(1:3) = [10, 10, 10]
integer(kind=int32), public :: leaf_division(1:3) = [10, 10, 10]

Type-Bound Procedures

procedure, public :: init => createArabidopsis

  • public subroutine createArabidopsis(this, config, debug)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: config
    logical, intent(in), optional :: debug

procedure, public :: create => createArabidopsis

  • public subroutine createArabidopsis(this, config, debug)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: config
    logical, intent(in), optional :: debug

procedure, public :: msh => mshArabidopsis

  • public subroutine mshArabidopsis(this, name, num_threads)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: name
    integer(kind=int32), intent(in), optional :: num_threads

procedure, public :: vtk => vtkArabidopsis

  • public subroutine vtkArabidopsis(this, name, num_threads, single_file, scalar_field, vector_field, tensor_field, field_name)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: name
    integer(kind=int32), intent(in), optional :: num_threads
    logical, intent(in), optional :: single_file
    real(kind=real64), intent(in), optional :: scalar_field(:)
    real(kind=real64), intent(in), optional :: vector_field(:,:)
    real(kind=real64), intent(in), optional :: tensor_field(:,:,:)
    character(len=*), intent(in), optional :: field_name

procedure, public :: stl => stlArabidopsis

  • public subroutine stlArabidopsis(this, name, num_threads, single_file)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: name
    integer(kind=int32), intent(in), optional :: num_threads
    logical, intent(in), optional :: single_file

procedure, public :: json => jsonArabidopsis

  • public subroutine jsonArabidopsis(this, name)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: name

procedure, public :: update => updateArabidopsis

  • public recursive subroutine updateArabidopsis(this, stem_id, root_id, leaf_id, overset_margin, debug)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    integer(kind=int32), intent(in), optional :: stem_id
    integer(kind=int32), intent(in), optional :: root_id
    integer(kind=int32), intent(in), optional :: leaf_id
    real(kind=real64), intent(in), optional :: overset_margin
    logical, intent(in), optional :: debug

procedure, public :: remove => removeArabidopsis

  • public subroutine removeArabidopsis(this, root)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    logical, intent(in), optional :: root

procedure, public :: rotate => rotateArabidopsis

  • public subroutine rotateArabidopsis(this, x, y, z)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in), optional :: x
    real(kind=real64), intent(in), optional :: y
    real(kind=real64), intent(in), optional :: z

procedure, public :: move => moveArabidopsis

  • public subroutine moveArabidopsis(this, x, y, z)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in), optional :: x
    real(kind=real64), intent(in), optional :: y
    real(kind=real64), intent(in), optional :: z

procedure, public :: getElementList => getElementListArabidopsis

  • public function getElementListArabidopsis(this, x_min, x_max, y_min, y_max, z_min, z_max, debug) result(ElementList)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in), optional :: x_min
    real(kind=real64), intent(in), optional :: x_max
    real(kind=real64), intent(in), optional :: y_min
    real(kind=real64), intent(in), optional :: y_max
    real(kind=real64), intent(in), optional :: z_min
    real(kind=real64), intent(in), optional :: z_max
    logical, intent(in), optional :: debug

    Return Value integer(kind=int32), allocatable, (:,:)

procedure, public :: ns => nsArabidopsis

  • public function nsArabidopsis(this) result(ret)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value integer(kind=int32)

procedure, public :: ne => neArabidopsis

  • public function neArabidopsis(this) result(ret)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value integer(kind=int32)

procedure, public :: nn => nnArabidopsis

  • public pure function nnArabidopsis(this) result(ret)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value integer(kind=int32)

procedure, public :: checkMemoryRequirement => checkMemoryRequirementArabidopsis

procedure, public :: numleaf => numleafArabidopsis

  • public function numleafArabidopsis(this) result(ret)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value integer(kind=int32)

procedure, public :: numstem => numStemArabidopsis

  • public function numStemArabidopsis(this) result(ret)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value integer(kind=int32)

procedure, public :: numroot => numRootArabidopsis

  • public function numRootArabidopsis(this) result(ret)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value integer(kind=int32)

procedure, public :: getFEMDomainPointers => getFEMDomainPointersArabidopsis

procedure, public :: checkYoungModulus => checkYoungModulusArabidopsis

procedure, public :: checkPoissonRatio => checkPoissonRatioArabidopsis

procedure, public :: checkDensity => checkDensityArabidopsis

  • public function checkDensityArabidopsis(this) result(all_young_modulus_is_set)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this

    Return Value logical

procedure, public :: getYoungModulus => getYoungModulusArabidopsis

  • public function getYoungModulusArabidopsis(this, DomainID, ElementID) result(YoungModulus)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this
    integer(kind=int32), intent(in), optional :: DomainID
    integer(kind=int32), intent(in), optional :: ElementID

    Return Value real(kind=real64)

procedure, public :: getPoissonRatio => getPoissonRatioArabidopsis

  • public function getPoissonRatioArabidopsis(this, DomainID, ElementID) result(PoissonRatio)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this
    integer(kind=int32), intent(in) :: DomainID
    integer(kind=int32), intent(in) :: ElementID

    Return Value real(kind=real64)

procedure, public :: getDensity => getDensityArabidopsis

  • public function getDensityArabidopsis(this, DomainID, ElementID) result(Density)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(in) :: this
    integer(kind=int32), intent(in) :: DomainID
    integer(kind=int32), intent(in) :: ElementID

    Return Value real(kind=real64)

procedure, public :: getYoungModulusField => getYoungModulusFieldArabidopsis

procedure, public :: getPoissonRatioField => getPoissonRatioFieldArabidopsis

procedure, public :: getDensityField => getDensityFieldArabidopsis

  • public function getDensityFieldArabidopsis(this) result(Density)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this

    Return Value real(kind=real64), allocatable, (:)

procedure, public :: getStressField => getStressFieldArabidopsis

  • public function getStressFieldArabidopsis(this, displacement, i, j, option) result(StressField)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in) :: displacement(:)
    integer(kind=int32), intent(in), optional :: i
    integer(kind=int32), intent(in), optional :: j
    character(len=*), intent(in), optional :: option

    Return Value real(kind=real64), allocatable, (:)

procedure, public :: setYoungModulus => setYoungModulusArabidopsis

  • public recursive subroutine setYoungModulusArabidopsis(this, YoungModulus, stem, root, leaf, ElementList)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in) :: YoungModulus
    logical, intent(in), optional :: stem
    logical, intent(in), optional :: root
    logical, intent(in), optional :: leaf
    integer(kind=int32), intent(in), optional :: ElementList(:,:)

procedure, public :: setPoissonRatio => setPoissonRatioArabidopsis

  • public recursive subroutine setPoissonRatioArabidopsis(this, PoissonRatio, stem, root, leaf)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in) :: PoissonRatio
    logical, intent(in), optional :: stem
    logical, intent(in), optional :: root
    logical, intent(in), optional :: leaf

procedure, public :: setDensity => setDensityArabidopsis

  • public recursive subroutine setDensityArabidopsis(this, Density, stem, root, leaf)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    real(kind=real64), intent(in) :: Density
    logical, intent(in), optional :: stem
    logical, intent(in), optional :: root
    logical, intent(in), optional :: leaf

procedure, public :: getEigenMode => getEigenModeArabidopsis

  • public function getEigenModeArabidopsis(this, ground_level, penalty, debug, Frequency, EbOM_Algorithm, num_mode) result(EigenVectors)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout), target :: this
    real(kind=real64), intent(in) :: ground_level
    real(kind=real64), intent(in), optional :: penalty
    logical, intent(in), optional :: debug
    real(kind=real64), intent(inout), allocatable :: Frequency(:)
    character(len=*), intent(in), optional :: EbOM_Algorithm
    integer(kind=int32), intent(in), optional :: num_mode

    Return Value real(kind=real64), allocatable, (:,:)

procedure, public :: getDisplacement => getDisplacementArabidopsis

  • public function getDisplacementArabidopsis(this, ground_level, penalty, debug, EbOM_Algorithm) result(displacement)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout), target :: this
    real(kind=real64), intent(in) :: ground_level
    real(kind=real64), intent(in), optional :: penalty
    logical, intent(in), optional :: debug
    character(len=*), intent(in), optional :: EbOM_Algorithm

    Return Value real(kind=real64), allocatable, (:)

procedure, public :: deform => deformArabidopsis

  • public subroutine deformArabidopsis(this, displacement)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout), target :: this
    real(kind=real64), intent(in), optional :: displacement(:)

procedure, public :: export_eig => export_eigArabidopsis

  • public subroutine export_eigArabidopsis(this, Name, Frequency, ModeVectors, stress_type)

    Arguments

    Type IntentOptional Attributes Name
    class(Arabidopsis_), intent(inout) :: this
    character(len=*), intent(in) :: Name
    real(kind=real64), intent(in) :: Frequency(:)
    real(kind=real64), intent(in) :: ModeVectors(:,:)
    character(len=*), intent(in), optional :: stress_type