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reaction_diffusion_equation_routines.f90
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reaction_diffusion_equation_routines.f90
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!> \file
!> \author Vijay Rajagopal
!> \brief This module handles all reaction diffusion equation routines.
!>
!> \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, the University of Oxford, Oxford, United
!> Kingdom and King's College, London, United Kingdom. Portions created
!> by the University of Auckland, the University of Oxford and King's
!> College, London are Copyright (C) 2007-2010 by the University of
!> Auckland, the University of Oxford and King's College, London.
!> All Rights Reserved.
!>
!> Contributor(s): Chris Bradley
!>
!> 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.
!>
!>This module handles all reaction diffusion equation routines.
MODULE REACTION_DIFFUSION_EQUATION_ROUTINES
USE BaseRoutines
USE BasisRoutines
USE BasisAccessRoutines
USE BOUNDARY_CONDITIONS_ROUTINES
USE ComputationEnvironment
USE Constants
USE CONTROL_LOOP_ROUTINES
USE ControlLoopAccessRoutines
USE DistributedMatrixVector
USE DOMAIN_MAPPINGS
USE EquationsRoutines
USE EquationsAccessRoutines
USE EquationsMappingRoutines
USE EquationsMatricesRoutines
USE EquationsSetConstants
USE EquationsSetAccessRoutines
USE FIELD_ROUTINES
USE FieldAccessRoutines
USE INPUT_OUTPUT
USE ISO_VARYING_STRING
USE Kinds
USE MatrixVector
#ifndef NOMPIMOD
USE MPI
#endif
USE PROBLEM_CONSTANTS
USE Strings
USE SOLVER_ROUTINES
USE SolverAccessRoutines
USE Timer
USE Types
USE REACTION_DIFFUSION_IO_ROUTINES
#include "macros.h"
IMPLICIT NONE
PRIVATE
#ifdef NOMPIMOD
#include "mpif.h"
#endif
!Module parameters
!Module types
!Module variables
!Interfaces
PUBLIC ReactionDiffusion_EquationsSetSetup
PUBLIC ReactionDiffusion_EquationsSetSolutionMethodSet
PUBLIC ReactionDiffusion_EquationsSetSpecificationSet
PUBLIC ReactionDiffusion_FiniteElementCalculate
PUBLIC ReactionDiffusion_PreSolve
PUBLIC REACTION_DIFFUSION_EQUATION_PROBLEM_SETUP
PUBLIC ReactionDiffusion_ProblemSpecificationSet
PUBLIC ReactionDiffusion_PostSolve
PUBLIC REACTION_DIFFUSION_CONTROL_LOOP_POST_LOOP
CONTAINS
!
!================================================================================================================================
!
!>Sets up the reaction diffusion equation type of a classical equations set class.
SUBROUTINE ReactionDiffusion_EquationsSetSetup(EQUATIONS_SET,EQUATIONS_SET_SETUP,err,error,*)
!Argument variables
TYPE(EQUATIONS_SET_TYPE), POINTER :: EQUATIONS_SET !<A pointer to the equations set to setup a bioelectric domain equation on.
TYPE(EQUATIONS_SET_SETUP_TYPE), INTENT(INOUT) :: EQUATIONS_SET_SETUP !<The equations set setup information
INTEGER(INTG), INTENT(OUT) :: err !<The error code
TYPE(VARYING_STRING), INTENT(OUT) :: error !<The error string
!Local Variables
INTEGER(INTG) :: component_idx,DIMENSION_MULTIPLIER,GEOMETRIC_COMPONENT_NUMBER,GEOMETRIC_SCALING_TYPE, &
& NUMBER_OF_DIMENSIONS,NUMBER_OF_MATERIALS_COMPONENTS,GEOMETRIC_MESH_COMPONENT
TYPE(DECOMPOSITION_TYPE), POINTER :: GEOMETRIC_DECOMPOSITION
TYPE(EquationsType), POINTER :: equations
TYPE(EquationsMappingVectorType), POINTER :: vectorMapping
TYPE(EquationsVectorType), POINTER :: vectorEquations
TYPE(EQUATIONS_SET_MATERIALS_TYPE), POINTER :: EQUATIONS_MATERIALS
TYPE(EquationsMatricesVectorType), POINTER :: vectorMatrices
TYPE(VARYING_STRING) :: localError
ENTERS("ReactionDiffusion_EquationsSetSetup",err,error,*999)
NULLIFY(EQUATIONS)
NULLIFY(vectorMapping)
NULLIFY(vectorMatrices)
NULLIFY(GEOMETRIC_DECOMPOSITION)
IF(ASSOCIATED(EQUATIONS_SET)) THEN
IF(.NOT.ALLOCATED(EQUATIONS_SET%SPECIFICATION)) THEN
CALL FlagError("Equations set specification is not allocated.",err,error,*999)
ELSE IF(SIZE(EQUATIONS_SET%SPECIFICATION,1)/=3) THEN
CALL FlagError("Equations set specification must have three entries for a reaction-diffusion type equations set.", &
& err,error,*999)
END IF
SELECT CASE(EQUATIONS_SET_SETUP%SETUP_TYPE)
CASE(EQUATIONS_SET_SETUP_INITIAL_TYPE)
SELECT CASE(EQUATIONS_SET_SETUP%ACTION_TYPE)
CASE(EQUATIONS_SET_SETUP_START_ACTION)
CALL ReactionDiffusion_EquationsSetSolutionMethodSet(EQUATIONS_SET, &
& EQUATIONS_SET_FEM_SOLUTION_METHOD,err,error,*999)
CASE(EQUATIONS_SET_SETUP_FINISH_ACTION)
!!Todo: CHECK VALID SETUP
CASE DEFAULT
localError="The action type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%ACTION_TYPE,"*",err,error))// &
& " for a setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for a reaction diffusion domain equation."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE(EQUATIONS_SET_SETUP_GEOMETRY_TYPE)
!\todo Check geometric dimension
CASE(EQUATIONS_SET_SETUP_DEPENDENT_TYPE)
SELECT CASE(EQUATIONS_SET_SETUP%ACTION_TYPE)
CASE(EQUATIONS_SET_SETUP_START_ACTION)
SELECT CASE(EQUATIONS_SET%SPECIFICATION(3))
CASE(EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE, &
& EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE)
IF(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD_AUTO_CREATED) THEN
!Create the auto created dependent field
CALL FIELD_CREATE_START(EQUATIONS_SET_SETUP%FIELD_USER_NUMBER,EQUATIONS_SET%REGION,EQUATIONS_SET%DEPENDENT% &
& DEPENDENT_FIELD,err,error,*999)
CALL FIELD_LABEL_SET(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,"Dependent Field",err,error,*999)
CALL FIELD_TYPE_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_GENERAL_TYPE,err,error,*999)
CALL FIELD_DEPENDENT_TYPE_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_DEPENDENT_TYPE,err,error,*999)
CALL FIELD_MESH_DECOMPOSITION_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,GEOMETRIC_DECOMPOSITION,err,error,*999)
CALL FIELD_MESH_DECOMPOSITION_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,GEOMETRIC_DECOMPOSITION, &
& err,error,*999)
CALL FIELD_GEOMETRIC_FIELD_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,EQUATIONS_SET%GEOMETRY% &
& GEOMETRIC_FIELD,err,error,*999)
CALL FIELD_NUMBER_OF_VARIABLES_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,2,err,error,*999)
CALL FIELD_VARIABLE_TYPES_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,[FIELD_U_VARIABLE_TYPE, &
& FIELD_DELUDELN_VARIABLE_TYPE],err,error,*999)
!CALL FIELD_VARIABLE_LABEL_SET
CALL FIELD_DIMENSION_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_SCALAR_DIMENSION_TYPE,err,error,*999)
CALL FIELD_DIMENSION_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_DELUDELN_VARIABLE_TYPE, &
& FIELD_SCALAR_DIMENSION_TYPE,err,error,*999)
CALL FIELD_DATA_TYPE_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_DP_TYPE,err,error,*999)
CALL FIELD_DATA_TYPE_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_DELUDELN_VARIABLE_TYPE, &
& FIELD_DP_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_U_VARIABLE_TYPE,1, &
& err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_DELUDELN_VARIABLE_TYPE,1, &
& err,error,*999)
!Default to the geometric interpolation setup
CALL FIELD_COMPONENT_MESH_COMPONENT_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE,1, &
& GEOMETRIC_MESH_COMPONENT,err,error,*999)
CALL FIELD_COMPONENT_MESH_COMPONENT_SET(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_U_VARIABLE_TYPE,1, &
& GEOMETRIC_MESH_COMPONENT,err,error,*999)
CALL FIELD_COMPONENT_MESH_COMPONENT_SET(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,FIELD_DELUDELN_VARIABLE_TYPE,1, &
& GEOMETRIC_MESH_COMPONENT,err,error,*999)
SELECT CASE(EQUATIONS_SET%SOLUTION_METHOD)
CASE(EQUATIONS_SET_FEM_SOLUTION_METHOD)
CALL FIELD_COMPONENT_INTERPOLATION_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD, &
& FIELD_U_VARIABLE_TYPE,1,FIELD_NODE_BASED_INTERPOLATION,err,error,*999)
CALL FIELD_COMPONENT_INTERPOLATION_SET_AND_LOCK(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD, &
& FIELD_DELUDELN_VARIABLE_TYPE,1,FIELD_NODE_BASED_INTERPOLATION,err,error,*999)
!Default the scaling to the geometric field scaling
CALL FIELD_SCALING_TYPE_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,GEOMETRIC_SCALING_TYPE,err,error,*999)
CALL FIELD_SCALING_TYPE_SET(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,GEOMETRIC_SCALING_TYPE,err,error,*999)
CASE(EQUATIONS_SET_BEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FD_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The solution method of "//TRIM(NumberToVString(EQUATIONS_SET%SOLUTION_METHOD,"*",err,error))// &
& " is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
ELSE
!Check the user specified field
CALL FIELD_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_GENERAL_TYPE,err,error,*999)
CALL FIELD_DEPENDENT_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_DEPENDENT_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_VARIABLES_CHECK(EQUATIONS_SET_SETUP%FIELD,2,err,error,*999)
CALL FIELD_VARIABLE_TYPES_CHECK(EQUATIONS_SET_SETUP%FIELD,[FIELD_U_VARIABLE_TYPE,FIELD_DELUDELN_VARIABLE_TYPE], &
& err,error,*999)
CALL FIELD_DIMENSION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,FIELD_SCALAR_DIMENSION_TYPE,err,error,*999)
CALL FIELD_DIMENSION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_DELUDELN_VARIABLE_TYPE,FIELD_SCALAR_DIMENSION_TYPE, &
& err,error,*999)
CALL FIELD_DATA_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,FIELD_DP_TYPE,err,error,*999)
CALL FIELD_DATA_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_DELUDELN_VARIABLE_TYPE,FIELD_DP_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,1,err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_DELUDELN_VARIABLE_TYPE,1,err,error,*999)
SELECT CASE(EQUATIONS_SET%SOLUTION_METHOD)
CASE(EQUATIONS_SET_FEM_SOLUTION_METHOD)
CALL FIELD_COMPONENT_INTERPOLATION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,1, &
& FIELD_NODE_BASED_INTERPOLATION,err,error,*999)
CALL FIELD_COMPONENT_INTERPOLATION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_DELUDELN_VARIABLE_TYPE,1, &
& FIELD_NODE_BASED_INTERPOLATION,err,error,*999)
CASE(EQUATIONS_SET_BEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FD_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The solution method of "//TRIM(NumberToVString(EQUATIONS_SET%SOLUTION_METHOD,"*",err,error))// &
& " is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
ENDIF
CASE(EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The equation set subtype of "//TRIM(NumberToVString(EQUATIONS_SET%SPECIFICATION(3),"*",err,error))// &
& " is invalid for a reaction diffusion equation set class."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE(EQUATIONS_SET_SETUP_FINISH_ACTION)
IF(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD_AUTO_CREATED) THEN
CALL FIELD_CREATE_FINISH(EQUATIONS_SET%DEPENDENT%DEPENDENT_FIELD,err,error,*999)
ENDIF
CASE DEFAULT
localError="The action type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%ACTION_TYPE,"*",err,error))// &
& " for a setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for a reaction diffusion equation"
CALL FlagError(localError,err,error,*999)
END SELECT
CASE(EQUATIONS_SET_SETUP_MATERIALS_TYPE)
SELECT CASE(EQUATIONS_SET_SETUP%ACTION_TYPE)
CASE(EQUATIONS_SET_SETUP_START_ACTION)
IF(EQUATIONS_SET%DEPENDENT%DEPENDENT_FINISHED) THEN
EQUATIONS_MATERIALS=>EQUATIONS_SET%MATERIALS
IF(ASSOCIATED(EQUATIONS_MATERIALS)) THEN
IF(EQUATIONS_MATERIALS%MATERIALS_FIELD_AUTO_CREATED) THEN
!Create the auto created materials field
CALL FIELD_CREATE_START(EQUATIONS_SET_SETUP%FIELD_USER_NUMBER,EQUATIONS_SET%REGION,EQUATIONS_MATERIALS% &
& MATERIALS_FIELD,err,error,*999)
CALL FIELD_TYPE_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_MATERIAL_TYPE,err,error,*999)
CALL FIELD_DEPENDENT_TYPE_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_INDEPENDENT_TYPE,err,error,*999)
CALL FIELD_MESH_DECOMPOSITION_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,GEOMETRIC_DECOMPOSITION,err,error,*999)
CALL FIELD_MESH_DECOMPOSITION_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,GEOMETRIC_DECOMPOSITION, &
& err,error,*999)
CALL FIELD_GEOMETRIC_FIELD_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,EQUATIONS_SET%GEOMETRY% &
& GEOMETRIC_FIELD,err,error,*999)
CALL FIELD_NUMBER_OF_VARIABLES_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,1,err,error,*999)
CALL FIELD_VARIABLE_TYPES_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,[FIELD_U_VARIABLE_TYPE], &
& err,error,*999)
CALL FIELD_DIMENSION_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_VECTOR_DIMENSION_TYPE,err,error,*999)
CALL FIELD_DATA_TYPE_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_DP_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE, &
& NUMBER_OF_DIMENSIONS,err,error,*999)
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE) THEN
!Reaction Diffusion. Materials field components are 1 diffusion coeff for each dimension
!plus one for the storage coefficient in alpha(delC/delt) = Div(-kgradC)+cellmlRC
NUMBER_OF_MATERIALS_COMPONENTS=NUMBER_OF_DIMENSIONS+1
DIMENSION_MULTIPLIER=1
ELSEIF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
!Constant reaction + diffusion. Materials field has 1 diffuse coeff for each dimension
!plus one for the storage coefficient om alpha(delC/delt) = Div(-kgradC)+const(x)_source
NUMBER_OF_MATERIALS_COMPONENTS=NUMBER_OF_DIMENSIONS+1
DIMENSION_MULTIPLIER=1
ENDIF
!Set the number of materials components
CALL FIELD_NUMBER_OF_COMPONENTS_SET_AND_LOCK(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& NUMBER_OF_MATERIALS_COMPONENTS,err,error,*999)
!Default the first three materials components for diffusivity param to the first component geometric interpolation with const interpolation
DO component_idx=1,NUMBER_OF_DIMENSIONS
CALL FIELD_COMPONENT_MESH_COMPONENT_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE, &
& 1,GEOMETRIC_COMPONENT_NUMBER,err,error,*999)
CALL FIELD_COMPONENT_MESH_COMPONENT_SET(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& component_idx,GEOMETRIC_COMPONENT_NUMBER,err,error,*999)
CALL FIELD_COMPONENT_INTERPOLATION_SET(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& component_idx,FIELD_CONSTANT_INTERPOLATION,err,error,*999)
ENDDO !components_idx
!Default the storage co-efficient to the first geometric interpolation setup with constant interpolation
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE) THEN
component_idx=NUMBER_OF_MATERIALS_COMPONENTS
CALL FIELD_COMPONENT_MESH_COMPONENT_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE, &
& 1,GEOMETRIC_COMPONENT_NUMBER,err,error,*999)
CALL FIELD_COMPONENT_MESH_COMPONENT_SET(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& component_idx,GEOMETRIC_COMPONENT_NUMBER,err,error,*999)
CALL FIELD_COMPONENT_INTERPOLATION_SET(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& component_idx,FIELD_CONSTANT_INTERPOLATION,err,error,*999)
ENDIF
!Default the field scaling to that of the geometric field
CALL FIELD_SCALING_TYPE_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,GEOMETRIC_SCALING_TYPE,err,error,*999)
CALL FIELD_SCALING_TYPE_SET(EQUATIONS_MATERIALS%MATERIALS_FIELD,GEOMETRIC_SCALING_TYPE,err,error,*999)
ELSE
!Check the user specified field
CALL FIELD_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_MATERIAL_TYPE,err,error,*999)
CALL FIELD_DEPENDENT_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_INDEPENDENT_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_VARIABLES_CHECK(EQUATIONS_SET_SETUP%FIELD,1,err,error,*999)
CALL FIELD_VARIABLE_TYPES_CHECK(EQUATIONS_SET_SETUP%FIELD,[FIELD_U_VARIABLE_TYPE],err,error,*999)
CALL FIELD_DIMENSION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,FIELD_VECTOR_DIMENSION_TYPE, &
& err,error,*999)
CALL FIELD_DATA_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,FIELD_DP_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE, &
& NUMBER_OF_DIMENSIONS,err,error,*999)
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE .OR. &
& EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
!Reaction Diffusion with cellml. Materials field components are 1 for storage coeff plus one for each dimension i.e., k
CALL FIELD_NUMBER_OF_COMPONENTS_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,NUMBER_OF_DIMENSIONS+1, &
& err,error,*999)
ENDIF
ENDIF
ELSE
CALL FlagError("Equations set materials is not associated.",err,error,*999)
ENDIF
ELSE
CALL FlagError("Equations set dependent field has not been finished.",err,error,*999)
ENDIF
CASE(EQUATIONS_SET_SETUP_FINISH_ACTION)
EQUATIONS_MATERIALS=>EQUATIONS_SET%MATERIALS
IF(ASSOCIATED(EQUATIONS_MATERIALS)) THEN
IF(EQUATIONS_MATERIALS%MATERIALS_FIELD_AUTO_CREATED) THEN
!Finish creating the materials field
CALL FIELD_CREATE_FINISH(EQUATIONS_MATERIALS%MATERIALS_FIELD,err,error,*999)
!Set the default values for the materials field
CALL FIELD_NUMBER_OF_COMPONENTS_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE, &
& NUMBER_OF_DIMENSIONS,err,error,*999)
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE .OR. &
& EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
!Reaction Diffusion with cellml. Materials field components are 1 plus one for each dimension i.e.,storage coeff, and k.
NUMBER_OF_MATERIALS_COMPONENTS=NUMBER_OF_DIMENSIONS+1
DIMENSION_MULTIPLIER=1
ENDIF
!set the diffusion coefficients to be 1.0
DO component_idx=1,NUMBER_OF_DIMENSIONS
CALL FIELD_COMPONENT_VALUES_INITIALISE(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_VALUES_SET_TYPE,component_idx,1.0_DP,err,error,*999)
ENDDO !component_idx
!Now set storage-coefficient
component_idx=NUMBER_OF_DIMENSIONS+1
CALL FIELD_COMPONENT_VALUES_INITIALISE(EQUATIONS_MATERIALS%MATERIALS_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_VALUES_SET_TYPE,component_idx,1.0_DP,err,error,*999)
ENDIF
ELSE
CALL FlagError("Equations set materials is not associated.",err,error,*999)
ENDIF
CASE DEFAULT
localError="The action type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%ACTION_TYPE,"*",err,error))// &
& " for a setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for a reaction diffusion equation."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE(EQUATIONS_SET_SETUP_SOURCE_TYPE)
SELECT CASE(EQUATIONS_SET_SETUP%ACTION_TYPE)
CASE(EQUATIONS_SET_SETUP_START_ACTION)
IF(ASSOCIATED(EQUATIONS_SET%MATERIALS)) THEN
IF(EQUATIONS_SET%MATERIALS%MATERIALS_FINISHED) THEN
IF(ASSOCIATED(EQUATIONS_SET%SOURCE)) THEN
IF(EQUATIONS_SET%SOURCE%SOURCE_FIELD_AUTO_CREATED) THEN
!Create the auto created source field
!Start field creation with name 'SOURCE_FIELD'
CALL FIELD_CREATE_START(EQUATIONS_SET_SETUP%FIELD_USER_NUMBER,EQUATIONS_SET%REGION, &
& EQUATIONS_SET%SOURCE%SOURCE_FIELD,err,error,*999)
!Create a general field
CALL FIELD_TYPE_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_GENERAL_TYPE,err,error,*999)
!Label the field
CALL FIELD_LABEL_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,"Source Field",err,error,*999)
!Set the dependent type
CALL FIELD_DEPENDENT_TYPE_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_INDEPENDENT_TYPE,err,error,*999)
!Set the field decomposition to be that of the geometric decomposition
CALL FIELD_MESH_DECOMPOSITION_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,GEOMETRIC_DECOMPOSITION,err,error,*999)
CALL FIELD_MESH_DECOMPOSITION_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,GEOMETRIC_DECOMPOSITION, &
& err,error,*999)
!Set the geometric field
CALL FIELD_GEOMETRIC_FIELD_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,EQUATIONS_SET% &
& GEOMETRY%GEOMETRIC_FIELD,err,error,*999)
!Set the field variables.
CALL FIELD_NUMBER_OF_VARIABLES_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,1,err,error,*999)
CALL FIELD_VARIABLE_TYPES_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,[FIELD_U_VARIABLE_TYPE],err,error,*999)
!Set the dimension
CALL FIELD_DIMENSION_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_SCALAR_DIMENSION_TYPE,err,error,*999)
!Set the data type
CALL FIELD_DATA_TYPE_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_U_VARIABLE_TYPE, &
& FIELD_DP_TYPE,err,error,*999)
!Set the number of components to one
CALL FIELD_NUMBER_OF_COMPONENTS_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_U_VARIABLE_TYPE,1, &
& err,error,*999)
!Get the geometric mesh component
CALL FIELD_COMPONENT_MESH_COMPONENT_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,FIELD_U_VARIABLE_TYPE, &
& 1,GEOMETRIC_MESH_COMPONENT,err,error,*999)
!Default to the geometric interpolation setup
CALL FIELD_COMPONENT_MESH_COMPONENT_SET(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_U_VARIABLE_TYPE,1, &
& GEOMETRIC_MESH_COMPONENT,err,error,*999)
!Specify the interpolation to be same as geometric interpolation
SELECT CASE(EQUATIONS_SET%SOLUTION_METHOD)
CASE(EQUATIONS_SET_FEM_SOLUTION_METHOD)
CALL FIELD_COMPONENT_INTERPOLATION_SET_AND_LOCK(EQUATIONS_SET%SOURCE%SOURCE_FIELD,FIELD_U_VARIABLE_TYPE,1, &
& FIELD_NODE_BASED_INTERPOLATION,err,error,*999)
CASE(EQUATIONS_SET_BEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FD_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The solution method of " &
& //TRIM(NumberToVString(EQUATIONS_SET%SOLUTION_METHOD,"*",err,error))// " is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
!Set the scaling to be the same as the geometric field
CALL FIELD_SCALING_TYPE_GET(EQUATIONS_SET%GEOMETRY%GEOMETRIC_FIELD,GEOMETRIC_SCALING_TYPE, &
& err,error,*999)
CALL FIELD_SCALING_TYPE_SET(EQUATIONS_SET%SOURCE%SOURCE_FIELD,GEOMETRIC_SCALING_TYPE, &
& err,error,*999)
ELSE
!Check the user specified field
CALL FIELD_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_GENERAL_TYPE,err,error,*999)
CALL FIELD_DEPENDENT_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_INDEPENDENT_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_VARIABLES_CHECK(EQUATIONS_SET_SETUP%FIELD,1,err,error,*999)
CALL FIELD_VARIABLE_TYPES_CHECK(EQUATIONS_SET_SETUP%FIELD,[FIELD_U_VARIABLE_TYPE],err,error,*999)
CALL FIELD_DIMENSION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,FIELD_SCALAR_DIMENSION_TYPE, &
& err,error,*999)
CALL FIELD_DATA_TYPE_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,FIELD_DP_TYPE,err,error,*999)
CALL FIELD_NUMBER_OF_COMPONENTS_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,1,err,error,*999)
SELECT CASE(EQUATIONS_SET%SOLUTION_METHOD)
CASE(EQUATIONS_SET_FEM_SOLUTION_METHOD)
CALL FIELD_COMPONENT_INTERPOLATION_CHECK(EQUATIONS_SET_SETUP%FIELD,FIELD_U_VARIABLE_TYPE,1, &
& FIELD_NODE_BASED_INTERPOLATION,err,error,*999)
CASE(EQUATIONS_SET_BEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FD_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The solution method of "//TRIM(NumberToVString(EQUATIONS_SET%SOLUTION_METHOD, &
&"*",err,error))//" is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
ENDIF
ELSE
CALL FlagError("Equations set source is not associated.",err,error,*999)
ENDIF
ELSE
CALL FlagError("Equations set materials field has not been finished.",err,error,*999)
ENDIF
ELSE
CALL FlagError("Equations set materials is not associated.",err,error,*999)
ENDIF
CASE(EQUATIONS_SET_SETUP_FINISH_ACTION)
IF(EQUATIONS_SET%SOURCE%SOURCE_FIELD_AUTO_CREATED) THEN
CALL FIELD_CREATE_FINISH(EQUATIONS_SET%SOURCE%SOURCE_FIELD,err,error,*999)
ENDIF
CASE DEFAULT
localError="The action type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%ACTION_TYPE,"*",err,error))// &
& " for a setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for a reaction diffusion equation."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE(EQUATIONS_SET_SETUP_ANALYTIC_TYPE)
SELECT CASE(EQUATIONS_SET_SETUP%ACTION_TYPE)
CASE(EQUATIONS_SET_SETUP_START_ACTION)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_SETUP_FINISH_ACTION)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The action type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%ACTION_TYPE,"*",err,error))// &
& " for a setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for a reaction diffusion equation."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE(EQUATIONS_SET_SETUP_EQUATIONS_TYPE)
SELECT CASE(EQUATIONS_SET_SETUP%ACTION_TYPE)
CASE(EQUATIONS_SET_SETUP_START_ACTION)
IF(ASSOCIATED(EQUATIONS_SET%SOURCE)) THEN
IF(EQUATIONS_SET%SOURCE%SOURCE_FINISHED) THEN
!Create the equations
CALL Equations_CreateStart(EQUATIONS_SET,EQUATIONS,err,error,*999)
SELECT CASE(EQUATIONS_SET%SPECIFICATION(3))
CASE(EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE)
CALL Equations_LinearityTypeSet(EQUATIONS,EQUATIONS_LINEAR,err,error,*999)
CASE(EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE)
CALL Equations_LinearityTypeSet(EQUATIONS,EQUATIONS_LINEAR,err,error,*999)
CASE(EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE)
CALL Equations_LinearityTypeSet(EQUATIONS,EQUATIONS_NONLINEAR,err,error,*999)
CASE DEFAULT
localError="The equations matrices linearity set up of "// &
& TRIM(NumberToVString(EQUATIONS%sparsityType,"*",err,error))//" is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
CALL Equations_TimeDependenceTypeSet(EQUATIONS,EQUATIONS_FIRST_ORDER_DYNAMIC,err,error,*999)
ELSE
CALL FlagError("Equations set source field has not been finished.",err,error,*999)
ENDIF
ELSE
CALL FlagError("Equations set source is not associated.",err,error,*999)
ENDIF
CASE(EQUATIONS_SET_SETUP_FINISH_ACTION)
SELECT CASE(EQUATIONS_SET%SOLUTION_METHOD)
CASE(EQUATIONS_SET_FEM_SOLUTION_METHOD)
!Finish the creation of the equations
CALL EquationsSet_EquationsGet(EQUATIONS_SET,equations,err,error,*999)
CALL Equations_CreateFinish(equations,err,error,*999)
NULLIFY(vectorEquations)
CALL Equations_VectorEquationsGet(equations,vectorEquations,err,error,*999)
!Create the equations mapping.
CALL EquationsMapping_VectorCreateStart(vectorEquations,FIELD_DELUDELN_VARIABLE_TYPE,vectorMapping,err,error,*999)
CALL EquationsMapping_DynamicMatricesSet(vectorMapping,.TRUE.,.TRUE.,err,error,*999)
CALL EquationsMapping_DynamicVariableTypeSet(vectorMapping,FIELD_U_VARIABLE_TYPE,err,error,*999)
CALL EquationsMapping_RHSVariableTypeSet(vectorMapping,FIELD_DELUDELN_VARIABLE_TYPE,err,error,*999)
CALL EquationsMapping_SourceVariableTypeSet(vectorMapping,FIELD_U_VARIABLE_TYPE,err,error,*999)
CALL EquationsMapping_VectorCreateFinish(vectorMapping,err,error,*999)
!Create the equations matrices
CALL EquationsMatrices_VectorCreateStart(vectorEquations,vectorMatrices,err,error,*999)
!Set up matrix storage and structure
IF(EQUATIONS%lumpingType==EQUATIONS_LUMPED_MATRICES) THEN
!Set up lumping
CALL EquationsMatrices_DynamicLumpingTypeSet(vectorMatrices, &
& [EQUATIONS_MATRIX_UNLUMPED,EQUATIONS_MATRIX_LUMPED],err,error,*999)
CALL EquationsMatrices_DynamicStorageTypeSet(vectorMatrices, &
& [DISTRIBUTED_MATRIX_COMPRESSED_ROW_STORAGE_TYPE,DISTRIBUTED_MATRIX_DIAGONAL_STORAGE_TYPE], &
& err,error,*999)
CALL EquationsMatrices_DynamicStructureTypeSet(vectorMatrices, &
[EQUATIONS_MATRIX_FEM_STRUCTURE,EQUATIONS_MATRIX_DIAGONAL_STRUCTURE],err,error,*999)
ELSE
SELECT CASE(EQUATIONS%sparsityType)
CASE(EQUATIONS_MATRICES_FULL_MATRICES)
CALL EquationsMatrices_DynamicStorageTypeSet(vectorMatrices, &
& [DISTRIBUTED_MATRIX_BLOCK_STORAGE_TYPE,DISTRIBUTED_MATRIX_BLOCK_STORAGE_TYPE],err,error,*999)
CASE(EQUATIONS_MATRICES_SPARSE_MATRICES)
CALL EquationsMatrices_DynamicStorageTypeSet(vectorMatrices, &
& [DISTRIBUTED_MATRIX_COMPRESSED_ROW_STORAGE_TYPE,DISTRIBUTED_MATRIX_COMPRESSED_ROW_STORAGE_TYPE], &
& err,error,*999)
CALL EquationsMatrices_DynamicStructureTypeSet(vectorMatrices, &
[EQUATIONS_MATRIX_FEM_STRUCTURE,EQUATIONS_MATRIX_FEM_STRUCTURE],err,error,*999)
CASE DEFAULT
localError="The equations matrices sparsity type of "// &
& TRIM(NumberToVString(EQUATIONS%sparsityType,"*",err,error))//" is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
ENDIF
CALL EquationsMatrices_VectorCreateFinish(vectorMatrices,err,error,*999)
CASE(EQUATIONS_SET_BEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FD_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The solution method of "//TRIM(NumberToVString(EQUATIONS_SET%SOLUTION_METHOD,"*",err,error))// &
& " is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE DEFAULT
localError="The action type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%ACTION_TYPE,"*",err,error))// &
& " for a setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for a bioelectric domain equation."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE DEFAULT
localError="The setup type of "//TRIM(NumberToVString(EQUATIONS_SET_SETUP%SETUP_TYPE,"*",err,error))// &
& " is invalid for reaction diffusion equation."
CALL FlagError(localError,err,error,*999)
END SELECT
ELSE
CALL FlagError("Equations set is not associated.",err,error,*999)
ENDIF
EXITS("ReactionDiffusion_EquationsSetSetup")
RETURN
999 ERRORSEXITS("ReactionDiffusion_EquationsSetSetup",err,error)
RETURN 1
END SUBROUTINE ReactionDiffusion_EquationsSetSetup
!
!================================================================================================================================
!
!>Sets/changes the solution method for a reaction diffusion equation type of a classical equations set class.
SUBROUTINE ReactionDiffusion_EquationsSetSolutionMethodSet(EQUATIONS_SET,SOLUTION_METHOD,err,error,*)
!Argument variables
TYPE(EQUATIONS_SET_TYPE), POINTER :: EQUATIONS_SET !<A pointer to the equations set to set the solution method for
INTEGER(INTG), INTENT(IN) :: SOLUTION_METHOD !<The solution method to set
INTEGER(INTG), INTENT(OUT) :: err !<The error code
TYPE(VARYING_STRING), INTENT(OUT) :: error !<The error string
!Local Variables
TYPE(VARYING_STRING) :: localError
ENTERS("ReactionDiffusion_EquationsSetSolutionMethodSet",err,error,*999)
IF(ASSOCIATED(EQUATIONS_SET)) THEN
IF(.NOT.ALLOCATED(EQUATIONS_SET%SPECIFICATION)) THEN
CALL FlagError("Equations set specification is not allocated.",err,error,*999)
ELSE IF(SIZE(EQUATIONS_SET%SPECIFICATION,1)/=3) THEN
CALL FlagError("Equations set specification must have three entries for a reaction-diffusion type equations set.", &
& err,error,*999)
END IF
SELECT CASE(EQUATIONS_SET%SPECIFICATION(3))
CASE(EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE, &
& EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE, &
& EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE)
SELECT CASE(SOLUTION_METHOD)
CASE(EQUATIONS_SET_FEM_SOLUTION_METHOD)
EQUATIONS_SET%SOLUTION_METHOD=EQUATIONS_SET_FEM_SOLUTION_METHOD
CASE(EQUATIONS_SET_BEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FD_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_FV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFEM_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_GFV_SOLUTION_METHOD)
CALL FlagError("Not implemented.",err,error,*999)
CASE DEFAULT
localError="The specified solution method of "//TRIM(NumberToVString(SOLUTION_METHOD,"*",err,error))//" is invalid."
CALL FlagError(localError,err,error,*999)
END SELECT
CASE DEFAULT
localError="Equations set subtype of "//TRIM(NumberToVString(EQUATIONS_SET%SPECIFICATION(3),"*",err,error))// &
& " is not valid for a reaction diffusion equation type of classical equations set class."
CALL FlagError(localError,err,error,*999)
END SELECT
ELSE
CALL FlagError("Equations set is not associated.",err,error,*999)
ENDIF
EXITS("ReactionDiffusion_EquationsSetSolutionMethodSet")
RETURN
999 ERRORS("ReactionDiffusion_EquationsSetSolutionMethodSet",err,error)
EXITS("ReactionDiffusion_EquationsSetSolutionMethodSet")
RETURN 1
END SUBROUTINE ReactionDiffusion_EquationsSetSolutionMethodSet
!
!================================================================================================================================
!
!>Sets the equation specification for a reaction diffusion equation type of a classical equations set class.
SUBROUTINE ReactionDiffusion_EquationsSetSpecificationSet(equationsSet,specification,err,error,*)
!Argument variables
TYPE(EQUATIONS_SET_TYPE), POINTER :: equationsSet !<A pointer to the equations set to set the specification for
INTEGER(INTG), INTENT(IN) :: specification(:) !<The equations set specification to set
INTEGER(INTG), INTENT(OUT) :: err !<The error code
TYPE(VARYING_STRING), INTENT(OUT) :: error !<The error string
!Local Variables
TYPE(VARYING_STRING) :: localError
INTEGER(INTG) :: subtype
ENTERS("ReactionDiffusion_EquationsSetSpecificationSet",err,error,*999)
IF(ASSOCIATED(equationsSet)) THEN
IF(SIZE(specification,1)>3) THEN
CALL FlagError("Equations set specification must have 3 entries for a reaction-diffusion type equations set.", &
& err,error,*999)
END IF
subtype=specification(3)
SELECT CASE(subtype)
CASE(EQUATIONS_SET_CELLML_REAC_SPLIT_REAC_DIFF_SUBTYPE)
!ok
CASE(EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE)
CALL FlagError("Not implemented.",err,error,*999)
CASE(EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE)
!ok
CASE DEFAULT
localError="The specified equations set subtype of "//TRIM(NumberToVstring(subtype,"*",err,error))// &
& " is not valid for reaction diffusion equation type of a classical equations set class."
CALL FlagError(localError,err,error,*999)
END SELECT
!Set full specification
IF(ALLOCATED(equationsSet%specification)) THEN
CALL FlagError("Equations set specification is already allocated.",err,error,*999)
ELSE
ALLOCATE(equationsSet%specification(3),stat=err)
IF(err/=0) CALL FlagError("Could not allocate equations set specification.",err,error,*999)
END IF
equationsSet%specification(1:3)=[EQUATIONS_SET_CLASSICAL_FIELD_CLASS,EQUATIONS_SET_REACTION_DIFFUSION_EQUATION_TYPE,subtype]
ELSE
CALL FlagError("Equations set is not associated.",err,error,*999)
END IF
EXITS("ReactionDiffusion_EquationsSetSpecificationSet")
RETURN
999 ERRORS("ReactionDiffusion_EquationsSetSpecificationSet",err,error)
EXITS("ReactionDiffusion_EquationsSetSpecificationSet")
RETURN 1
END SUBROUTINE ReactionDiffusion_EquationsSetSpecificationSet
!
!================================================================================================================================
!
!>Calculates the element stiffness matrices and RHS for a reaction diffusion equation finite element equations set.
SUBROUTINE ReactionDiffusion_FiniteElementCalculate(EQUATIONS_SET,ELEMENT_NUMBER,err,error,*)
!Argument variables
TYPE(EQUATIONS_SET_TYPE), POINTER :: EQUATIONS_SET !<A pointer to the equations set to perform the finite element calculations on
INTEGER(INTG), INTENT(IN) :: ELEMENT_NUMBER !<The element number to calculate
INTEGER(INTG), INTENT(OUT) :: err !<The error code
TYPE(VARYING_STRING), INTENT(OUT) :: error !<The error string
!Local Variables
INTEGER(INTG) FIELD_VAR_TYPE,mh,mhs,ms,ng,nh,nhs,ni,nj,ns,component_idx
LOGICAL :: USE_FIBRES
REAL(DP) :: DIFFUSIVITY(3,3),DPHIDX(3,64),RWG,SUM,STORAGE_COEFFICIENT,C_PARAM
TYPE(BASIS_TYPE), POINTER :: DEPENDENT_BASIS,GEOMETRIC_BASIS,FIBRE_BASIS
TYPE(EquationsType), POINTER :: equations
TYPE(EquationsMappingVectorType), POINTER :: vectorMapping
TYPE(EquationsMappingDynamicType), POINTER :: dynamicMapping
TYPE(EquationsMatricesVectorType), POINTER :: vectorMatrices
TYPE(EquationsMatricesDynamicType), POINTER :: dynamicMatrices
TYPE(EquationsMatricesRHSType), POINTER :: rhsVector
TYPE(EquationsMatricesSourceType), POINTER :: sourceVector
TYPE(EquationsMatrixType), POINTER :: dampingMatrix,stiffnessMatrix
TYPE(EquationsVectorType), POINTER :: vectorEquations
TYPE(FIELD_TYPE), POINTER :: dependentField,geometricField,fibreField,materialsField,sourceField
TYPE(FIELD_VARIABLE_TYPE), POINTER :: FIELD_VARIABLE,GEOMETRIC_VARIABLE
TYPE(QUADRATURE_SCHEME_TYPE), POINTER :: QUADRATURE_SCHEME
ENTERS("ReactionDiffusion_FiniteElementCalculate",err,error,*999)
IF(ASSOCIATED(EQUATIONS_SET)) THEN
IF(.NOT.ALLOCATED(EQUATIONS_SET%SPECIFICATION)) THEN
CALL FlagError("Equations set specification is not allocated.",err,error,*999)
ELSE IF(SIZE(EQUATIONS_SET%SPECIFICATION,1)/=3) THEN
CALL FlagError("Equations set specification must have three entries for a reaction-diffusion type equations set.", &
& err,error,*999)
END IF
EQUATIONS=>EQUATIONS_SET%EQUATIONS
IF(ASSOCIATED(EQUATIONS)) THEN
NULLIFY(vectorEquations)
CALL Equations_VectorEquationsGet(equations,vectorEquations,err,error,*999)
dependentField=>equations%interpolation%dependentField
geometricField=>equations%interpolation%geometricField
materialsField=>equations%interpolation%materialsField
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE .OR. &
& EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
sourceField=>equations%interpolation%sourceField
ENDIF
fibreField=>equations%interpolation%fibreField
USE_FIBRES=ASSOCIATED(fibreField)
vectorMapping=>vectorEquations%vectorMapping
vectorMatrices=>vectorEquations%vectorMatrices
DEPENDENT_BASIS=>dependentField%DECOMPOSITION%DOMAIN(dependentField%DECOMPOSITION%MESH_COMPONENT_NUMBER)%ptr% &
& TOPOLOGY%ELEMENTS%ELEMENTS(ELEMENT_NUMBER)%BASIS
GEOMETRIC_BASIS=>geometricField%DECOMPOSITION%DOMAIN(geometricField%DECOMPOSITION%MESH_COMPONENT_NUMBER)%ptr% &
& TOPOLOGY%ELEMENTS%ELEMENTS(ELEMENT_NUMBER)%BASIS
GEOMETRIC_VARIABLE=>geometricField%VARIABLE_TYPE_MAP(FIELD_U_VARIABLE_TYPE)%ptr
IF(USE_FIBRES) FIBRE_BASIS=>fibreField%DECOMPOSITION%DOMAIN(geometricField%DECOMPOSITION%MESH_COMPONENT_NUMBER)%ptr% &
& TOPOLOGY%ELEMENTS%ELEMENTS(ELEMENT_NUMBER)%BASIS
QUADRATURE_SCHEME=>DEPENDENT_BASIS%QUADRATURE%QUADRATURE_SCHEME_MAP(BASIS_DEFAULT_QUADRATURE_SCHEME)%ptr
CALL FIELD_INTERPOLATION_PARAMETERS_ELEMENT_GET(FIELD_VALUES_SET_TYPE,ELEMENT_NUMBER,equations%interpolation% &
& geometricInterpParameters(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
CALL FIELD_INTERPOLATION_PARAMETERS_ELEMENT_GET(FIELD_VALUES_SET_TYPE,ELEMENT_NUMBER,equations%interpolation% &
& materialsInterpParameters(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
IF(USE_FIBRES) CALL FIELD_INTERPOLATION_PARAMETERS_ELEMENT_GET(FIELD_VALUES_SET_TYPE,ELEMENT_NUMBER,equations% &
& interpolation%fibreInterpParameters(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE .OR. &
& EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
CALL FIELD_INTERPOLATION_PARAMETERS_ELEMENT_GET(FIELD_VALUES_SET_TYPE,ELEMENT_NUMBER,equations%interpolation% &
& sourceInterpParameters(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
ENDIF
dynamicMatrices=>vectorMatrices%dynamicMatrices
stiffnessMatrix=>dynamicMatrices%matrices(1)%ptr
dampingMatrix=>dynamicMatrices%matrices(2)%ptr
rhsVector=>vectorMatrices%rhsVector
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE .OR. &
& EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
sourceVector=>vectorMatrices%sourceVector
ENDIF
dynamicMapping=>vectorMapping%dynamicMapping
FIELD_VARIABLE=>dynamicMapping%equationsMatrixToVarMaps(1)%variable
FIELD_VAR_TYPE=FIELD_VARIABLE%VARIABLE_TYPE
IF(stiffnessMatrix%updateMatrix.OR.dampingMatrix%updateMatrix.OR.rhsVector%updateVector) THEN
!Loop over gauss points
DO ng=1,QUADRATURE_SCHEME%NUMBER_OF_GAUSS
CALL FIELD_INTERPOLATE_GAUSS(FIRST_PART_DERIV,BASIS_DEFAULT_QUADRATURE_SCHEME,ng,equations%interpolation% &
& geometricInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
CALL FIELD_INTERPOLATED_POINT_METRICS_CALCULATE(GEOMETRIC_BASIS%NUMBER_OF_XI,equations%interpolation% &
& geometricInterpPointMetrics(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
CALL FIELD_INTERPOLATE_GAUSS(NO_PART_DERIV,BASIS_DEFAULT_QUADRATURE_SCHEME,ng,equations%interpolation% &
& materialsInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
IF(USE_FIBRES) THEN
CALL FIELD_INTERPOLATE_GAUSS(FIRST_PART_DERIV,BASIS_DEFAULT_QUADRATURE_SCHEME,ng,equations%interpolation% &
& fibreInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
CALL FIELD_INTERPOLATED_POINT_METRICS_CALCULATE(FIBRE_BASIS%NUMBER_OF_XI,equations%interpolation% &
& fibreInterpPointMetrics(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
ENDIF
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CELLML_REAC_NO_SPLIT_REAC_DIFF_SUBTYPE .OR. &
& EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
CALL FIELD_INTERPOLATE_GAUSS(NO_PART_DERIV,BASIS_DEFAULT_QUADRATURE_SCHEME,ng,equations%interpolation% &
& sourceInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr,err,error,*999)
ENDIF
!Calculate RWG.
RWG=equations%interpolation%geometricInterpPointMetrics(FIELD_U_VARIABLE_TYPE)%ptr%JACOBIAN* &
& QUADRATURE_SCHEME%GAUSS_WEIGHTS(ng)
!Calculate the diffusivity tensor
DIFFUSIVITY=0.0_DP
IF(USE_FIBRES) THEN
!Calculate the diffusivity tensor in fibre coordinates
CALL FlagError("Not implemented.",err,error,*999)
ELSE
!Use the diffusivity tensor in geometric coordinates
DO nj=1,GEOMETRIC_VARIABLE%NUMBER_OF_COMPONENTS !first three components of material field are the diffusivities
DIFFUSIVITY(nj,nj)=equations%interpolation%materialsInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr%VALUES(nj,1)
ENDDO !nj
ENDIF
!Get the storage Coefficient, stored in the component after the diffusivities for each dimension
component_idx=GEOMETRIC_VARIABLE%NUMBER_OF_COMPONENTS+1
STORAGE_COEFFICIENT=equations%interpolation%materialsInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr%VALUES(component_idx,1)
!Compute basis dPhi/dx terms
DO nj=1,GEOMETRIC_VARIABLE%NUMBER_OF_COMPONENTS
DO ms=1,DEPENDENT_BASIS%NUMBER_OF_ELEMENT_PARAMETERS
DPHIDX(nj,ms)=0.0_DP
DO ni=1,DEPENDENT_BASIS%NUMBER_OF_XI
DPHIDX(nj,ms)=DPHIDX(nj,ms)+ &
& QUADRATURE_SCHEME%GAUSS_BASIS_FNS(ms,PARTIAL_DERIVATIVE_FIRST_DERIVATIVE_MAP(ni),ng)* &
& equations%interpolation%geometricInterpPointMetrics(FIELD_U_VARIABLE_TYPE)%ptr%DXI_DX(ni,nj)
ENDDO !ni
ENDDO !ms
ENDDO !nj
!Loop over field components
mhs=0
DO mh=1,FIELD_VARIABLE%NUMBER_OF_COMPONENTS
!Loop over element rows
DO ms=1,DEPENDENT_BASIS%NUMBER_OF_ELEMENT_PARAMETERS
mhs=mhs+1
nhs=0
!Loop over element columns
DO nh=1,FIELD_VARIABLE%NUMBER_OF_COMPONENTS
DO ns=1,DEPENDENT_BASIS%NUMBER_OF_ELEMENT_PARAMETERS
nhs=nhs+1
SUM=0.0_DP
IF(stiffnessMatrix%updateMatrix) THEN
DO ni=1,GEOMETRIC_VARIABLE%NUMBER_OF_COMPONENTS
DO nj=1,GEOMETRIC_VARIABLE%NUMBER_OF_COMPONENTS
SUM=SUM+DIFFUSIVITY(ni,nj)*DPHIDX(ni,mhs)*DPHIDX(nj,nhs)
ENDDO !nj
ENDDO !ni
stiffnessMatrix%elementMatrix%matrix(mhs,nhs)=stiffnessMatrix%elementMatrix%matrix(mhs,nhs)+(SUM*RWG)
ENDIF
IF(dampingMatrix%updateMatrix) THEN
dampingMatrix%elementMatrix%matrix(mhs,nhs)=dampingMatrix%elementMatrix%matrix(mhs,nhs)+ &
& QUADRATURE_SCHEME%GAUSS_BASIS_FNS(ms,NO_PART_DERIV,ng)* &
& QUADRATURE_SCHEME%GAUSS_BASIS_FNS(ns,NO_PART_DERIV,ng)*STORAGE_COEFFICIENT*RWG
ENDIF
ENDDO !ns
ENDDO !nh
IF(rhsVector%updateVector) rhsVector%elementVector%vector(mhs)=0.0_DP
ENDDO !ms
ENDDO !mh
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
IF(sourceVector%updateVector) THEN
C_PARAM=equations%interpolation%sourceInterpPoint(FIELD_U_VARIABLE_TYPE)%ptr%VALUES(1,NO_PART_DERIV)
mhs=0
DO mh=1,FIELD_VARIABLE%NUMBER_OF_COMPONENTS
!Loop over element rows
DO ms=1,DEPENDENT_BASIS%NUMBER_OF_ELEMENT_PARAMETERS
mhs=mhs+1
sourceVector%elementVector%vector(mhs)=sourceVector%elementVector%vector(mhs)+ &
& QUADRATURE_SCHEME%GAUSS_BASIS_FNS(ms,NO_PART_DERIV,ng)*C_PARAM*RWG
ENDDO
ENDDO
ENDIF
ENDIF
IF(rhsVector%updateVector) rhsVector%elementVector%vector(mhs)=0.0_DP
ENDDO !ng
ENDIF
!Scale factor adjustment
IF(dependentField%SCALINGS%SCALING_TYPE/=FIELD_NO_SCALING) THEN
CALL Field_InterpolationParametersScaleFactorsElementGet(ELEMENT_NUMBER,equations%interpolation% &
& dependentInterpParameters(FIELD_VAR_TYPE)%ptr,err,error,*999)
mhs=0
DO mh=1,FIELD_VARIABLE%NUMBER_OF_COMPONENTS
!Loop over element rows
DO ms=1,DEPENDENT_BASIS%NUMBER_OF_ELEMENT_PARAMETERS
mhs=mhs+1
nhs=0
IF(stiffnessMatrix%updateMatrix.OR.dampingMatrix%updateMatrix) THEN
!Loop over element columns
DO nh=1,FIELD_VARIABLE%NUMBER_OF_COMPONENTS
DO ns=1,DEPENDENT_BASIS%NUMBER_OF_ELEMENT_PARAMETERS
nhs=nhs+1
IF(stiffnessMatrix%updateMatrix) THEN
stiffnessMatrix%elementMatrix%matrix(mhs,nhs)=stiffnessMatrix%elementMatrix%matrix(mhs,nhs)* &
& equations%interpolation%dependentInterpParameters(FIELD_VAR_TYPE)%ptr%SCALE_FACTORS(ms,mh)* &
& equations%interpolation%dependentInterpParameters(FIELD_VAR_TYPE)%ptr%SCALE_FACTORS(ns,nh)
ENDIF
IF(dampingMatrix%updateMatrix) THEN
dampingMatrix%elementMatrix%matrix(mhs,nhs)=dampingMatrix%elementMatrix%matrix(mhs,nhs)* &
& equations%interpolation%dependentInterpParameters(FIELD_VAR_TYPE)%ptr%SCALE_FACTORS(ms,mh)* &
& equations%interpolation%dependentInterpParameters(FIELD_VAR_TYPE)%ptr%SCALE_FACTORS(ns,nh)
ENDIF
ENDDO !ns
ENDDO !nh
ENDIF
IF(rhsVector%updateVector) rhsVector%elementVector%vector(mhs)=rhsVector%elementVector%vector(mhs)* &
& equations%interpolation%dependentInterpParameters(FIELD_VAR_TYPE)%ptr%SCALE_FACTORS(ms,mh)
IF(EQUATIONS_SET%SPECIFICATION(3)==EQUATIONS_SET_CONSTANT_REAC_DIFF_SUBTYPE) THEN
IF(sourceVector%updateVector) sourceVector%elementVector%vector(mhs)= &
& sourceVector%elementVector%vector(mhs)* &
& equations%interpolation%dependentInterpParameters(FIELD_VAR_TYPE)%ptr%SCALE_FACTORS(ms,mh)
ENDIF
ENDDO !ms
ENDDO !mh
ENDIF
ELSE
CALL FlagError("Equations set equations is not associated.",err,error,*999)
ENDIF
ELSE
CALL FlagError("Equations set is not associated.",err,error,*999)
ENDIF
EXITS("ReactionDiffusion_FiniteElementCalculate")
RETURN
999 ERRORS("ReactionDiffusion_FiniteElementCalculate",err,error)
EXITS("ReactionDiffusion_FiniteElementCalculate")
RETURN 1
END SUBROUTINE ReactionDiffusion_FiniteElementCalculate