species_element_config_type

type, public, extends(abstract_config_type) :: species_element_config_type

Used to represent the input configuration of species

Type-Bound Procedures

is_initialised init setup write_namelist_header get_name get_requires_index write_namelist_footer write_key_val read write reset broadcast get_default_name get_default_requires_index

Source Code

species_element_config_type

Components

Type	Visibility		Name		Initial
logical,	public	::	exist	=	.false.	Does the related namelist exist in the target input file?
integer,	public	::	index	=	0	Used to hold the specific index of numbered namelists
logical,	public	::	skip_read	=	.false.	Do we want to skip the read step in init?
logical,	public	::	skip_broadcast	=	.false.	Do we want to skip the broadcast step in init?
real,	public	::	bess_fac	=	1.0	Multiplies the argument of the Bessel function for this species. Useful for exploring the effect of the Bessel functions.
real,	public	::	dens	=	1.0	Set the normalised density for this species
real,	public	::	dens0	=	1.0	Parameter used for a few specific initial condition types. Todo Consider moving this parameter to init_g_knobs.
character(len=20),	public	::	f0type	=	"default"	Select which type of background distribution should be assumed for this species. Must be one of: 'default' : equivalent to maxwellian 'maxwellian' : Standard maxwellian 'tabulated' : A general tabulated form 'sdanalytic' : A analytic slowing down form. See G. Wilkie thesis.
real,	public	::	fprim	=	2.2	Normalised inverse density gradient: $-\frac{1}{n}\frac{dn}{d \rho_N}$ (Note here $\rho_N$ is the normalised radius $\frac{\rho}{L_\textrm{ref}}$ .
real,	public	::	mass	=	1.0	Normalised mass of this species
real,	public	::	nu_h	=	0.0	Set the species hyper collision frequency used in the pitch angle scattering collision operator if [[collision_knobs::hypermult]] is `true`.
real,	public	::	temp	=	1.0	Set the normalised species temperature
real,	public	::	tpar0	=	0.	Parameter used for a few specific initial condition types. Todo Consider moving this parameter to init_g_knobs.
real,	public	::	tperp0	=	0.	Parameter used for a few specific initial condition types. Todo Consider moving this parameter to init_g_knobs.
real,	public	::	tprim	=	6.9	Normalised inverse temperature gradient: $-\frac{1}{T}\frac{dT}{d \rho_N}$ (Note here $\rho_N$ is the normalised radius $\frac{\rho}{L_\textrm{ref}}$ .
character(len=20),	public	::	type	=	"default"	Sets the characterisation of the species. Should be one of 'ion' : Thermal ion species 'default' : Same as 'ion' 'electron' : Thermal electron species 'e' : Same as 'electron' 'trace' : Tracer species 'hybrid_electron' : Adiabatic passing electrons, full trapped electron treatment. NOTE: This option is currently considered experimental and is intended for use in electrostatic simulations. This primarily controls the treatment in the collision operator, the detection of adiabatic species. Tracer species do not contribute to velocity space integrals.
real,	public	::	u0	=	1.0	Parameter used for a few specific initial condition types. Todo Consider moving this parameter to init_g_knobs.
real,	public	::	uprim	=	0.0	Controls an energy independent part of a source term. Note Documentation needs improving, looks like it's an early attempt at adding in the parallel flow shear drive term. This effectively provides a constant offset to the parallel flow shear term, allowing one to add a species dependent shift.
real,	public	::	uprim2	=	0.0	Controls an energy dependent part of a source term. Note Documentation needs improving, looks like it's an early attempt at adding in the parallel flow shear drive term. This effectively provides a energy dependent offset to the parallel flow shear term, allowing one to add a species and energy dependent shift.
real,	public	::	vcprim	=	-999.9	Part of the `sdanalytic` slowing down model. See G. Wilkie thesis.
real,	public	::	vcrit	=	-1.0	Part of the `sdanalytic` slowing down model. See G. Wilkie thesis.
real,	public	::	vnewk	=	0.0	Sets the normalised species-species collisionality frequency. For species s, `vnewk = nu_ss Lref/vref` where Lref is the reference length, `vref` is the reference thermal speed (not the thermal speed of species s!), $\nu_{ss}=\sqrt{2}\pi n_s Z_s^4 e^4 \log(\lambda)/\sqrt{m_s}T^{3/2}_s$ is a dimensional collision frequency, e is the proton charge, $\log(\lambda)$ is the Coloumb logarithm, and $Z_s,T_s,n_s,m_s$ are the (charge, temperature, density, mass) of species s. (The dimensional collision frequency given here is in Gaussian units. For SI units, include an extra factor $(4\pi\epsilon_0)^2$ in the denominator of the definition of $\nu_{ss}$ .
real,	public	::	z	=	1.0	Normalised species charge

Type-Bound Procedures

procedure, public, :: is_initialised => is_initialised_generic

private function is_initialised_generic(self)

Is this instance initialised?

Arguments

Type	Intent	Optional	Attributes		Name
class(abstract_config_type),	intent(in)			::	self

Return Value logical

procedure, public, :: init => init_generic

private subroutine init_generic(self, name, requires_index, index)

Fully initialise the config object

Arguments

Type	Intent	Optional		Name
class(abstract_config_type),	intent(inout)		::	self
character(len=*),	intent(in),	optional	::	name
logical,	intent(in),	optional	::	requires_index
integer,	intent(in),	optional	::	index

procedure, public, :: setup => setup_generic

private subroutine setup_generic(self, name, requires_index, index)

Do some standard setup/checking

Arguments

Type	Intent	Optional		Name
class(abstract_config_type),	intent(inout)		::	self
character(len=*),	intent(in),	optional	::	name
logical,	intent(in),	optional	::	requires_index
integer,	intent(in),	optional	::	index

procedure, public, :: write_namelist_header

private subroutine write_namelist_header(self, unit)

Write the namelist header for this instance

Arguments

Type	Intent	Optional	Attributes		Name
class(abstract_config_type),	intent(in)			::	self
integer,	intent(in)			::	unit

procedure, public, :: get_name => get_name_generic

private function get_name_generic(self)

Returns the namelist name. Not very useful at the moment but may want to do more interesting things in the future

Arguments

Type	Intent	Optional	Attributes		Name
class(abstract_config_type),	intent(in)			::	self

Return Value character(len=CONFIG_MAX_NAME_LEN)

procedure, public, :: get_requires_index => get_requires_index_generic

private function get_requires_index_generic(self)

Returns the requires_index value. Allows access whilst keeping the variable private

Arguments

Type	Intent	Optional	Attributes		Name
class(abstract_config_type),	intent(in)			::	self

Return Value logical

procedure, public, nopass :: write_namelist_footer

private subroutine write_namelist_footer(unit)

Write the namelist footer

Arguments

Type	Intent	Optional	Attributes		Name
integer,	intent(in)			::	unit

generic, public, :: write_key_val => write_key_val_string, write_key_val_real, write_key_val_complex, write_key_val_integer, write_key_val_logical, write_key_val_real_array, write_key_val_complex_array, write_key_val_integer_array

private subroutine write_key_val_string(key, val, unit)

Writes a {key,val} pair where the value is of type character

Arguments

Type	Intent		Name
character(len=*),	intent(in)	::	key
character(len=*),	intent(in)	::	val
integer,	intent(in)	::	unit

private subroutine write_key_val_real(key, val, unit)

Writes a {key,val} pair where the value is of type real

Arguments

Type	Intent		Name
character(len=*),	intent(in)	::	key
real,	intent(in)	::	val
integer,	intent(in)	::	unit

private subroutine write_key_val_complex(key, val, unit)

Writes a {key,val} pair where the value is of type complex

Arguments

Type	Intent		Name
character(len=*),	intent(in)	::	key
complex,	intent(in)	::	val
integer,	intent(in)	::	unit

private subroutine write_key_val_integer(key, val, unit)

Writes a {key,val} pair where the value is of type integer

Arguments

Type	Intent		Name
character(len=*),	intent(in)	::	key
integer,	intent(in)	::	val
integer,	intent(in)	::	unit

private subroutine write_key_val_logical(key, val, unit)

Writes a {key,val} pair where the value is of type logical

Arguments

Type	Intent		Name
character(len=*),	intent(in)	::	key
logical,	intent(in)	::	val
integer,	intent(in)	::	unit

private subroutine write_key_val_real_array(self, key, val, unit)

Writes a {key,val} pair where the value is of type real array

Arguments

Type	Intent	Attributes		Name
class(abstract_config_type),	intent(in)		::	self
character(len=*),	intent(in)		::	key
real,	intent(in),	dimension(:)	::	val
integer,	intent(in)		::	unit

private subroutine write_key_val_complex_array(self, key, val, unit)

Writes a {key,val} pair where the value is of type complex array

Arguments

Type	Intent	Attributes		Name
class(abstract_config_type),	intent(in)		::	self
character(len=*),	intent(in)		::	key
complex,	intent(in),	dimension(:)	::	val
integer,	intent(in)		::	unit

private subroutine write_key_val_integer_array(self, key, val, unit)

Writes a {key,val} pair where the value is of type integer array

Arguments

Type	Intent	Attributes		Name
class(abstract_config_type),	intent(in)		::	self
character(len=*),	intent(in)		::	key
integer,	intent(in),	dimension(:)	::	val
integer,	intent(in)		::	unit

procedure, public :: read => read_species_element_config

private subroutine read_species_element_config(self)

Reads in the species_parameters namelist and populates the member variables

Arguments

Type	Intent	Optional	Attributes		Name
class(species_element_config_type),	intent(inout)			::	self

procedure, public :: write => write_species_element_config

private subroutine write_species_element_config(self, unit)

Writes out a namelist representing the current state of the config object

Arguments

Type	Intent	Optional	Attributes		Name
class(species_element_config_type),	intent(in)			::	self
integer,	intent(in),	optional		::	unit

procedure, public :: reset => reset_species_element_config

private subroutine reset_species_element_config(self)

Resets the config object to the initial empty state

Arguments

Type	Intent	Optional	Attributes		Name
class(species_element_config_type),	intent(inout)			::	self

procedure, public :: broadcast => broadcast_species_element_config

private subroutine broadcast_species_element_config(self)

Broadcasts all config parameters so object is populated identically on all processors

Arguments

Type	Intent	Optional	Attributes		Name
class(species_element_config_type),	intent(inout)			::	self

procedure, public, nopass :: get_default_name => get_default_name_species_element_config

private function get_default_name_species_element_config()

Gets the default name for this namelist

Arguments
None
Return Value character(len=CONFIG_MAX_NAME_LEN)

procedure, public, nopass :: get_default_requires_index => get_default_requires_index_species_element_config

private function get_default_requires_index_species_element_config()

Gets the default requires index for this namelist

Arguments
None
Return Value logical

Source Code

  type, extends(abstract_config_type) :: species_element_config_type
     ! namelist : species_parameters
     ! indexed : true
     !> Multiplies the argument of the Bessel function for this
     !> species. Useful for exploring the effect of the Bessel
     !> functions.
     real :: bess_fac = 1.0
     !> Set the normalised density for this species
     real :: dens = 1.0
     !> Parameter used for a few specific initial condition types.
     !>
     !> @todo Consider moving this parameter to [[init_g_knobs]].
     real :: dens0 = 1.0
     !> Select which type of background distribution should be assumed
     !> for this species. Must be one of:
     !>
     !> - 'default' : equivalent to maxwellian
     !> - 'maxwellian' : Standard maxwellian
     !> - 'tabulated' : A general tabulated form
     !> - 'sdanalytic' : A analytic slowing down form.
     !>
     !> See [G. Wilkie
     !> thesis](https://drum.lib.umd.edu/handle/1903/17302).
     character(len = 20) :: f0type = "default"
     !> Normalised inverse density gradient: \(-\frac{1}{n}\frac{dn}{d
     !> \rho_N}\) (Note here \(\rho_N\) is the normalised radius
     !> \(\frac{\rho}{L_\textrm{ref}}\).
     real :: fprim = 2.2
     !> Normalised mass of this species
     real :: mass = 1.0
     !> Set the species hyper collision frequency used in the pitch
     !> angle scattering collision operator if
     !> [[collision_knobs::hypermult]] is `true`.
     real :: nu_h = 0.0
     !> Set the normalised species temperature
     real :: temp = 1.0
     !> Parameter used for a few specific initial condition types.
     !>
     !> @todo Consider moving this parameter to [[init_g_knobs]].
     real :: tpar0 = 0.
     !> Parameter used for a few specific initial condition types.
     !>
     !> @todo Consider moving this parameter to [[init_g_knobs]].
     real :: tperp0 = 0.
     !> Normalised inverse temperature gradient: \(-\frac{1}{T}\frac{dT}{d
     !> \rho_N}\) (Note here \(\rho_N\) is the normalised radius
     !> \(\frac{\rho}{L_\textrm{ref}}\).
     real :: tprim = 6.9
     !> Sets the characterisation of the species. Should be one of
     !>
     !> - 'ion' : Thermal ion species
     !> - 'default' :  Same as 'ion'
     !> - 'electron' : Thermal electron species
     !> - 'e' : Same as 'electron'
     !> - 'trace' : Tracer species
     !> - 'hybrid_electron' : Adiabatic passing electrons, full
     !>    trapped electron treatment. *NOTE: This option is currently
     !>    considered experimental and is intended for use in
     !>    electrostatic simulations.*
     !>
     !> This primarily controls the treatment in the collision
     !> operator, the detection of adiabatic species. Tracer species
     !> do not contribute to velocity space integrals.
     character(len = 20) :: type = "default"
     !> Parameter used for a few specific initial condition types.
     !>
     !> @todo Consider moving this parameter to [[init_g_knobs]].
     real :: u0 = 1.0
     !> Controls an energy independent part of a source term.
     !>
     !> @note Documentation needs improving, looks like it's an early
     !> attempt at adding in the parallel flow shear drive term. This
     !> effectively provides a constant offset to the parallel flow
     !> shear term, allowing one to add a species dependent shift.
     real :: uprim = 0.0
     !> Controls an energy dependent part of a source term.
     !>
     !> @note Documentation needs improving, looks like it's an early
     !> attempt at adding in the parallel flow shear drive term. This
     !> effectively provides a energy dependent offset to the parallel
     !> flow shear term, allowing one to add a species and energy
     !> dependent shift.
     real :: uprim2 = 0.0
     !> Part of the `sdanalytic` slowing down model. See [G. Wilkie
     !> thesis](https://drum.lib.umd.edu/handle/1903/17302).
     real :: vcprim = -999.9
     !> Part of the `sdanalytic` slowing down model. See [G. Wilkie
     !> thesis](https://drum.lib.umd.edu/handle/1903/17302).
     real :: vcrit = -1.0
     !> Sets the normalised species-species collisionality
     !> frequency. For species s, `vnewk = nu_ss Lref/vref` where Lref
     !> is the reference length, `vref` is the reference thermal speed
     !> (not the thermal speed of species s!), \(\nu_{ss}=\sqrt{2}\pi
     !> n_s Z_s^4 e^4 \log(\lambda)/\sqrt{m_s}T^{3/2}_s\) is a
     !> dimensional collision frequency, e is the proton charge,
     !> \(\log(\lambda)\) is the Coloumb logarithm, and
     !> \(Z_s,T_s,n_s,m_s\) are the (charge, temperature, density,
     !> mass) of species s. (The dimensional collision frequency given
     !> here is in Gaussian units. For SI units, include an extra
     !> factor \((4\pi\epsilon_0)^2\) in the denominator of the
     !> definition of \(\nu_{ss}\).
     real :: vnewk = 0.0
     !> Normalised species charge
     real :: z = 1.0
   contains
     procedure, public :: read => read_species_element_config
     procedure, public :: write => write_species_element_config
     procedure, public :: reset => reset_species_element_config
     procedure, public :: broadcast => broadcast_species_element_config
     procedure, public, nopass :: get_default_name => get_default_name_species_element_config
     procedure, public, nopass :: get_default_requires_index => get_default_requires_index_species_element_config
  end type species_element_config_type

species_element_config_type Derived Type

Contents

Variables

Type-Bound Procedures

Source Code

type, public, extends(abstract_config_type) :: species_element_config_type

Contents

Variables

Type-Bound Procedures

Source Code

Components

Todo

Todo

Todo

Todo

Note

Note

Type-Bound Procedures

procedure, public, :: is_initialised => is_initialised_generic

private function is_initialised_generic(self)

Arguments

Return Value logical

procedure, public, :: init => init_generic

private subroutine init_generic(self, name, requires_index, index)

Arguments

procedure, public, :: setup => setup_generic

private subroutine setup_generic(self, name, requires_index, index)

Arguments

procedure, public, :: write_namelist_header

private subroutine write_namelist_header(self, unit)

Arguments

procedure, public, :: get_name => get_name_generic

private function get_name_generic(self)

Arguments

Return Value character(len=CONFIG_MAX_NAME_LEN)

procedure, public, :: get_requires_index => get_requires_index_generic

private function get_requires_index_generic(self)

Arguments

Return Value logical

procedure, public, nopass :: write_namelist_footer

private subroutine write_namelist_footer(unit)

Arguments

generic, public, :: write_key_val => write_key_val_string, write_key_val_real, write_key_val_complex, write_key_val_integer, write_key_val_logical, write_key_val_real_array, write_key_val_complex_array, write_key_val_integer_array

private subroutine write_key_val_string(key, val, unit)

Arguments

private subroutine write_key_val_real(key, val, unit)

Arguments

private subroutine write_key_val_complex(key, val, unit)

Arguments

private subroutine write_key_val_integer(key, val, unit)

Arguments

private subroutine write_key_val_logical(key, val, unit)

Arguments

private subroutine write_key_val_real_array(self, key, val, unit)

Arguments

private subroutine write_key_val_complex_array(self, key, val, unit)

Arguments

private subroutine write_key_val_integer_array(self, key, val, unit)

Arguments

procedure, public :: read => read_species_element_config

private subroutine read_species_element_config(self)

Arguments

procedure, public :: write => write_species_element_config

private subroutine write_species_element_config(self, unit)

Arguments

procedure, public :: reset => reset_species_element_config

private subroutine reset_species_element_config(self)

Arguments

procedure, public :: broadcast => broadcast_species_element_config

private subroutine broadcast_species_element_config(self)

Arguments

procedure, public, nopass :: get_default_name => get_default_name_species_element_config

private function get_default_name_species_element_config()

Arguments

Return Value character(len=CONFIG_MAX_NAME_LEN)

procedure, public, nopass :: get_default_requires_index => get_default_requires_index_species_element_config

private function get_default_requires_index_species_element_config()

Arguments

Return Value logical

Source Code