!-----------------------------------------------------------------------------------------------------------------------------------
! This file is part of ReMKiT1D.
!
! ReMKiT1D is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as
! published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
!
! ReMKiT1D is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
!
! You should have received a copy of the GNU General Public License along with ReMKiT1D. If not, see <https://www.gnu.org/licenses/>.
!
! Copyright 2023 United Kingdom Atomic Energy Authority (stefan.mijin@ukaea.uk)
!-----------------------------------------------------------------------------------------------------------------------------------
module initialization_support
!! author: Stefan Mijin
!!
!! Contains various support routines used in data initialization
use data_kinds ,only: rk, ik
use runtime_constants ,only: debugging, assertions, assertionLvl
use assertion_utility ,only: assert, assertIdentical, assertPure
use variable_container_class ,only: VariableContainer, CalculationRule
use variable_list_class ,only: VariableList
use indexing_class ,only: Indexing
use json_controller_class ,only: JSONController
use mpi_controller_class ,only: MPIController ,CommunicationData
use derivation_abstract_class ,only: Derivation
use textbook_class ,only: Textbook
use grid_class ,only: Grid
use v_space_class ,only: VSpace
use partition_class ,only: Partition
use geometry_class ,only: Geometry
use petsc_controller_class ,only: PETScController, SolverOptions
use hdf5_controller_class ,only: HDF5Controller
use species_list_class ,only: SpeciesList
use species_class ,only: Species
use simple_derivation_class ,only: SimpleDerivation
use additive_derivation_class ,only: AdditiveDerivation
use moment_derivation_class ,only: MomentDerivation
use sheath_gamma_derivation_class ,only: ElectronSheathGammaDerivation
use normalization_abstract_class ,only: Normalization
use implicit_PicardBDE_integrator_class ,only: PicardBDEIntegrator ,InternalControllerOptions
use composite_integrator_class ,only: CompositeIntegrator, IntegratorCallStep
use explicit_rk_integrator_class ,only: ExplicitRKIntegrator
use simple_timestep_controller_class ,only: SimpleTimestepController
use signal_collection_class ,only: SignalCollection
use constant_signal_class ,only: ConstSignal
use hat_signal_class ,only: HatSignal
use cut_sine_signal_class ,only: CutSineSignal
use interpolation_derivation_class ,only: InterpolationDerivation
use central_diff_grad_derivation_class ,only: CentralDiffDerivation
use coulomb_log_derivation_class ,only: CoulombLogDerivation
use maxwellian_derivation_class ,only: MaxwellianDerivation
use ccl_diff_derivation_class ,only: CCLDiffDerivation
use ccl_drag_derivation_class ,only: CCLDragDerivation
use ccl_weight_derivation_class ,only: CCLWeightDerivation
use status_printing
use custom_derivation_support
use support_types
use key_names
use physical_constants
implicit none
!-----------------------------------------------------------------------------------------------------------------------------------
interface
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initVarListFromJSON(varList,jsonCont,mpiCont,isDerivedList)
!! Initialize variable list based on variable data from a JSON file. If isDerivedList = .true. the list is initialized
!! based on derived list data, otherwise it uses the implicit list.
type(VariableList) ,intent(inout) :: varList
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
logical ,optional ,intent(in) :: isDerivedList
end subroutine initVarListFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initGridFromJSON(gridObj,jsonCont,mpiCont,lengthNorm)
!! Initialize grid object based on data from a JSON file.
type(Grid) ,intent(inout) :: gridObj
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
real(rk) ,optional ,intent(in) :: lengthNorm !! Length normalization if the supplied grid is in meters, defaults to 1
end subroutine initGridFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initPartFromJSON(partObj,gridObj,jsonCont,mpiCont)
!! Initialize simple partition object based on data from a JSON file and grid object
type(Partition) ,intent(inout) :: partObj
type(Grid) ,intent(in) :: gridObj !! Grid object used to get numX and numH
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
end subroutine initPartFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initGeometryFromJSON(geometryObj,gridObj,jsonCont,mpiCont)
!! Initialize geometry object based on data from a JSON file and grid object
type(Geometry) ,intent(inout) :: geometryObj
type(Grid) ,intent(in) :: gridObj !! Grid object used to infer cell widths for consistency
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
end subroutine initGeometryFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initPETScContFromJSON(petscCont,indexingObj,jsonCont,mpiCont)
!! Initialize PETSc controller object based on data from a JSON file and indexing object
type(PETScController) ,intent(inout) :: petscCont
type(Indexing) ,intent(in) :: indexingObj
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController and to initialize PETSc
end subroutine initPETScContFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initHDF5ContFromJSON(hdf5Cont,varCont,jsonCont,mpiCont)
!! Initialize HDF5 controller object based on data from a JSON file and variable container object
type(HDF5Controller) ,intent(inout) :: hdf5Cont
type(VariableContainer) ,intent(in) :: varCont
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController and to initialize HDF5
end subroutine initHDF5ContFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initVarContFromJSON(varCont,indexingObj,partObj,textbookObj,jsonCont,mpiCont)
!! Initialize variable container based on variable data from a JSON file.
type(VariableContainer) ,intent(inout) :: varCont
type(Indexing) ,intent(in) :: indexingObj !! Indexing object used in variable container initialization
type(Partition) ,intent(in) :: partObj !! Partition object used in variable container initialization
type(Textbook) ,intent(in) :: textbookObj !! Textbook object used to retrieve derivation rules for variable container
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
end subroutine initVarContFromJSON
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initStandardIntegrator(integratorObj,varCont,indexingObj,jsonCont,mpiCont)
!! Initialize standard integrator based on data from a JSON file. The standard integrator is a composit integrator containing
!! either RK or BDE integrators.
type(CompositeIntegrator) ,intent(inout) :: integratorObj
type(VariableContainer) ,intent(in) :: varCont
type(Indexing) ,intent(in) :: indexingObj !! Indexing object used in BDE integrator initialization
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
end subroutine initStandardIntegrator
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initStandardTextbook(textbookObj,gridObj,geometryObj,partObj,&
vSpaceObj,normObj,speciesListObj,varList,jsonCont,mpiCont)
! Initialize standard textbook object based on grid, geometry, partition, species, and normalization data as well as a JSON file.
!! Assumes that the velocity grid is normalized to electron thermal speed.
!! The textbook includes (passed variables are in appearance order unless otherwise specified):
!!
!! "flowSpeedFromFlux" = flux/density (normalized to n_0 * u_0)
!! "sonicSpeed" for each ion species (negative IDs) = sqrt((poly_e * T_e + poly_i * T_i)/m_i) where i is the index of the ion species (normalized to u_0)
!! "tempFromEnergy" for each species specified in config file as requiring temperature derivation = 2/3 * energy/density - mass * flux**2/(3*density**2)
!! "leftElectronGamma" = sheath heat transmission coeffiecient for electrons at the left boundary using T_e and T_i
!! "rightElectronGamma" = sheath heat transmission coefficient for electrons at the right boundary using T_e and T_i
!! "densityMoment" = zeroth moment of f_0
!! "energyMoment" = second order of f_0
!! "cclDragCoeff" = Chang-Cooper-Langdon drag coefficient - assumes passed variable is the single harmonic f_0
!! "cclDiffusionCoeff" = Chang-Cooper-Langdon diffusion coefficient - assumes passed variables are the single harmonic f_0 and cclWeight
!! "cclWeight" = Chang-Cooper-Langdon interpolation weight - assumes passed variables are the single harmonic cclDragCoeff and cclDiffusionCoeff
!! if l=1 is resolved:
!! "fluxMoment" = first moment of f_1/3 (normalized to n_0*u_0)
!! "heatFluxMoment" = third moment of f_1/3 (normalized to m_e * n_0 * v_th**3 / 2)
!! if l=2 is resolved:
!! "viscosityTensorxxMoment" = second moment of 2*f_2/15 (normalized to n_0 * e * T_0)
!! Interpolation for staggered grids:
!! "gridToDual" = interpolates one variable from regular to staggered(dual) grid
!! "dualToGrid" = interpolates one variable from staggered(dual) to regular grid
!! "distributionInterp" = interpolates one distribution function (even harmonics to dual, odd to regular grid)
!! Other useful derivations:
!! "gradDeriv" = calculates gradient of variable on regular grid, interpolating on cell faces and extrapolating at boundaries
!! "logLei" = calculates electron-ion Coulomb log taking in electron temperature and density (derivations added for each ion species)
!! "logLee" = calculates electron self collision Coulomb log taking in electron temperature and density
!! "logLii" = calculates ion-ion collision frequency for each ion collision combination taking in the two species temperatures and
!! densities (used as"logLiis_S" where s and S are the first and second ion species name)
!! "maxwellianDistribution" = calculates distribution function with Maxwellian l=0 harmonic and all other harmonics 0. Takes in temperature and density
!! Also automatically includes all defined custom derivations
type(Textbook) ,intent(inout) :: textbookObj
type(Grid) ,intent(in) :: gridObj
type(Geometry) ,intent(in) :: geometryObj
type(Partition) ,intent(in) :: partObj
type(VSpace) ,intent(in) :: vSpaceObj
class(Normalization) ,intent(in) :: normObj
type(SpeciesList) ,intent(in) :: speciesListObj
type(VariableList) ,intent(in) :: varList
type(JSONController) ,intent(inout) :: jsonCont !! JSONController used to get parameters from ./config.json
type(MPIController) ,intent(inout) :: mpiCont !! MPIController used with JSONController
end subroutine
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine initStandardSignals(signalCollectionObj)
!! Initialize signal collection with commonly used signals and their names. The signals are:
!! 1. constant signal
!! 2. hat signal
!! 3. cut sine signal
type(SignalCollection) ,intent(inout) :: signalCollectionObj
end subroutine initStandardSignals
!-----------------------------------------------------------------------------------------------------------------------------------
module subroutine setDistHarmonic(dist,h,xArr,vArr)
!! Set the h-th harmonic of distribution function variable dist to xArr*vArr at corresponding x, and v coordinates.
!! vArr should be either rank 1 or 2, and if it is rank 2 it should be size(numV,size(xArr))
real(rk) ,dimension(:) ,intent(inout) :: dist
integer(ik) ,intent(in) :: h
real(rk) ,dimension(:) ,intent(in) :: xArr
real(rk) ,dimension(..) ,intent(in) :: vArr
end subroutine setDistHarmonic
!-----------------------------------------------------------------------------------------------------------------------------------
end interface
!-----------------------------------------------------------------------------------------------------------------------------------
end module initialization_support
!-----------------------------------------------------------------------------------------------------------------------------------
