Active contraction (from Mario)

src/data_projection_access_routines.F90

@@ -62,10 +62,11 @@ MODULE DataProjectionAccessRoutines
   !> \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
   !>@{ 
   INTEGER(INTG), PARAMETER :: DATA_PROJECTION_CANCELLED=0 !<Data projection has been cancelled. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
-  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_CONVERGED=1 !<Data projection exited due to it being converged \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
-  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_BOUNDS=2 !<Data projection exited due to it hitting the bound and continue to travel out of the element. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
-  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_MAX_ITERATION=3 !<Data projection exited due to it attaining maximum number of iteration specified by user. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
-  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_NO_ELEMENT=4 !<Data projection exited due to no local element found, this happens when none of the candidate elements are within this computational node, and before MPI communication with other nodes. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
+  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_USER_SPECIFIED=1 !<Data projection was specified by the user. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
+  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_CONVERGED=2 !<Data projection exited due to it being converged \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
+  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_BOUNDS=3 !<Data projection exited due to it hitting the bound and continue to travel out of the element. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
+  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_MAX_ITERATION=4 !<Data projection exited due to it attaining maximum number of iteration specified by user. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
+  INTEGER(INTG), PARAMETER :: DATA_PROJECTION_EXIT_TAG_NO_ELEMENT=5 !<Data projection exited due to no local element found, this happens when none of the candidate elements are within this computational node, and before MPI communication with other nodes. \see DataProjectionRoutines,OPENCMISS_DataProjectionExitTags
   !>@}
 
   !Module types
@@ -74,8 +75,8 @@ MODULE DataProjectionAccessRoutines
 
   !Interfaces
 
-  PUBLIC DATA_PROJECTION_CANCELLED,DATA_PROJECTION_EXIT_TAG_CONVERGED,DATA_PROJECTION_EXIT_TAG_BOUNDS, &
-    & DATA_PROJECTION_EXIT_TAG_MAX_ITERATION,DATA_PROJECTION_EXIT_TAG_NO_ELEMENT
+  PUBLIC DATA_PROJECTION_CANCELLED,DATA_PROJECTION_USER_SPECIFIED,DATA_PROJECTION_EXIT_TAG_CONVERGED, &
+    & DATA_PROJECTION_EXIT_TAG_BOUNDS,DATA_PROJECTION_EXIT_TAG_MAX_ITERATION,DATA_PROJECTION_EXIT_TAG_NO_ELEMENT
 
   PUBLIC DataProjection_DataPointsGet
 

src/equations_set_constants.F90

@@ -154,6 +154,8 @@ MODULE EquationsSetConstants
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_ANISOTROPIC_POLYNOMIAL_ACTIVE_SUBTYPE=30
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_HOLZAPFEL_OGDEN_ACTIVECONTRACTION_SUBTYPE=31
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_GUCCIONE_ACTIVECONTRACTION_SUBTYPE=32
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_GUCCIONE_ACTIVECONTRACTION_NOLENDEP_SUBTYPE=44
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_GUCCIONE_ACTIVECONTRACTION_2NDPIOLA_SUBTYPE=45
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_CONSTITUTIVE_AND_GROWTH_LAW_IN_CELLML_SUBTYPE=33
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_GROWTH_LAW_IN_CELLML_SUBTYPE=34
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_ACTIVE_STRAIN_SUBTYPE=35
@@ -406,14 +408,17 @@ MODULE EquationsSetConstants
   !> \see EquationsSetConstants
   !>@{
   INTEGER(INTG), PARAMETER :: EQUATIONS_SET_DEFORMATION_GRADIENT_TENSOR=1 !<Deformation gradient tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_R_CAUCHY_GREEN_DEFORMATION_TENSOR=2 !<Right Cauchy-Green deformation field \see EquationsSetConstants_TensorTypes,EquationsSetConstants
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_L_CAUCHY_GREEN_DEFORMATION_TENSOR=3 !<Right Cauchy-Green deformation field \see EquationsSetConstants_TensorTypes,EquationsSetConstants
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_GREEN_LAGRANGE_STRAIN_TENSOR=4 !<Green-Lagrange strain tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_CAUCHY_STRESS_TENSOR=5 !<Cauchy stress tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_FIRST_PK_STRESS_TENSOR=6 !<First Piola Kirchhoff stress tensor \see EquationsSetConstants_TensorEvaluateTypes,EquationsSetConstants
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_SECOND_PK_STRESS_TENSOR=7 !<Second Piola Kirchhoff stress tensor \see EquationsSetConstants_TensorEvaluateTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_DEFORMATION_GRADIENT_TENSOR_SPATIAL=2 !<Deformation gradient tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_DEFORMATION_GRADIENT_TENSOR_FIBRE=3 !<Deformation gradient tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_R_CAUCHY_GREEN_DEFORMATION_TENSOR=4 !<Right Cauchy-Green deformation field \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_L_CAUCHY_GREEN_DEFORMATION_TENSOR=5 !<Right Cauchy-Green deformation field \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_GREEN_LAGRANGE_STRAIN_TENSOR=6 !<Green-Lagrange strain tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_CAUCHY_STRESS_TENSOR=7 !<Cauchy stress tensor \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_CAUCHY_STRESS_TENSOR_FIBRE=8 !<Cauchy stress tensor wrt deformed fibres \see EquationsSetConstants_TensorTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_FIRST_PK_STRESS_TENSOR=9 !<First Piola Kirchhoff stress tensor \see EquationsSetConstants_TensorEvaluateTypes,EquationsSetConstants
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_SECOND_PK_STRESS_TENSOR=10 !<Second Piola Kirchhoff stress tensor \see EquationsSetConstants_TensorEvaluateTypes,EquationsSetConstants
   !>@}
-  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_NUMBER_OF_TENSOR_TYPES=7
+  INTEGER(INTG), PARAMETER :: EQUATIONS_SET_NUMBER_OF_TENSOR_TYPES=10
 
   !> \addtogroup EquationsSetConstants_DynamicMatrixTypes EquationsSetConstants::DynamicMatrixTypes
   !> \brief Type of matrix in a dynamic equations set

src/equations_set_routines.F90

@@ -2772,6 +2772,8 @@ SUBROUTINE EquationsSet_FiniteElementJacobianEvaluate(equationsSet,elementNumber
           CALL FlagError("Not implemented.",err,error,*999)
         CASE(EQUATIONS_SET_CLASSICAL_FIELD_CLASS)
           CALL ClassicalField_FiniteElementJacobianEvaluate(equationsSet,elementNumber,err,error,*999)
+        CASE(EQUATIONS_SET_FITTING_CLASS)
+          CALL FlagError("Not implemented.",err,error,*999)
         CASE(EQUATIONS_SET_BIOELECTRICS_CLASS)
           CALL FlagError("Not implemented.",err,error,*999)
         CASE(EQUATIONS_SET_MODAL_CLASS)
@@ -2907,6 +2909,10 @@ SUBROUTINE EquationsSet_FiniteElementJacobianEvaluateFD(equationsSet,elementNumb
       ! so let's just loop over component, node/el, derivative
       column=0  ! element jacobian matrix column number
       DO componentIdx=1,columnVariable%NUMBER_OF_COMPONENTS
+        ! adjusts the pertubation for the hydrostatic pressure to not use the L2Norm
+        IF(componentIdx==4) THEN
+          delta=(1.0_DP)*nonlinearMatrices%jacobians(jacobianNumber)%ptr%jacobianFiniteDifferenceStepSize
+        ENDIF
         elementsTopology=>columnVariable%COMPONENTS(componentIdx)%DOMAIN%TOPOLOGY%ELEMENTS
         componentInterpolationType=columnVariable%COMPONENTS(componentIdx)%INTERPOLATION_TYPE
         SELECT CASE(componentInterpolationType)
@@ -3012,6 +3018,8 @@ SUBROUTINE EquationsSet_FiniteElementResidualEvaluate(equationsSet,elementNumber
       CALL FlagError("Not implemented.",err,error,*999)
     CASE(EQUATIONS_SET_CLASSICAL_FIELD_CLASS)
       CALL ClassicalField_FiniteElementResidualEvaluate(equationsSet,elementNumber,err,error,*999)
+    CASE(EQUATIONS_SET_FITTING_CLASS)
+      CALL FlagError("Not implemented.",err,error,*999)
     CASE(EQUATIONS_SET_BIOELECTRICS_CLASS)
       CALL FlagError("Not implemented.",err,error,*999)
     CASE(EQUATIONS_SET_MODAL_CLASS)

src/field_routines.F90

@@ -1290,6 +1290,8 @@ MODULE FIELD_ROUTINES
 
   PUBLIC FieldVariable_ParameterSetGet
 
+  PUBLIC Fields_AddField
+
   PUBLIC Fields_Finalise,Fields_Initialise
 
   PUBLIC MESH_EMBEDDING_PUSH_DATA, MESH_EMBEDDING_PULL_GAUSS_POINT_DATA, FIELD_PARAMETER_SET_GET_GAUSS_POINT_COORD
@@ -32067,6 +32069,79 @@ END SUBROUTINE FieldVariable_ParameterSetsCopyIfExists
   !================================================================================================================================
   !
 
+  !>Adds a field to a fields list
+  SUBROUTINE Fields_AddField(fields,field,err,error,*)
+
+    !Argument variables
+    TYPE(FIELDS_TYPE), POINTER :: fields !<A pointer to the fields to add a field to
+    TYPE(FIELD_TYPE), POINTER :: field !<The field to add
+    INTEGER(INTG), INTENT(OUT) :: err !<The error code
+    TYPE(VARYING_STRING), INTENT(OUT) :: error !<The error string
+    !Local Variables
+    INTEGER(INTG) :: fieldIdx
+    TYPE(FIELD_PTR_TYPE), POINTER :: newFields(:)
+
+    ENTERS("Fields_AddField",err,error,*999)
+
+    IF(.NOT.ASSOCIATED(field)) CALL FlagError("Field is not associated.",err,error,*999)
+    IF(.NOT.ASSOCIATED(fields)) THEN
+      ALLOCATE(fields,STAT=err)
+      IF(err/=0) CALL FlagError("Could not allocate fields.",err,error,*999)
+      CALL FIELDS_INITIALISE_GENERIC(fields,err,error,*999)      
+    ENDIF
+    NULLIFY(newFields)
+    ALLOCATE(newFields(fields%NUMBER_OF_FIELDS+1),STAT=err)
+    IF(err/=0) CALL FlagError("Could not allocate new fields.",err,error,*999)
+    IF(fields%NUMBER_OF_FIELDS>0) THEN
+      IF(ASSOCIATED(fields%region)) THEN
+        IF(ASSOCIATED(field%region)) THEN
+          IF(.NOT.ASSOCIATED(fields%region,field%region)) &
+            & CALL FlagError("The specified field does not have the same region as the specified fields.",err,error,*999)
+        ELSE IF(ASSOCIATED(field%INTERFACE)) THEN
+          CALL FlagError("Can not add a field from an interface to fields that are from a region.",err,error,*999)
+        ELSE
+          CALL FlagError("Field does not have an associated region or interface.",err,error,*999)
+        ENDIF
+      ELSE IF(ASSOCIATED(fields%INTERFACE)) THEN
+       IF(ASSOCIATED(field%interface)) THEN
+          IF(.NOT.ASSOCIATED(fields%interface,field%interface)) &
+            & CALL FlagError("The specified field does not have the same interface as the specified fields.",err,error,*999)
+        ELSE IF(ASSOCIATED(field%region)) THEN
+          CALL FlagError("Can not add a field from a region to fields that are from an interface.",err,error,*999)
+        ELSE
+          CALL FlagError("Field does not have an associated region or interface.",err,error,*999)
+        ENDIF
+      ELSE
+        CALL FlagError("Fields does not have a region or interface.",err,error,*999)
+      ENDIF
+    ELSE
+      IF(ASSOCIATED(field%region)) THEN
+        fields%region=>field%region
+      ELSE IF(ASSOCIATED(field%INTERFACE)) THEN
+        fields%interface=>field%interface
+      ELSE
+          CALL FlagError("Field does not have an associated region or interface.",err,error,*999)
+      ENDIF
+    ENDIF
+    DO fieldIdx=1,fields%NUMBER_OF_FIELDS
+      newFields(fieldIdx)%ptr=>fields%fields(fieldIdx)%ptr
+    ENDDO !fieldIdx
+    newFields(fields%NUMBER_OF_FIELDS+1)%ptr=>field
+    IF(ASSOCIATED(fields%fields)) DEALLOCATE(fields%fields)
+    fields%fields=>newFields
+    fields%NUMBER_OF_FIELDS=fields%NUMBER_OF_FIELDS+1
+
+    EXITS("Fields_AddField")
+    RETURN
+999 ERRORSEXITS("Fields_AddField",err,error)
+    RETURN 1
+
+  END SUBROUTINE Fields_AddField
+
+  !
+  !================================================================================================================================
+  !
+
   !>Finalises the fields and deallocates all memory.
   SUBROUTINE FIELDS_FINALISE(FIELDS,ERR,ERROR,*)