vfetk.h

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#ifndef _VFETK_H_
#define _VFETK_H_

#include "maloc/maloc.h"
#include "mc/mc.h"
#include "apbs/vhal.h"
#include "apbs/vatom.h"
/* #include "apbs/valist.h" */
#include "apbs/vcsm.h"
#include "apbs/vpbe.h"
#include "apbs/vunit.h"
#include "apbs/vgreen.h"
#include "apbs/vcap.h"
#include "apbs/pbeparm.h"
#include "apbs/femparm.h"

enum eVfetk_LsolvType {
    VLT_SLU=0,  
    VLT_MG=1,  
    VLT_CG=2,  
    VLT_BCG=3  
};

typedef enum eVfetk_LsolvType Vfetk_LsolvType;

enum eVfetk_NsolvType {
    VNT_NEW=0,  
    VNT_INC=1,  
    VNT_ARC=2  
};

typedef enum eVfetk_NsolvType Vfetk_NsolvType;

enum eVfetk_GuessType {
    VGT_ZERO=0,  
    VGT_DIRI=1,  
    VGT_PREV=2  
};

typedef enum eVfetk_GuessType Vfetk_GuessType;

enum eVfetk_PrecType {
    VPT_IDEN=0,  
    VPT_DIAG=1,  
    VPT_MG=2  
};

typedef enum eVfetk_PrecType Vfetk_PrecType;

struct sVfetk { 

  Vmem *vmem;  
  Gem *gm;  
  AM *am;  
  Aprx *aprx;  
  PDE *pde;  
  Vpbe *pbe;  
  Vcsm *csm;  
  Vfetk_LsolvType lkey;  
  int lmax;  
  double ltol;  
  Vfetk_NsolvType nkey;  
  int nmax;  
  double ntol;  
  Vfetk_GuessType gues;  
  Vfetk_PrecType lprec;  
  int pjac;  
  PBEparm *pbeparm;  
  FEMparm *feparm;  
  Vhal_PBEType type;  
  int level;  
};

typedef struct sVfetk Vfetk;

struct sVfetk_LocalVar {
    double nvec[VAPBS_DIM];  
    double vx[4][VAPBS_DIM];  
    double xq[VAPBS_DIM];  
    double U[MAXV];  
    double dU[MAXV][VAPBS_DIM];  
    double W;  
    double dW[VAPBS_DIM];  
    double d2W;  
    int sType;  
    int fType;  
    double diel;  
    double kappa2;  
    double A;  
    double F;  
    double B;  
    double DB;  
    double jumpDiel;  
    Vfetk *fetk;  
    Vgreen *green;  
    int initGreen;  
    SS *simp;  
    VV *verts[4];  
    int nverts;  
    double ionConc[MAXION];  
    double ionQ[MAXION];  
    double ionRadii[MAXION];  
    double zkappa2; 
    double zks2; 
    double ionstr; 
    int nion;  
    double Fu_v;  
    double DFu_wv;  
    double delta;  
    double u_D;  
    double u_T;  
};

typedef struct sVfetk_LocalVar Vfetk_LocalVar;

#if !defined(VINLINE_VFETK)

    Gem* Vfetk_getGem(
            Vfetk *thee 
            );

    AM* Vfetk_getAM(
            Vfetk *thee 
            );

    Vpbe* Vfetk_getVpbe(
            Vfetk *thee 
            );

    Vcsm* Vfetk_getVcsm(
            Vfetk *thee 
            );

    int Vfetk_getAtomColor(
            Vfetk *thee, 
            int iatom  
            );

#else /* if defined(VINLINE_VFETK) */
#   define Vfetk_getGem(thee) ((thee)->gm)
#   define Vfetk_getAM(thee) ((thee)->am)
#   define Vfetk_getVpbe(thee) ((thee)->pbe)
#   define Vfetk_getVcsm(thee) ((thee)->csm)
#   define Vfetk_getAtomColor(thee, iatom) (Vatom_getPartID(Valist_getAtom(Vpbe_getValist(thee->pbe), iatom)))
#endif /* if !defined(VINLINE_VFETK) */

/* ///////////////////////////////////////////////////////////////////////////
// Class Vfetk: Non-Inlineable methods (vfetk.c)

Vfetk* Vfetk_ctor(
        Vpbe *pbe, 
        Vhal_PBEType type 
        );

int Vfetk_ctor2(
        Vfetk *thee, 
        Vpbe *pbe, 
        Vhal_PBEType type 
        );

void Vfetk_dtor(
        Vfetk **thee 
        );

void Vfetk_dtor2(
        Vfetk *thee 
        );

double* Vfetk_getSolution(
        Vfetk *thee, 
        int *length 
        );

void Vfetk_setParameters(
        Vfetk *thee, 
        PBEparm *pbeparm, 
        FEMparm *feparm 
        );

double  Vfetk_energy(
        Vfetk *thee, 
        int color, 
        int nonlin 
        );

double  Vfetk_dqmEnergy(
        Vfetk *thee, 
        int color  
        );

double Vfetk_qfEnergy(
        Vfetk *thee, 
        int color 
        );

unsigned long int Vfetk_memChk(
        Vfetk *thee 
        );

void Vfetk_setAtomColors(
        Vfetk *thee 
        );

void Bmat_printHB(
        Bmat *thee, 
        char *fname 
        );

int Vfetk_genCube(
        Vfetk *thee, 
        double center[VAPBS_DIM], 
        double length[VAPBS_DIM] 
        );

PDE* Vfetk_PDE_ctor(
        Vfetk *fetk 
        );

int Vfetk_PDE_ctor2(
        PDE *thee, 
        Vfetk *fetk 
        );

void Vfetk_PDE_dtor(
        PDE **thee 
        );

void Vfetk_PDE_dtor2(
        PDE *thee 
        );

void Vfetk_PDE_initAssemble(
        PDE *thee, 
        int ip[], 
        double rp[] 
        );

void Vfetk_PDE_initElement(
        PDE *thee,  
        int elementType,  
        int chart,  
        double tvx[][VAPBS_DIM],  
        void *data 
        );

void Vfetk_PDE_initFace(
        PDE *thee, 
        int faceType, 
        int chart, 
        double tnvec[] 
        );

void Vfetk_PDE_initPoint(
        PDE *thee,  
        int pointType, 
        int chart,  
        double txq[],  
        double tU[],  
        double tdU[][VAPBS_DIM] 
        );

void Vfetk_PDE_Fu(
        PDE *thee, 
        int key, 
        double F[] 
        );

double Vfetk_PDE_Fu_v(
        PDE *thee, 
        int key, 
        double V[],  
        double dV[][VAPBS_DIM] 
        );

double Vfetk_PDE_DFu_wv(
        PDE *thee, 
        int key, 
        double W[], 
        double dW[][VAPBS_DIM], 
        double V[], 
        double dV[][VAPBS_DIM] 
        );

void Vfetk_PDE_delta(
        PDE *thee, 
        int type, 
        int chart, 
        double txq[], 
        void *user, 
        double F[] 
        );

void Vfetk_PDE_u_D(
        PDE *thee, 
        int type, 
        int chart, 
        double txq[], 
        double F[] 
        );

void Vfetk_PDE_u_T(
        PDE *thee, 
        int type, 
        int chart, 
        double txq[], 
        double F[] 
        );

void Vfetk_PDE_bisectEdge(
        int dim, 
        int dimII, 
        int edgeType,  
        int chart[], 
        double vx[][VAPBS_DIM] 
        );

void Vfetk_PDE_mapBoundary(
        int dim, 
        int dimII, 
        int vertexType,  
        int chart, 
        double vx[VAPBS_DIM] 
        );

int Vfetk_PDE_markSimplex(
        int dim, 
        int dimII, 
        int simplexType,  
        int faceType[VAPBS_NVS], 
        int vertexType[VAPBS_NVS], 
        int chart[], 
        double vx[][VAPBS_DIM], 
        void *simplex 
        );

void Vfetk_PDE_oneChart(
        int dim, 
        int dimII, 
        int objType, 
        int chart[], 
        double vx[][VAPBS_DIM], 
        int dimV 
        );

double Vfetk_PDE_Ju(
        PDE *thee, 
        int key 
        );

void Vfetk_externalUpdateFunction(
        SS **simps, 
        int num 
        );


int Vfetk_PDE_simplexBasisInit(
        int key, 
        int dim, 
        int comp, 
        int *ndof,  
        int dof[] 
        );

void Vfetk_PDE_simplexBasisForm(
        int key, 
        int dim, 
        int comp ,
        int pdkey, 
        double xq[], 
        double basis[] 
        );

void Vfetk_readMesh(
        Vfetk *thee, 
        int skey, 
        Vio *sock 
        );

void Vfetk_dumpLocalVar();

int Vfetk_fillArray(
        Vfetk *thee, 
        Bvec *vec, 
        Vdata_Type type 
        );

int Vfetk_write(
        Vfetk *thee, 
        const char *iodev, 
        const char *iofmt, 
        const char *thost, 
        const char *fname, 
        Bvec *vec, 
        Vdata_Format format 
        );


#endif /* ifndef _VFETK_H_ */

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