!> \file
!> \author Chris Bradley
!> \brief This is an example program to solve a diffusion equation using openCMISS calls.
!>
!> \section LICENSE
!>
!> Version: MPL 1.1/GPL 2.0/LGPL 2.1
!>
!> The contents of this file are subject to the Mozilla Public License
!> Version 1.1 (the "License"); you may not use this file except in
!> compliance with the License. You may obtain a copy of the License at
!> http://www.mozilla.org/MPL/
!>
!> Software distributed under the License is distributed on an "AS IS"
!> basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
!> License for the specific language governing rights and limitations
!> under the License.
!>
!> The Original Code is openCMISS
!>
!> The Initial Developer of the Original Code is University of Auckland,
!> Auckland, New Zealand and University of Oxford, Oxford, United
!> Kingdom. Portions created by the University of Auckland and University
!> of Oxford are Copyright (C) 2007 by the University of Auckland and
!> the University of Oxford. All Rights Reserved.
!>
!> Contributor(s):
!>
!> Alternatively, the contents of this file may be used under the terms of
!> either the GNU General Public License Version 2 or later (the "GPL"), or
!> the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
!> in which case the provisions of the GPL or the LGPL are applicable instead
!> of those above. If you wish to allow use of your version of this file only
!> under the terms of either the GPL or the LGPL, and not to allow others to
!> use your version of this file under the terms of the MPL, indicate your
!> decision by deleting the provisions above and replace them with the notice
!> and other provisions required by the GPL or the LGPL. If you do not delete
!> the provisions above, a recipient may use your version of this file under
!> the terms of any one of the MPL, the GPL or the LGPL.
!>

!> \example ClassicalField/Diffusion/DiffusionConstantSource/src/DiffusionConstantSourceExample.f90
!! Example program to solve a diffusion equation using openCMISS calls.
!! \htmlinclude ClassicalField/Diffusion/DiffusionConstantSource/history.html
!<

!> Main program
PROGRAM DIFFUSIONCONSTANTSOURCEEXAMPLE



  USE OPENCMISS
  USE MPI


#ifdef WIN32
  USE IFQWIN
#endif

  IMPLICIT NONE

  INTEGER(CMISSIntg), PARAMETER :: EquationsSetFieldUserNumber=1337
  TYPE(CMISSFieldType) :: EquationsSetField


  !Test program parameters

  REAL(CMISSDP), PARAMETER :: HEIGHT=1.0_CMISSDP
  REAL(CMISSDP), PARAMETER :: WIDTH=1.0_CMISSDP
  REAL(CMISSDP), PARAMETER :: LENGTH=1.0_CMISSDP
  
  INTEGER(CMISSIntg), PARAMETER :: CoordinateSystemUserNumber=1
  INTEGER(CMISSIntg), PARAMETER :: RegionUserNumber=2
  INTEGER(CMISSIntg), PARAMETER :: BasisUserNumber=3
  INTEGER(CMISSIntg), PARAMETER :: GeneratedMeshUserNumber=4
  INTEGER(CMISSIntg), PARAMETER :: MeshUserNumber=5
  INTEGER(CMISSIntg), PARAMETER :: DecompositionUserNumber=6
  INTEGER(CMISSIntg), PARAMETER :: GeometricFieldUserNumber=7
  INTEGER(CMISSIntg), PARAMETER :: DependentFieldUserNumber=8
  INTEGER(CMISSIntg), PARAMETER :: MaterialsFieldUserNumber=9
  INTEGER(CMISSIntg), PARAMETER :: EquationsSetUserNumber=10
  INTEGER(CMISSIntg), PARAMETER :: ProblemUserNumber=11
  INTEGER(CMISSIntg), PARAMETER :: ControlLoopNode=0
  INTEGER(CMISSIntg), PARAMETER :: SourceFieldUserNumber=12
  INTEGER(CMISSIntg), PARAMETER :: AnalyticFieldUserNumber=13

  !Program types
  
  !Program variables

  INTEGER(CMISSIntg) :: NUMBER_GLOBAL_X_ELEMENTS,NUMBER_GLOBAL_Y_ELEMENTS,NUMBER_GLOBAL_Z_ELEMENTS
  INTEGER(CMISSIntg) :: NUMBER_OF_DOMAINS
  
  INTEGER(CMISSIntg) :: MPI_IERROR
  
    !CMISS variables

  TYPE(CMISSBasisType) :: Basis
  TYPE(CMISSBoundaryConditionsType) :: BoundaryConditions
  TYPE(CMISSCoordinateSystemType) :: CoordinateSystem,WorldCoordinateSystem
  TYPE(CMISSDecompositionType) :: Decomposition
  TYPE(CMISSEquationsType) :: Equations
  TYPE(CMISSEquationsSetType) :: EquationsSet
  TYPE(CMISSFieldType) :: GeometricField,DependentField,MaterialsField,SourceField,AnalyticField
  TYPE(CMISSFieldsType) :: Fields
  TYPE(CMISSGeneratedMeshType) :: GeneratedMesh  
  TYPE(CMISSMeshType) :: Mesh
  TYPE(CMISSProblemType) :: Problem
  TYPE(CMISSControlLoopType) :: ControlLoop
  TYPE(CMISSRegionType) :: Region,WorldRegion
  TYPE(CMISSSolverType) :: Solver, LinearSolver
  TYPE(CMISSSolverEquationsType) :: SolverEquations

  LOGICAL :: EXPORT_FIELD,IMPORT_FIELD
 

#ifdef WIN32
  !Quickwin type
  LOGICAL :: QUICKWIN_STATUS=.FALSE.
  TYPE(WINDOWCONFIG) :: QUICKWIN_WINDOW_CONFIG
#endif
  
  !Generic CMISS variables
  
  INTEGER(CMISSIntg) :: EquationsSetIndex
  INTEGER(CMISSIntg) :: FirstNodeNumber,LastNodeNumber
  INTEGER(CMISSIntg) :: Err
  
#ifdef WIN32
  !Initialise QuickWin
  QUICKWIN_WINDOW_CONFIG%TITLE="General Output" !Window title
  QUICKWIN_WINDOW_CONFIG%NUMTEXTROWS=-1 !Max possible number of rows
  QUICKWIN_WINDOW_CONFIG%MODE=QWIN$SCROLLDOWN
  !Set the window parameters
  QUICKWIN_STATUS=SETWINDOWCONFIG(QUICKWIN_WINDOW_CONFIG)
  !If attempt fails set with system estimated values
  IF(.NOT.QUICKWIN_STATUS) QUICKWIN_STATUS=SETWINDOWCONFIG(QUICKWIN_WINDOW_CONFIG)
#endif

  !Intialise OpenCMISS
  CALL CMISSInitialise(WorldCoordinateSystem,WorldRegion,Err)

  CALL CMISSErrorHandlingModeSet(CMISS_ERRORS_TRAP_ERROR,Err)

  NUMBER_GLOBAL_X_ELEMENTS=10
  NUMBER_GLOBAL_Y_ELEMENTS=10
  NUMBER_GLOBAL_Z_ELEMENTS=10
  NUMBER_OF_DOMAINS=1


  CALL MPI_BCAST(NUMBER_GLOBAL_X_ELEMENTS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
  CALL MPI_BCAST(NUMBER_GLOBAL_Y_ELEMENTS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
  CALL MPI_BCAST(NUMBER_GLOBAL_Z_ELEMENTS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)
  CALL MPI_BCAST(NUMBER_OF_DOMAINS,1,MPI_INTEGER,0,MPI_COMM_WORLD,MPI_IERROR)

    !Start the creation of a new RC coordinate system
    CALL CMISSCoordinateSystem_Initialise(CoordinateSystem,Err)
    CALL CMISSCoordinateSystem_CreateStart(CoordinateSystemUserNumber,CoordinateSystem,Err)
    IF(NUMBER_GLOBAL_Z_ELEMENTS==0) THEN
      !Set the coordinate system to be 2D
      CALL CMISSCoordinateSystem_DimensionSet(CoordinateSystem,2,Err)
    ELSE
      !Set the coordinate system to be 3D
      CALL CMISSCoordinateSystem_DimensionSet(CoordinateSystem,3,Err)
    ENDIF
    !Finish the creation of the coordinate system
    CALL CMISSCoordinateSystem_CreateFinish(CoordinateSystem,Err)


    !Start the creation of the region
    CALL CMISSRegion_Initialise(Region,Err)
    CALL CMISSRegion_CreateStart(RegionUserNumber,WorldRegion,Region,Err)
    !Set the regions coordinate system to the 2D RC coordinate system that we have created
    CALL CMISSRegion_CoordinateSystemSet(Region,CoordinateSystem,Err)
    !Finish the creation of the region
    CALL CMISSRegion_CreateFinish(Region,Err)

    !Start the creation of a basis (default is trilinear lagrange)
    CALL CMISSBasis_Initialise(Basis,Err)
    CALL CMISSBasis_CreateStart(BasisUserNumber,Basis,Err)
    IF(NUMBER_GLOBAL_Z_ELEMENTS==0) THEN
      !Set the basis to be a bilinear Lagrange basis
      CALL CMISSBasis_NumberOfXiSet(Basis,2,Err)
    ELSE
      !Set the basis to be a trilinear Lagrange basis
      CALL CMISSBasis_NumberOfXiSet(Basis,3,Err)
    ENDIF
    !Finish the creation of the basis
    CALL CMISSBasis_CreateFinish(BASIS,Err)

    !Start the creation of a generated mesh in the region
    CALL CMISSGeneratedMesh_Initialise(GeneratedMesh,Err)
    CALL CMISSGeneratedMesh_CreateStart(GeneratedMeshUserNumber,Region,GeneratedMesh,Err)
    !Set up a regular x*y*z mesh
    CALL CMISSGeneratedMesh_TypeSet(GeneratedMesh,CMISS_GENERATED_MESH_REGULAR_MESH_TYPE,Err)
    !Set the default basis
    CALL CMISSGeneratedMesh_BasisSet(GeneratedMesh,Basis,Err)   
    !Define the mesh on the region
    IF(NUMBER_GLOBAL_Z_ELEMENTS==0) THEN
      CALL CMISSGeneratedMesh_ExtentSet(GeneratedMesh,(/WIDTH,HEIGHT/),Err)
      CALL CMISSGeneratedMesh_NumberOfElementsSet(GeneratedMesh,(/NUMBER_GLOBAL_X_ELEMENTS,NUMBER_GLOBAL_Y_ELEMENTS/),Err)
    ELSE
      CALL CMISSGeneratedMesh_ExtentSet(GeneratedMesh,(/WIDTH,HEIGHT,LENGTH/),Err)
      CALL CMISSGeneratedMesh_NumberOfElementsSet(GeneratedMesh,(/NUMBER_GLOBAL_X_ELEMENTS,NUMBER_GLOBAL_Y_ELEMENTS, &
        & NUMBER_GLOBAL_Z_ELEMENTS/),Err)
    ENDIF    
    !Finish the creation of a generated mesh in the region
    CALL CMISSMesh_Initialise(Mesh,Err)
    CALL CMISSGeneratedMesh_CreateFinish(GeneratedMesh,MeshUserNumber,Mesh,Err)

    !Create a decomposition
    CALL CMISSDecomposition_Initialise(Decomposition,Err)
    CALL CMISSDecomposition_CreateStart(DecompositionUserNumber,Mesh,Decomposition,Err)
    !Set the decomposition to be a general decomposition with the specified number of domains
    CALL CMISSDecomposition_TypeSet(Decomposition,CMISS_DECOMPOSITION_CALCULATED_TYPE,Err)
    CALL CMISSDecomposition_NumberOfDomainsSet(Decomposition,NUMBER_OF_DOMAINS,Err)
    !Finish the decomposition
    CALL CMISSDecomposition_CreateFinish(Decomposition,Err)

  !Start to create a default (geometric) field on the region
  CALL CMISSField_Initialise(GeometricField,Err)
  CALL CMISSField_CreateStart(GeometricFieldUserNumber,Region,GeometricField,Err)
  !Set the decomposition to use
  CALL CMISSField_MeshDecompositionSet(GeometricField,Decomposition,Err)
  !Set the domain to be used by the field components.
  CALL CMISSField_ComponentMeshComponentSet(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,1,1,Err)
  CALL CMISSField_ComponentMeshComponentSet(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,2,1,Err)
  IF(NUMBER_GLOBAL_Z_ELEMENTS/=0) THEN
    CALL CMISSField_ComponentMeshComponentSet(GeometricField,CMISS_FIELD_U_VARIABLE_TYPE,3,1,Err)
  ENDIF
  !Finish creating the field
  CALL CMISSField_CreateFinish(GeometricField,Err)

       
    !Update the geometric field parameters
    CALL CMISSGeneratedMesh_GeometricParametersCalculate(GeneratedMesh,GeometricField,Err)
!  ENDIF

  !IF(.NOT.ASSOCIATED(GEOMETRIC_FIELD)) GEOMETRIC_FIELD=>REGION%FIELDS%FIELDS(1)%PTR
  
  !Create the equations_set
  CALL CMISSEquationsSet_Initialise(EquationsSet,Err)
    CALL CMISSField_Initialise(EquationsSetField,Err)
CALL CMISSEquationsSet_CreateStart(EquationsSetUserNumber,Region,GeometricField,CMISS_EQUATIONS_SET_CLASSICAL_FIELD_CLASS, &
    & CMISS_EQUATIONS_SET_DIFFUSION_EQUATION_TYPE,CMISS_EQUATIONS_SET_CONSTANT_SOURCE_DIFFUSION_SUBTYPE, &
      & EquationsSetFieldUserNumber, &
    & EquationsSetField,EquationsSet,Err)
  !Set the equations set to be a standard Laplace problem
  
  !Finish creating the equations set
  CALL CMISSEquationsSet_CreateFinish(EquationsSet,Err)

  !Create the equations set dependent field variables
  CALL CMISSField_Initialise(DependentField,Err)
  CALL CMISSEquationsSet_DependentCreateStart(EquationsSet,DependentFieldUserNumber,DependentField,Err)
  !Finish the equations set dependent field variables
  CALL CMISSEquationsSet_DependentCreateFinish(EquationsSet,Err)

  !Create the equations set material field variables
  CALL CMISSField_Initialise(MaterialsField,Err)
  CALL CMISSEquationsSet_MaterialsCreateStart(EquationsSet,MaterialsFieldUserNumber,MaterialsField,Err)
  !Finish the equations set dependent field variables
  CALL CMISSEquationsSet_MaterialsCreateFinish(EquationsSet,Err)

  !Create the equations set source field variables
  CALL CMISSField_Initialise(SourceField,Err)
  CALL CMISSEquationsSet_SourceCreateStart(EquationsSet,SourceFieldUserNumber,SourceField,Err)
  !Finish the equations set dependent field variables
  CALL CMISSEquationsSet_SourceCreateFinish(EquationsSet,Err)

  !Create the equations set analytic field variables
  CALL CMISSField_Initialise(AnalyticField,Err)
  CALL CMISSEquationsSet_AnalyticCreateStart(EquationsSet,CMISS_EQUATIONS_SET_DIFFUSION_EQUATION_THREE_DIM_1, &
    & AnalyticFieldUserNumber, &
    & AnalyticField,Err)
  !Finish the equations set analytic field variables
  CALL CMISSEquationsSet_AnalyticCreateFinish(EquationsSet,Err)

  !Create the equations set equations
  CALL CMISSEquations_Initialise(Equations,Err)
  CALL CMISSEquationsSet_EquationsCreateStart(EquationsSet,Equations,Err)
  !Set the equations matrices sparsity type
  CALL CMISSEquations_SparsityTypeSet(Equations,CMISS_EQUATIONS_SPARSE_MATRICES,Err)
  !Set the equations set output
  CALL CMISSEquations_OutputTypeSet(Equations,CMISS_EQUATIONS_NO_OUTPUT,Err)
  !CALL CMISSEquations_OutputTypeSet(Equations,CMISS_EQUATIONS_TIMING_OUTPUT,Err)
  !CALL CMISSEquations_OutputTypeSet(Equations,CMISS_EQUATIONS_MATRIX_OUTPUT,Err)
  !CALL CMISSEquations_OutputTypeSet(Equations,CMISS_EQUATIONS_ELEMENT_MATRIX_OUTPUT,Err)
  !Finish the equations set equations
  CALL CMISSEquationsSet_EquationsCreateFinish(EquationsSet,Err)
  
  !Create the equations set boundary conditions
!   CALL CMISSBoundaryConditions_Initialise(BoundaryConditions,Err)
!   CALL CMISSEquationsSetBoundaryConditionsCreateStart(EquationsSet,BoundaryConditions,Err)
!   !Set the first node to 0.0 and the last node to 1.0
! !   FirstNodeNumber=1
! !   IF(NUMBER_GLOBAL_Z_ELEMENTS==0) THEN
! !     LastNodeNumber=(NUMBER_GLOBAL_X_ELEMENTS+1)*(NUMBER_GLOBAL_Y_ELEMENTS+1)
! !   ELSE
! !     LastNodeNumber=(NUMBER_GLOBAL_X_ELEMENTS+1)*(NUMBER_GLOBAL_Y_ELEMENTS+1)*(NUMBER_GLOBAL_Z_ELEMENTS+1)
! !   ENDIF
! !   CALL CMISSBoundaryConditions_SetNode(BoundaryConditions,CMISS_FIELD_U_VARIABLE_TYPE,1,FirstNodeNumber,1, &
! !     & CMISS_BOUNDARY_CONDITION_FIXED,0.0_CMISSDP,Err)
! !   CALL CMISSBoundaryConditions_SetNode(BoundaryConditions,CMISS_FIELD_DELUDELN_VARIABLE_TYPE,1,LastNodeNumber,1, &
! !     & CMISS_BOUNDARY_CONDITION_FIXED,1.0_CMISSDP,Err)
!   !Finish the creation of the equations set boundary conditions
!   CALL CMISSEquationsSetBoundaryConditionsCreateFinish(EquationsSet,Err)




  !Create the problem
  CALL CMISSProblem_Initialise(Problem,Err)
  CALL CMISSProblem_CreateStart(ProblemUserNumber,Problem,Err)
  !Set the problem to be a linear source Diffusion problem
  CALL CMISSProblem_SpecificationSet(Problem,CMISS_PROBLEM_CLASSICAL_FIELD_CLASS,CMISS_PROBLEM_DIFFUSION_EQUATION_TYPE, &
    & CMISS_PROBLEM_LINEAR_SOURCE_DIFFUSION_SUBTYPE,Err)
  !Finish the creation of a problem.
  CALL CMISSProblem_CreateFinish(Problem,Err)


  !Create the problem control
  CALL CMISSProblem_ControlLoopCreateStart(Problem,Err)
  CALL CMISSControlLoop_Initialise(ControlLoop,Err)
  !Get the control loop
  CALL CMISSProblem_ControlLoopGet(Problem,ControlLoopNode,ControlLoop,Err)
  !Set the times
  CALL CMISSControlLoop_TimesSet(ControlLoop,0.0_CMISSDP,1.0001_CMISSDP,0.01_CMISSDP,Err)
  !Finish creating the problem control loop
  CALL CMISSProblem_ControlLoopCreateFinish(Problem,Err)


  !Start the creation of the problem solvers
!  
! !   !For the Direct Solver MUMPS, uncomment the below two lines and comment out the above five
! !   CALL SOLVER_LINEAR_TYPE_SET(LINEAR_SOLVER,SOLVER_LINEAR_DIRECT_SOLVE_TYPE,ERR,ERROR,*999)
! !   CALL SOLVER_LINEAR_DIRECT_TYPE_SET(LINEAR_SOLVER,SOLVER_DIRECT_MUMPS,ERR,ERROR,*999) 
! 

  CALL CMISSSolver_Initialise(Solver,Err)
  CALL CMISSSolver_Initialise(LinearSolver,Err)
  CALL CMISSProblem_SolversCreateStart(Problem,Err)
  CALL CMISSProblem_SolverGet(Problem,CMISS_CONTROL_LOOP_NODE,1,Solver,Err)
  !CALL CMISSSolver_OutputTypeSet(Solver,CMISS_SOLVER_NO_OUTPUT,Err)
  !CALL CMISSSolver_OutputTypeSet(Solver,CMISS_SOLVER_PROGRESS_OUTPUT,Err)
  !CALL CMISSSolver_OutputTypeSet(Solver,CMISS_SOLVER_TIMING_OUTPUT,Err)
  !CALL CMISSSolver_OutputTypeSet(Solver,CMISS_SOLVER_MATRIX_OUTPUT,Err)
  CALL CMISSSolver_OutputTypeSet(Solver,CMISS_SOLVER_PROGRESS_OUTPUT,Err)
  CALL CMISSSolver_DynamicLinearSolverGet(Solver,LinearSolver,Err)
  CALL CMISSSolver_LinearIterativeMaximumIterationsSet(LinearSolver,10000,Err)
  !Finish the creation of the problem solver
  CALL CMISSProblem_SolversCreateFinish(Problem,Err)


  !Create the problem solver equations
  CALL CMISSSolver_Initialise(Solver,Err)
  CALL CMISSSolverEquations_Initialise(SolverEquations,Err)
  CALL CMISSProblem_SolverEquationsCreateStart(Problem,Err)
  !Get the solve equations
  CALL CMISSProblem_SolverGet(Problem,CMISS_CONTROL_LOOP_NODE,1,Solver,Err)
  CALL CMISSSolver_SolverEquationsGet(Solver,SolverEquations,Err)
  !Set the solver equations sparsity
  !CALL CMISSSolverEquations_SparsityTypeSet(SolverEquations,CMISS_SOLVER_SPARSE_MATRICES,Err)
  !CALL CMISSSolverEquations_SparsityTypeSet(SolverEquations,CMISS_SOLVER_FULL_MATRICES,Err)  
  !Add in the equations set
  CALL CMISSSolverEquations_EquationsSetAdd(SolverEquations,EquationsSet,EquationsSetIndex,Err)
  !Finish the creation of the problem solver equations
  CALL CMISSProblem_SolverEquationsCreateFinish(Problem,Err)

  CALL CMISSBoundaryConditions_Initialise(BoundaryConditions,Err)
  CALL CMISSSolverEquations_BoundaryConditionsCreateStart(SolverEquations,BoundaryConditions,Err)
  CALL CMISSSolverEquations_BoundaryConditionsAnalytic(SolverEquations,Err)
  CALL CMISSSolverEquations_BoundaryConditionsCreateFinish(SolverEquations,Err)

  !Solve the problem
  CALL CMISSProblem_Solve(Problem,Err)

  !Output Analytic analysis
  CALL CMISSAnalyticAnalysisOutput(DependentField,"DiffusionAnalytics_x10_y10_z10_L_T1",Err)


  EXPORT_FIELD=.TRUE.
  IF(EXPORT_FIELD) THEN
    CALL CMISSFields_Initialise(Fields,Err)
    CALL CMISSFields_Create(Region,Fields,Err)
    CALL CMISSFields_NodesExport(Fields,"DiffusionConstantSourceAnalytic_x10_y10_z10_L_T1","FORTRAN",Err)
    CALL CMISSFields_ElementsExport(Fields,"DiffusionConstantSourceAnalytic_x10_y10_z10_L_T1","FORTRAN",Err)
    CALL CMISSFields_Finalise(Fields,Err)

  ENDIF

  !CALL CMISSFinalise(Err)
  WRITE(*,'(A)') "Program successfully completed."
  

  STOP
 
END PROGRAM DIFFUSIONCONSTANTSOURCEEXAMPLE