source: issm/trunk/src/c/objects/Inputs/PentaVertexInput.cpp@ 4039

/*!\file PentaVertexInput.c
 * \brief: implementation of the PentaVertexInput object
 */

#ifdef HAVE_CONFIG_H
        #include "config.h"
#else
#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
#endif

#include "stdio.h"
#include <string.h>
#include "../objects.h"
#include "../../EnumDefinitions/EnumDefinitions.h"
#include "../../shared/shared.h"
#include "../../DataSet/DataSet.h"
#include "../../include/include.h"

/*Object constructors and destructor*/
/*FUNCTION PentaVertexInput::PentaVertexInput(){{{1*/
PentaVertexInput::PentaVertexInput(){
        return;
}
/*}}}*/
/*FUNCTION PentaVertexInput::PentaVertexInput(int in_enum_type,double* values){{{1*/
PentaVertexInput::PentaVertexInput(int in_enum_type,double* in_values){

        enum_type=in_enum_type;
        values[0]=in_values[0];
        values[1]=in_values[1];
        values[2]=in_values[2];
        values[3]=in_values[3];
        values[4]=in_values[4];
        values[5]=in_values[5];
}
/*}}}*/
/*FUNCTION PentaVertexInput::~PentaVertexInput(){{{1*/
PentaVertexInput::~PentaVertexInput(){
        return;
}
/*}}}*/

/*Object management*/
/*FUNCTION PentaVertexInput::copy{{{1*/
Object* PentaVertexInput::copy() {
        
        return new PentaVertexInput(this->enum_type,this->values);

}
/*}}}*/
/*FUNCTION PentaVertexInput::DeepEcho{{{1*/
void PentaVertexInput::DeepEcho(void){

        printf("PentaVertexInput:\n");
        printf("   enum: %i (%s)\n",this->enum_type,EnumAsString(this->enum_type));
        printf("   values: [%g %g %g %g %g %g]\n",this->values[0],this->values[1],this->values[2],this->values[3],this->values[4],this->values[5]);
}
/*}}}*/
/*FUNCTION PentaVertexInput::Demarshall{{{1*/
void  PentaVertexInput::Demarshall(char** pmarshalled_dataset){

        char* marshalled_dataset=NULL;
        int   i;

        /*recover marshalled_dataset: */
        marshalled_dataset=*pmarshalled_dataset;

        /*this time, no need to get enum type, the pointer directly points to the beginning of the 
         *object data (thanks to DataSet::Demarshall):*/
        memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type);
        memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values);

        /*return: */
        *pmarshalled_dataset=marshalled_dataset;
        return;
}
/*}}}*/
/*FUNCTION PentaVertexInput::Echo {{{1*/
void PentaVertexInput::Echo(void){
        this->DeepEcho();
}
/*}}}*/
/*FUNCTION PentaVertexInput::Enum{{{1*/
int PentaVertexInput::Enum(void){

        return PentaVertexInputEnum;

}
/*}}}*/
/*FUNCTION PentaVertexInput::EnumType{{{1*/
int PentaVertexInput::EnumType(void){

        return this->enum_type;

}
/*}}}*/
/*FUNCTION PentaVertexInput::Id{{{1*/
int    PentaVertexInput::Id(void){ return -1; }
/*}}}*/
/*FUNCTION PentaVertexInput::Marshall{{{1*/
void  PentaVertexInput::Marshall(char** pmarshalled_dataset){

        char* marshalled_dataset=NULL;
        int   enum_value=0;

        /*recover marshalled_dataset: */
        marshalled_dataset=*pmarshalled_dataset;

        /*get enum value of PentaVertexInput: */
        enum_value=PentaVertexInputEnum;
        
        /*marshall enum: */
        memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value);
        
        /*marshall PentaVertexInput data: */
        memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type);
        memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values);

        *pmarshalled_dataset=marshalled_dataset;
}
/*}}}*/
/*FUNCTION PentaVertexInput::MarshallSize{{{1*/
int   PentaVertexInput::MarshallSize(){
        
        return sizeof(values)+
                +sizeof(enum_type)+
                +sizeof(int); //sizeof(int) for enum value
}
/*}}}*/
/*FUNCTION PentaVertexInput::MyRank{{{1*/
int    PentaVertexInput::MyRank(void){ 
        extern int my_rank;
        return my_rank; 
}
/*}}}*/
/*FUNCTION PentaVertexInput::SpawnSingInput{{{1*/
Input* PentaVertexInput::SpawnSingInput(int index){

        /*output*/
        SingVertexInput* outinput=NULL;

        /*Create new Sing input (copy of current input)*/
        ISSMASSERT(index<6 && index>=0);
        outinput=new SingVertexInput(this->enum_type,this->values[index]);

        /*Assign output*/
        return outinput;

}
/*}}}*/
/*FUNCTION PentaVertexInput::SpawnBeamInput{{{1*/
Input* PentaVertexInput::SpawnBeamInput(int* indices){

        /*output*/
        BeamVertexInput* outinput=NULL;
        double newvalues[2];

        /*Loop over the new indices*/
        for(int i=0;i<2;i++){

                /*Check index value*/
                ISSMASSERT(indices[i]>=0 && indices[i]<6);

                /*Assign value to new input*/
                newvalues[i]=this->values[indices[i]];
        }

        /*Create new Beam input*/
        outinput=new BeamVertexInput(this->enum_type,&newvalues[0]);

        /*Assign output*/
        return outinput;

}
/*}}}*/
/*FUNCTION PentaVertexInput::SpawnTriaInput{{{1*/
Input* PentaVertexInput::SpawnTriaInput(int* indices){

        /*output*/
        TriaVertexInput* outinput=NULL;
        double newvalues[3];

        /*Loop over the new indices*/
        for(int i=0;i<3;i++){

                /*Check index value*/
                ISSMASSERT(indices[i]>=0 && indices[i]<6);

                /*Assign value to new input*/
                newvalues[i]=this->values[indices[i]];
        }

        /*Create new Tria input*/
        outinput=new TriaVertexInput(this->enum_type,&newvalues[0]);

        /*Assign output*/
        return outinput;

}
/*}}}*/
/*FUNCTION PentaVertexInput::SpawnResult{{{1*/
Result* PentaVertexInput::SpawnResult(int step, double time){

        return new PentaVertexResult(this->enum_type,this->values,step,time);

}
/*}}}*/

/*Object functions*/
/*FUNCTION PentaVertexInput::GetParameterValue(bool* pvalue) {{{1*/
void PentaVertexInput::GetParameterValue(bool* pvalue){ISSMERROR(" not supported yet!");}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValue(int* pvalue){{{1*/
void PentaVertexInput::GetParameterValue(int* pvalue){ISSMERROR(" not supported yet!");}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValue(double* pvalue){{{1*/
void PentaVertexInput::GetParameterValue(double* pvalue){ISSMERROR(" not supported yet!");}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValue(double* pvalue,Node* node){{{1*/
void PentaVertexInput::GetParameterValue(double* pvalue,Node* node){ISSMERROR(" not supported yet!");}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValue(double* pvalue,Node* node1,Node* node2,double gauss_coord){{{1*/
void PentaVertexInput::GetParameterValue(double* pvalue,Node* node1,Node* node2,double gauss_coord){ISSMERROR(" not supported yet!");}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValue(double* pvalue,double* gauss){{{1*/
void PentaVertexInput::GetParameterValue(double* pvalue,double* gauss){
        /*P1 interpolation on Gauss point*/

        /*intermediary*/
        double l1l6[6];

        /*nodal functions: */
        GetNodalFunctionsP1(&l1l6[0],gauss);

        /*Assign output pointers:*/
        *pvalue=l1l6[0]*values[0]+l1l6[1]*values[1]+l1l6[2]*values[2]+l1l6[3]*values[3]+l1l6[4]*values[4]+l1l6[5]*values[5];

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValue(double* pvalue,double* gauss,double defaultvalue){{{1*/
void PentaVertexInput::GetParameterValue(double* pvalue,double* gauss,double defaultvalue){ISSMERROR(" not supported yet!");}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterValues(double* values,double* gauss_pointers, int numgauss){{{1*/
void PentaVertexInput::GetParameterValues(double* values,double* gauss_pointers, int numgauss){
        /*It is assumed that output values has been correctly allocated*/

        int i,j;
        double gauss[4];

        for (i=0;i<numgauss;i++){

                /*Get current Gauss point coordinates*/
                for (j=0;j<4;j++) gauss[j]=gauss_pointers[i*4+j];

                /*Assign parameter value*/
                GetParameterValue(&values[i],&gauss[0]);
        }
}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterDerivativeValue(double* derivativevalues, double* xyz_list, double* gauss){{{1*/
void PentaVertexInput::GetParameterDerivativeValue(double* p, double* xyz_list, double* gauss){
        /*From grid values of parameter p (p_list[0], p_list[1], p_list[2], p_list[3], p_list[4] and p_list[4]), return parameter derivative value at gaussian point specified by gauss_coord:
         *   dp/dx=p_list[0]*dh1/dx+p_list[1]*dh2/dx+p_list[2]*dh3/dx+p_list[3]*dh4/dx+p_list[4]*dh5/dx+p_list[5]*dh6/dx;
         *   dp/dy=p_list[0]*dh1/dy+p_list[1]*dh2/dy+p_list[2]*dh3/dy+p_list[3]*dh4/dy+p_list[4]*dh5/dy+p_list[5]*dh6/dy;
         *   dp/dz=p_list[0]*dh1/dz+p_list[1]*dh2/dz+p_list[2]*dh3/dz+p_list[3]*dh4/dz+p_list[4]*dh5/dz+p_list[5]*dh6/dz;
         *
         *   p is a vector of size 3x1 already allocated.
         */

        const int NDOF3=3;
        const int numgrids=6;
        double dh1dh6[NDOF3][numgrids];

        /*Get nodal funnctions derivatives in actual coordinate system: */
        GetNodalFunctionsP1Derivatives(&dh1dh6[0][0],xyz_list, gauss);

        p[0]=this->values[0]*dh1dh6[0][0]+this->values[1]*dh1dh6[0][1]+this->values[2]*dh1dh6[0][2]+this->values[3]*dh1dh6[0][3]+this->values[4]*dh1dh6[0][4]+this->values[5]*dh1dh6[0][5];
        p[1]=this->values[0]*dh1dh6[1][0]+this->values[1]*dh1dh6[1][1]+this->values[2]*dh1dh6[1][2]+this->values[3]*dh1dh6[1][3]+this->values[4]*dh1dh6[1][4]+this->values[5]*dh1dh6[1][5];
        p[2]=this->values[0]*dh1dh6[2][0]+this->values[1]*dh1dh6[2][1]+this->values[2]*dh1dh6[2][2]+this->values[3]*dh1dh6[2][3]+this->values[4]*dh1dh6[2][4]+this->values[5]*dh1dh6[2][5];

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetVxStrainRate3d(double* epsilonvx,double* xyz_list, double* gauss) {{{1*/
void PentaVertexInput::GetVxStrainRate3d(double* epsilonvx,double* xyz_list, double* gauss){
        int i,j;

        const int numgrids=6;
        const int DOFVELOCITY=3;
        double B[8][27];
        double B_reduced[6][DOFVELOCITY*numgrids];
        double velocity[numgrids][DOFVELOCITY];

        /*Get B matrix: */
        GetBStokes(&B[0][0], xyz_list, gauss);
        /*Create a reduced matrix of B to get rid of pressure */
        for (i=0;i<6;i++){
                for (j=0;j<3;j++){
                        B_reduced[i][j]=B[i][j];
                }
                for (j=4;j<7;j++){
                        B_reduced[i][j-1]=B[i][j];
                }
                for (j=8;j<11;j++){
                        B_reduced[i][j-2]=B[i][j];
                }
                for (j=12;j<15;j++){
                        B_reduced[i][j-3]=B[i][j];
                }
                for (j=16;j<19;j++){
                        B_reduced[i][j-4]=B[i][j];
                }
                for (j=20;j<23;j++){
                        B_reduced[i][j-5]=B[i][j];
                }
        }

        /*Here, we are computing the strain rate of (vx,0,0)*/
        for(i=0;i<numgrids;i++){
                velocity[i][0]=this->values[i];
                velocity[i][1]=0.0;
                velocity[i][2]=0.0;
        }
        /*Multiply B by velocity, to get strain rate: */
        MatrixMultiply(&B_reduced[0][0],6,DOFVELOCITY*numgrids,0,&velocity[0][0],DOFVELOCITY*numgrids,1,0,epsilonvx,0);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetVyStrainRate3d(double* epsilonvy,double* xyz_list, double* gauss) {{{1*/
void PentaVertexInput::GetVyStrainRate3d(double* epsilonvy,double* xyz_list, double* gauss){
        int i,j;

        const int numgrids=6;
        const int DOFVELOCITY=3;
        double B[8][27];
        double B_reduced[6][DOFVELOCITY*numgrids];
        double velocity[numgrids][DOFVELOCITY];

        /*Get B matrix: */
        GetBStokes(&B[0][0], xyz_list, gauss);
        /*Create a reduced matrix of B to get rid of pressure */
        for (i=0;i<6;i++){
                for (j=0;j<3;j++){
                        B_reduced[i][j]=B[i][j];
                }
                for (j=4;j<7;j++){
                        B_reduced[i][j-1]=B[i][j];
                }
                for (j=8;j<11;j++){
                        B_reduced[i][j-2]=B[i][j];
                }
                for (j=12;j<15;j++){
                        B_reduced[i][j-3]=B[i][j];
                }
                for (j=16;j<19;j++){
                        B_reduced[i][j-4]=B[i][j];
                }
                for (j=20;j<23;j++){
                        B_reduced[i][j-5]=B[i][j];
                }
        }

        /*Here, we are computing the strain rate of (0,vy,0)*/
        for(i=0;i<numgrids;i++){
                velocity[i][0]=0.0;
                velocity[i][1]=this->values[i];
                velocity[i][2]=0.0;
        }
        /*Multiply B by velocity, to get strain rate: */
        MatrixMultiply(&B_reduced[0][0],6,DOFVELOCITY*numgrids,0,&velocity[0][0],DOFVELOCITY*numgrids,1,0,epsilonvy,0);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetVzStrainRate3d(double* epsilonvz,double* xyz_list, double* gauss) {{{1*/
void PentaVertexInput::GetVzStrainRate3d(double* epsilonvz,double* xyz_list, double* gauss){
        int i,j;

        const int numgrids=6;
        const int DOFVELOCITY=3;
        double B[8][27];
        double B_reduced[6][DOFVELOCITY*numgrids];
        double velocity[numgrids][DOFVELOCITY];

        /*Get B matrix: */
        GetBStokes(&B[0][0], xyz_list, gauss);
        /*Create a reduced matrix of B to get rid of pressure */
        for (i=0;i<6;i++){
                for (j=0;j<3;j++){
                        B_reduced[i][j]=B[i][j];
                }
                for (j=4;j<7;j++){
                        B_reduced[i][j-1]=B[i][j];
                }
                for (j=8;j<11;j++){
                        B_reduced[i][j-2]=B[i][j];
                }
                for (j=12;j<15;j++){
                        B_reduced[i][j-3]=B[i][j];
                }
                for (j=16;j<19;j++){
                        B_reduced[i][j-4]=B[i][j];
                }
                for (j=20;j<23;j++){
                        B_reduced[i][j-5]=B[i][j];
                }
        }

        /*Here, we are computing the strain rate of (0,0,vz)*/
        for(i=0;i<numgrids;i++){
                velocity[i][0]=0.0;
                velocity[i][1]=0.0;
                velocity[i][2]=this->values[i];
        }

        /*Multiply B by velocity, to get strain rate: */
        MatrixMultiply(&B_reduced[0][0],6,DOFVELOCITY*numgrids,0,&velocity[0][0],DOFVELOCITY*numgrids,1,0,epsilonvz,0);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetVxStrainRate3dPattyn(double* epsilonvx,double* xyz_list, double* gauss) {{{1*/
void PentaVertexInput::GetVxStrainRate3dPattyn(double* epsilonvx,double* xyz_list, double* gauss){

        int i;
        const int numgrids=6;
        const int NDOF2=2;
        double B[5][NDOF2*numgrids];
        double velocity[numgrids][NDOF2];

        /*Get B matrix: */
        GetBPattyn(&B[0][0], xyz_list, gauss);

        /*Here, we are computing the strain rate of (vx,0)*/
        for(i=0;i<numgrids;i++){
                velocity[i][0]=this->values[i];
                velocity[i][1]=0.0;
        }

        /*Multiply B by velocity, to get strain rate: */
        MatrixMultiply( &B[0][0],5,NDOF2*numgrids,0,
                                &velocity[0][0],NDOF2*numgrids,1,0,
                                epsilonvx,0);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetVyStrainRate3dPattyn(double* epsilonvy,double* xyz_list, double* gauss) {{{1*/
void PentaVertexInput::GetVyStrainRate3dPattyn(double* epsilonvy,double* xyz_list, double* gauss){

        int i;
        const int numgrids=6;
        const int NDOF2=2;
        double B[5][NDOF2*numgrids];
        double velocity[numgrids][NDOF2];

        /*Get B matrix: */
        GetBPattyn(&B[0][0], xyz_list, gauss);

        /*Here, we are computing the strain rate of (0,vy)*/
        for(i=0;i<numgrids;i++){
                velocity[i][0]=0.0;
                velocity[i][1]=this->values[i];
        }

        /*Multiply B by velocity, to get strain rate: */
        MatrixMultiply( &B[0][0],5,NDOF2*numgrids,0,
                                &velocity[0][0],NDOF2*numgrids,1,0,
                                epsilonvy,0);

}
/*}}}*/
/*FUNCTION PentaVertexInput::ChangeEnum(int newenumtype){{{1*/
void PentaVertexInput::ChangeEnum(int newenumtype){
        this->enum_type=newenumtype;
}
/*}}}*/
/*FUNCTION PentaVertexInput::GetParameterAverage(double* pvalue){{{1*/
void PentaVertexInput::GetParameterAverage(double* pvalue){
        *pvalue=1./6.*(values[0]+values[1]+values[2]+values[3]+values[4]+values[5]);
}
/*}}}*/

/*Intermediary*/
/*FUNCTION PentaVertexInput::GetNodalFunctionsP1 {{{1*/
void PentaVertexInput::GetNodalFunctionsP1(double* l1l6, double* gauss_coord){

        /*This routine returns the values of the nodal functions  at the gaussian point.*/

        l1l6[0]=gauss_coord[0]*(1-gauss_coord[3])/2.0;

        l1l6[1]=gauss_coord[1]*(1-gauss_coord[3])/2.0;

        l1l6[2]=gauss_coord[2]*(1-gauss_coord[3])/2.0;

        l1l6[3]=gauss_coord[0]*(1+gauss_coord[3])/2.0;

        l1l6[4]=gauss_coord[1]*(1+gauss_coord[3])/2.0;

        l1l6[5]=gauss_coord[2]*(1+gauss_coord[3])/2.0;

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetNodalFunctionsMINI{{{1*/
void PentaVertexInput::GetNodalFunctionsMINI(double* l1l7, double* gauss_coord){

        /*This routine returns the values of the nodal functions  at the gaussian point.*/

        /*First nodal function: */
        l1l7[0]=gauss_coord[0]*(1.0-gauss_coord[3])/2.0;

        /*Second nodal function: */
        l1l7[1]=gauss_coord[1]*(1.0-gauss_coord[3])/2.0;

        /*Third nodal function: */
        l1l7[2]=gauss_coord[2]*(1.0-gauss_coord[3])/2.0;

        /*Fourth nodal function: */
        l1l7[3]=gauss_coord[0]*(1.0+gauss_coord[3])/2.0;

        /*Fifth nodal function: */
        l1l7[4]=gauss_coord[1]*(1.0+gauss_coord[3])/2.0;

        /*Sixth nodal function: */
        l1l7[5]=gauss_coord[2]*(1.0+gauss_coord[3])/2.0;

        /*Seventh nodal function: */
        l1l7[6]=27*gauss_coord[0]*gauss_coord[1]*gauss_coord[2]*(1.0+gauss_coord[3])*(1.0-gauss_coord[3]);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetNodalFunctionsP1Derivatives {{{1*/
void PentaVertexInput::GetNodalFunctionsP1Derivatives(double* dh1dh6,double* xyz_list, double* gauss_coord){

        /*This routine returns the values of the nodal functions derivatives  (with respect to the actual coordinate system: */
        int i;
        const int NDOF3=3;
        const int numgrids=6;

        double dh1dh6_ref[NDOF3][numgrids];
        double Jinv[NDOF3][NDOF3];

        /*Get derivative values with respect to parametric coordinate system: */
        GetNodalFunctionsP1DerivativesReference(&dh1dh6_ref[0][0], gauss_coord); 

        /*Get Jacobian invert: */
        GetJacobianInvert(&Jinv[0][0], xyz_list, gauss_coord);

        /*Build dh1dh3: 
         *
         * [dhi/dx]= Jinv*[dhi/dr]
         * [dhi/dy]       [dhi/ds]
         * [dhi/dz]       [dhi/dn]
         */

        for (i=0;i<numgrids;i++){
                *(dh1dh6+numgrids*0+i)=Jinv[0][0]*dh1dh6_ref[0][i]+Jinv[0][1]*dh1dh6_ref[1][i]+Jinv[0][2]*dh1dh6_ref[2][i];
                *(dh1dh6+numgrids*1+i)=Jinv[1][0]*dh1dh6_ref[0][i]+Jinv[1][1]*dh1dh6_ref[1][i]+Jinv[1][2]*dh1dh6_ref[2][i];
                *(dh1dh6+numgrids*2+i)=Jinv[2][0]*dh1dh6_ref[0][i]+Jinv[2][1]*dh1dh6_ref[1][i]+Jinv[2][2]*dh1dh6_ref[2][i];
        }

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetNodalFunctionsMINIDerivatives{{{1*/
void PentaVertexInput::GetNodalFunctionsMINIDerivatives(double* dh1dh7,double* xyz_list, double* gauss_coord){

        /*This routine returns the values of the nodal functions derivatives  (with respect to the 
         * actual coordinate system: */

        int i;

        const  int numgrids=7;
        double dh1dh7_ref[3][numgrids];
        double Jinv[3][3];


        /*Get derivative values with respect to parametric coordinate system: */
        GetNodalFunctionsMINIDerivativesReference(&dh1dh7_ref[0][0], gauss_coord); 

        /*Get Jacobian invert: */
        GetJacobianInvert(&Jinv[0][0], xyz_list, gauss_coord);

        /*Build dh1dh6: 
         *
         * [dhi/dx]= Jinv'*[dhi/dr]
         * [dhi/dy]        [dhi/ds]
         * [dhi/dz]        [dhi/dzeta]
         */

        for (i=0;i<numgrids;i++){
                *(dh1dh7+numgrids*0+i)=Jinv[0][0]*dh1dh7_ref[0][i]+Jinv[0][1]*dh1dh7_ref[1][i]+Jinv[0][2]*dh1dh7_ref[2][i];
                *(dh1dh7+numgrids*1+i)=Jinv[1][0]*dh1dh7_ref[0][i]+Jinv[1][1]*dh1dh7_ref[1][i]+Jinv[1][2]*dh1dh7_ref[2][i];
                *(dh1dh7+numgrids*2+i)=Jinv[2][0]*dh1dh7_ref[0][i]+Jinv[2][1]*dh1dh7_ref[1][i]+Jinv[2][2]*dh1dh7_ref[2][i];
        }

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetNodalFunctionsP1DerivativesReference {{{1*/
void PentaVertexInput::GetNodalFunctionsP1DerivativesReference(double* dl1dl6,double* gauss_coord){

        /*This routine returns the values of the nodal functions derivatives  (with respect to the 
         * natural coordinate system) at the gaussian point. Those values vary along xi,eta,z */

        const int numgrids=6;
        double A1,A2,A3,z;

        A1=gauss_coord[0]; //first area coordinate value. In term of xi and eta: A1=(1-xi)/2-eta/(2*SQRT3);
        A2=gauss_coord[1]; //second area coordinate value In term of xi and eta: A2=(1+xi)/2-eta/(2*SQRT3);
        A3=gauss_coord[2]; //third area coordinate value  In term of xi and eta: A3=y/SQRT3;
        z=gauss_coord[3]; //fourth vertical coordinate value. Corresponding nodal function: (1-z)/2 and (1+z)/2


        /*First nodal function derivatives. The corresponding nodal function is N=A1*(1-z)/2. Its derivatives follow*/
        *(dl1dl6+numgrids*0+0)=-0.5*(1.0-z)/2.0;
        *(dl1dl6+numgrids*1+0)=-0.5/SQRT3*(1.0-z)/2.0;
        *(dl1dl6+numgrids*2+0)=-0.5*A1;

        /*Second nodal function: The corresponding nodal function is N=A2*(1-z)/2. Its derivatives follow*/
        *(dl1dl6+numgrids*0+1)=0.5*(1.0-z)/2.0;
        *(dl1dl6+numgrids*1+1)=-0.5/SQRT3*(1.0-z)/2.0;
        *(dl1dl6+numgrids*2+1)=-0.5*A2;

        /*Third nodal function: The corresponding nodal function is N=A3*(1-z)/2. Its derivatives follow*/
        *(dl1dl6+numgrids*0+2)=0.0;
        *(dl1dl6+numgrids*1+2)=1.0/SQRT3*(1.0-z)/2.0;
        *(dl1dl6+numgrids*2+2)=-0.5*A3;

        /*Fourth nodal function: The corresponding nodal function is N=A1*(1+z)/2. Its derivatives follow*/
        *(dl1dl6+numgrids*0+3)=-0.5*(1.0+z)/2.0;
        *(dl1dl6+numgrids*1+3)=-0.5/SQRT3*(1.0+z)/2.0;
        *(dl1dl6+numgrids*2+3)=0.5*A1;

        /*Fifth nodal function: The corresponding nodal function is N=A2*(1+z)/2. Its derivatives follow*/
        *(dl1dl6+numgrids*0+4)=0.5*(1.0+z)/2.0;
        *(dl1dl6+numgrids*1+4)=-0.5/SQRT3*(1.0+z)/2.0;
        *(dl1dl6+numgrids*2+4)=0.5*A2;

        /*Sixth nodal function: The corresponding nodal function is N=A3*(1+z)/2. Its derivatives follow*/
        *(dl1dl6+numgrids*0+5)=0.0;
        *(dl1dl6+numgrids*1+5)=1.0/SQRT3*(1.0+z)/2.0;
        *(dl1dl6+numgrids*2+5)=0.5*A3;
}
/*}}}*/
/*FUNCTION PentaVertexInput::GetNodalFunctionsMINIDerivativesReference{{{1*/
void PentaVertexInput::GetNodalFunctionsMINIDerivativesReference(double* dl1dl7,double* gauss_coord){

        /*This routine returns the values of the nodal functions derivatives  (with respect to the 
         * natural coordinate system) at the gaussian point. */

        int    numgrids=7; //six plus bubble grids

        double r=gauss_coord[1]-gauss_coord[0];
        double s=-3.0/SQRT3*(gauss_coord[0]+gauss_coord[1]-2.0/3.0);
        double zeta=gauss_coord[3];

        /*First nodal function: */
        *(dl1dl7+numgrids*0+0)=-0.5*(1.0-zeta)/2.0;
        *(dl1dl7+numgrids*1+0)=-SQRT3/6.0*(1.0-zeta)/2.0;
        *(dl1dl7+numgrids*2+0)=-0.5*(-0.5*r-SQRT3/6.0*s+ONETHIRD);

        /*Second nodal function: */
        *(dl1dl7+numgrids*0+1)=0.5*(1.0-zeta)/2.0;
        *(dl1dl7+numgrids*1+1)=-SQRT3/6.0*(1.0-zeta)/2.0;
        *(dl1dl7+numgrids*2+1)=-0.5*(0.5*r-SQRT3/6.0*s+ONETHIRD);

        /*Third nodal function: */
        *(dl1dl7+numgrids*0+2)=0;
        *(dl1dl7+numgrids*1+2)=SQRT3/3.0*(1.0-zeta)/2.0;
        *(dl1dl7+numgrids*2+2)=-0.5*(SQRT3/3.0*s+ONETHIRD);

        /*Fourth nodal function: */
        *(dl1dl7+numgrids*0+3)=-0.5*(1.0+zeta)/2.0;
        *(dl1dl7+numgrids*1+3)=-SQRT3/6.0*(1.0+zeta)/2.0;
        *(dl1dl7+numgrids*2+3)=0.5*(-0.5*r-SQRT3/6.0*s+ONETHIRD);

        /*Fith nodal function: */
        *(dl1dl7+numgrids*0+4)=0.5*(1.0+zeta)/2.0;
        *(dl1dl7+numgrids*1+4)=-SQRT3/6.0*(1.0+zeta)/2.0;
        *(dl1dl7+numgrids*2+4)=0.5*(0.5*r-SQRT3/6.0*s+ONETHIRD);

        /*Sixth nodal function: */
        *(dl1dl7+numgrids*0+5)=0;
        *(dl1dl7+numgrids*1+5)=SQRT3/3.0*(1.0+zeta)/2.0;
        *(dl1dl7+numgrids*2+5)=0.5*(SQRT3/3.0*s+ONETHIRD);

        /*Seventh nodal function: */
        *(dl1dl7+numgrids*0+6)=9.0/2.0*r*(1.0+zeta)*(zeta-1.0)*(SQRT3*s+1.0);
        *(dl1dl7+numgrids*1+6)=9.0/4.0*(1+zeta)*(1-zeta)*(SQRT3*pow(s,2.0)-2.0*s-SQRT3*pow(r,2.0));
        *(dl1dl7+numgrids*2+6)=27*gauss_coord[0]*gauss_coord[1]*gauss_coord[2]*(-2.0*zeta);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetJacobian {{{1*/
void PentaVertexInput::GetJacobian(double* J, double* xyz_list,double* gauss_coord){

        const int NDOF3=3;
        int i,j;

        /*The Jacobian is constant over the element, discard the gaussian points. 
         * J is assumed to have been allocated of size NDOF2xNDOF2.*/

        double A1,A2,A3; //area coordinates
        double xi,eta,zi; //parametric coordinates

        double x1,x2,x3,x4,x5,x6;
        double y1,y2,y3,y4,y5,y6;
        double z1,z2,z3,z4,z5,z6;

        /*Figure out xi,eta and zi (parametric coordinates), for this gaussian point: */
        A1=gauss_coord[0];
        A2=gauss_coord[1];
        A3=gauss_coord[2];

        xi=A2-A1;
        eta=SQRT3*A3;
        zi=gauss_coord[3];

        x1=*(xyz_list+3*0+0);
        x2=*(xyz_list+3*1+0);
        x3=*(xyz_list+3*2+0);
        x4=*(xyz_list+3*3+0);
        x5=*(xyz_list+3*4+0);
        x6=*(xyz_list+3*5+0);

        y1=*(xyz_list+3*0+1);
        y2=*(xyz_list+3*1+1);
        y3=*(xyz_list+3*2+1);
        y4=*(xyz_list+3*3+1);
        y5=*(xyz_list+3*4+1);
        y6=*(xyz_list+3*5+1);

        z1=*(xyz_list+3*0+2);
        z2=*(xyz_list+3*1+2);
        z3=*(xyz_list+3*2+2);
        z4=*(xyz_list+3*3+2);
        z5=*(xyz_list+3*4+2);
        z6=*(xyz_list+3*5+2);

        *(J+NDOF3*0+0)=0.25*(x1-x2-x4+x5)*zi+0.25*(-x1+x2-x4+x5);
        *(J+NDOF3*1+0)=SQRT3/12.0*(x1+x2-2*x3-x4-x5+2*x6)*zi+SQRT3/12.0*(-x1-x2+2*x3-x4-x5+2*x6);
        *(J+NDOF3*2+0)=SQRT3/12.0*(x1+x2-2*x3-x4-x5+2*x6)*eta+1/4*(x1-x2-x4+x5)*xi +0.25*(-x1+x5-x2+x4);

        *(J+NDOF3*0+1)=0.25*(y1-y2-y4+y5)*zi+0.25*(-y1+y2-y4+y5);
        *(J+NDOF3*1+1)=SQRT3/12.0*(y1+y2-2*y3-y4-y5+2*y6)*zi+SQRT3/12.0*(-y1-y2+2*y3-y4-y5+2*y6);
        *(J+NDOF3*2+1)=SQRT3/12.0*(y1+y2-2*y3-y4-y5+2*y6)*eta+0.25*(y1-y2-y4+y5)*xi+0.25*(y4-y1+y5-y2);

        *(J+NDOF3*0+2)=0.25*(z1-z2-z4+z5)*zi+0.25*(-z1+z2-z4+z5);
        *(J+NDOF3*1+2)=SQRT3/12.0*(z1+z2-2*z3-z4-z5+2*z6)*zi+SQRT3/12.0*(-z1-z2+2*z3-z4-z5+2*z6);
        *(J+NDOF3*2+2)=SQRT3/12.0*(z1+z2-2*z3-z4-z5+2*z6)*eta+0.25*(z1-z2-z4+z5)*xi+0.25*(-z1+z5-z2+z4);

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetJacobianInvert {{{1*/
void PentaVertexInput::GetJacobianInvert(double*  Jinv, double* xyz_list,double* gauss_coord){

        double Jdet;
        const int NDOF3=3;

        /*Call Jacobian routine to get the jacobian:*/
        GetJacobian(Jinv, xyz_list, gauss_coord);

        /*Invert Jacobian matrix: */
        MatrixInverse(Jinv,NDOF3,NDOF3,NULL,0,&Jdet);
}
/*}}}*/
/*FUNCTION PentaVertexInput::GetBPattyn {{{1*/
void PentaVertexInput::GetBPattyn(double* B, double* xyz_list, double* gauss_coord){
        /*Compute B  matrix. B=[B1 B2 B3 B4 B5 B6] where Bi is of size 5*NDOF2. 
         * For grid i, Bi can be expressed in the actual coordinate system
         * by: 
         *       Bi=[ dh/dx          0      ]
         *          [   0           dh/dy   ]
         *          [ 1/2*dh/dy  1/2*dh/dx  ]
         *          [ 1/2*dh/dz      0      ]
         *          [  0         1/2*dh/dz  ]
         * where h is the interpolation function for grid i.
         *
         * We assume B has been allocated already, of size: 5x(NDOF2*numgrids)
         */

        int i;
        const int numgrids=6;
        const int NDOF3=3;
        const int NDOF2=2;

        double dh1dh6[NDOF3][numgrids];

        /*Get dh1dh6 in actual coordinate system: */
        GetNodalFunctionsP1Derivatives(&dh1dh6[0][0],xyz_list, gauss_coord);

        /*Build B: */
        for (i=0;i<numgrids;i++){
                *(B+NDOF2*numgrids*0+NDOF2*i)=dh1dh6[0][i]; 
                *(B+NDOF2*numgrids*0+NDOF2*i+1)=0.0;

                *(B+NDOF2*numgrids*1+NDOF2*i)=0.0;
                *(B+NDOF2*numgrids*1+NDOF2*i+1)=dh1dh6[1][i];

                *(B+NDOF2*numgrids*2+NDOF2*i)=(float).5*dh1dh6[1][i]; 
                *(B+NDOF2*numgrids*2+NDOF2*i+1)=(float).5*dh1dh6[0][i]; 

                *(B+NDOF2*numgrids*3+NDOF2*i)=(float).5*dh1dh6[2][i]; 
                *(B+NDOF2*numgrids*3+NDOF2*i+1)=0.0;

                *(B+NDOF2*numgrids*4+NDOF2*i)=0.0;
                *(B+NDOF2*numgrids*4+NDOF2*i+1)=(float).5*dh1dh6[2][i]; 
        }

}
/*}}}*/
/*FUNCTION PentaVertexInput::GetBStokes {{{1*/
void PentaVertexInput::GetBStokes(double* B, double* xyz_list, double* gauss_coord){

        /*Compute B  matrix. B=[B1 B2 B3 B4 B5 B6] where Bi is of size 3*DOFPERGRID. 
         * For grid i, Bi can be expressed in the actual coordinate system
         * by:          Bi=[ dh/dx          0             0       0  ]
         *                                      [   0           dh/dy           0       0  ]
         *                                      [   0             0           dh/dy     0  ]
         *                                      [ 1/2*dh/dy    1/2*dh/dx        0       0  ]
         *                                      [ 1/2*dh/dz       0         1/2*dh/dx   0  ]
         *                                      [   0          1/2*dh/dz    1/2*dh/dy   0  ]
         *                                      [   0             0             0       h  ]
         *                                      [ dh/dx         dh/dy         dh/dz     0  ]
         *      where h is the interpolation function for grid i.
         *      Same thing for Bb except the last column that does not exist.
         */

        int i;
        const int calculationdof=3;
        const int numgrids=6;
        int DOFPERGRID=4;

        double dh1dh7[calculationdof][numgrids+1];
        double l1l6[numgrids];


        /*Get dh1dh7 in actual coordinate system: */
        GetNodalFunctionsMINIDerivatives(&dh1dh7[0][0],xyz_list, gauss_coord);
        GetNodalFunctionsP1(l1l6, gauss_coord);

        /*Build B: */
        for (i=0;i<numgrids+1;i++){
                *(B+(DOFPERGRID*numgrids+3)*0+DOFPERGRID*i)=dh1dh7[0][i]; //B[0][DOFPERGRID*i]=dh1dh6[0][i];
                *(B+(DOFPERGRID*numgrids+3)*0+DOFPERGRID*i+1)=0;
                *(B+(DOFPERGRID*numgrids+3)*0+DOFPERGRID*i+2)=0;
                *(B+(DOFPERGRID*numgrids+3)*1+DOFPERGRID*i)=0;
                *(B+(DOFPERGRID*numgrids+3)*1+DOFPERGRID*i+1)=dh1dh7[1][i];
                *(B+(DOFPERGRID*numgrids+3)*1+DOFPERGRID*i+2)=0;
                *(B+(DOFPERGRID*numgrids+3)*2+DOFPERGRID*i)=0;
                *(B+(DOFPERGRID*numgrids+3)*2+DOFPERGRID*i+1)=0;
                *(B+(DOFPERGRID*numgrids+3)*2+DOFPERGRID*i+2)=dh1dh7[2][i];
                *(B+(DOFPERGRID*numgrids+3)*3+DOFPERGRID*i)=(float).5*dh1dh7[1][i]; 
                *(B+(DOFPERGRID*numgrids+3)*3+DOFPERGRID*i+1)=(float).5*dh1dh7[0][i]; 
                *(B+(DOFPERGRID*numgrids+3)*3+DOFPERGRID*i+2)=0;
                *(B+(DOFPERGRID*numgrids+3)*4+DOFPERGRID*i)=(float).5*dh1dh7[2][i];
                *(B+(DOFPERGRID*numgrids+3)*4+DOFPERGRID*i+1)=0;
                *(B+(DOFPERGRID*numgrids+3)*4+DOFPERGRID*i+2)=(float).5*dh1dh7[0][i];
                *(B+(DOFPERGRID*numgrids+3)*5+DOFPERGRID*i)=0;
                *(B+(DOFPERGRID*numgrids+3)*5+DOFPERGRID*i+1)=(float).5*dh1dh7[2][i];
                *(B+(DOFPERGRID*numgrids+3)*5+DOFPERGRID*i+2)=(float).5*dh1dh7[1][i];
                *(B+(DOFPERGRID*numgrids+3)*6+DOFPERGRID*i)=0;
                *(B+(DOFPERGRID*numgrids+3)*6+DOFPERGRID*i+1)=0;
                *(B+(DOFPERGRID*numgrids+3)*6+DOFPERGRID*i+2)=0;
                *(B+(DOFPERGRID*numgrids+3)*7+DOFPERGRID*i)=dh1dh7[0][i];
                *(B+(DOFPERGRID*numgrids+3)*7+DOFPERGRID*i+1)=dh1dh7[1][i];
                *(B+(DOFPERGRID*numgrids+3)*7+DOFPERGRID*i+2)=dh1dh7[2][i];
        }

        for (i=0;i<numgrids;i++){ //last column not for the bubble function
                *(B+(DOFPERGRID*numgrids+3)*0+DOFPERGRID*i+3)=0;
                *(B+(DOFPERGRID*numgrids+3)*1+DOFPERGRID*i+3)=0;
                *(B+(DOFPERGRID*numgrids+3)*2+DOFPERGRID*i+3)=0;
                *(B+(DOFPERGRID*numgrids+3)*3+DOFPERGRID*i+3)=0;
                *(B+(DOFPERGRID*numgrids+3)*4+DOFPERGRID*i+3)=0;
                *(B+(DOFPERGRID*numgrids+3)*5+DOFPERGRID*i+3)=0;
                *(B+(DOFPERGRID*numgrids+3)*6+DOFPERGRID*i+3)=l1l6[i];
                *(B+(DOFPERGRID*numgrids+3)*7+DOFPERGRID*i+3)=0;
        }

}
/*}}}*/