APBS: vpbe.h Source File

00001 
00064 #ifndef _VPBE_H_
00065 #define _VPBE_H_
00066 
00067 /* Generic headers */
00068 #include "maloc/maloc.h"
00069 #include "apbs/vhal.h"
00070 
00071 /* Specific headers */
00072 #include "apbs/vunit.h"
00073 #include "apbs/vatom.h"
00074 #include "apbs/vacc.h"
00075 #include "apbs/vclist.h"
00076 
00082 struct sVpbe { 
00083         
00084         Vmem *vmem;         
00086         Valist *alist;      
00087         Vclist *clist;      
00088         Vacc *acc;          
00090         double T;           
00091         double soluteDiel;  
00092         double solventDiel; 
00093         double solventRadius;
00097         double bulkIonicStrength; 
00098         double maxIonRadius;      
00101         int    numIon;            
00102         double ionConc[MAXION];   
00103         double ionRadii[MAXION];  
00104         double ionQ[MAXION];      
00106         double xkappa;      
00107         double deblen;      
00108         double zkappa2;     
00109         double zmagic;      
00111         double soluteCenter[3]; 
00112         double soluteRadius; 
00113         double soluteXlen;  
00114         double soluteYlen;  
00115         double soluteZlen;  
00116         double soluteCharge; 
00118         double smvolume;        
00119         double smsize;          
00120         int ipkey;                      
00123         int paramFlag;      
00125         /*-------------------------------------------------------*/
00126         /* Added by Michael Grabe                                */
00127         /*-------------------------------------------------------*/
00128         
00129         double z_mem;        /* Z value of the botton of the membrane (A) */
00130         double L;            /* Length of the membrane (A) */
00131         double membraneDiel; /* Membrane dielectric constant */
00132         double V;            /* Membrane potential */
00133         int param2Flag;     /* Check to see if bcfl=3 parms have been set */
00134         /*-------------------------------------------------------*/
00135         
00136 };
00137 
00142 typedef struct sVpbe Vpbe;
00143 
00144 /* ///////////////////////////////////////////////////////////////////////////
00145    // Class Vpbe: Inlineable methods (vpbe.c)
00147 
00148 #if !defined(VINLINE_VPBE)
00149 
00156 Valist* Vpbe_getValist(Vpbe *thee);
00157 
00164 Vacc*   Vpbe_getVacc(Vpbe *thee);
00165 
00172 double  Vpbe_getBulkIonicStrength(Vpbe *thee);
00173 
00180 double  Vpbe_getMaxIonRadius(Vpbe *thee);
00181 
00188 double  Vpbe_getTemperature(Vpbe *thee);           
00189 
00196 double  Vpbe_getSoluteDiel(Vpbe *thee); 
00197 
00204 double  Vpbe_getGamma(Vpbe *thee);
00205 
00212 double  Vpbe_getSoluteRadius(Vpbe *thee);
00213 
00220 double  Vpbe_getSoluteXlen(Vpbe *thee);
00221 
00228 double  Vpbe_getSoluteYlen(Vpbe *thee);
00229 
00236 double  Vpbe_getSoluteZlen(Vpbe *thee);
00237 
00244 double* Vpbe_getSoluteCenter(Vpbe *thee);
00245 
00252 double  Vpbe_getSoluteCharge(Vpbe *thee);
00253 
00260 double  Vpbe_getSolventDiel(Vpbe *thee);
00261 
00268 double  Vpbe_getSolventRadius(Vpbe *thee);
00269 
00276 double  Vpbe_getXkappa(Vpbe *thee);
00277 
00284 double  Vpbe_getDeblen(Vpbe *thee);
00285 
00292 double  Vpbe_getZkappa2(Vpbe *thee);
00293 
00300 double  Vpbe_getZmagic(Vpbe *thee);
00301 
00302 /*--------------------------------------------------------------*/
00303 /* Added by Michael Grabe                                       */
00304 /*--------------------------------------------------------------*/
00305 
00312 double  Vpbe_getzmem(Vpbe *thee);
00313 
00320 double  Vpbe_getLmem(Vpbe *thee);
00321 
00328 double  Vpbe_getmembraneDiel(Vpbe *thee);
00329 
00335 double  Vpbe_getmemv(Vpbe *thee);
00336 
00337 /*--------------------------------------------------------------*/
00338 
00339 #else /* if defined(VINLINE_VPBE) */
00340 #   define Vpbe_getValist(thee) ((thee)->alist)
00341 #   define Vpbe_getVacc(thee) ((thee)->acc)
00342 #   define Vpbe_getBulkIonicStrength(thee) ((thee)->bulkIonicStrength)
00343 #   define Vpbe_getTemperature(thee) ((thee)->T)           
00344 #   define Vpbe_getSoluteDiel(thee) ((thee)->soluteDiel) 
00345 #   define Vpbe_getSoluteCenter(thee) ((thee)->soluteCenter)
00346 #   define Vpbe_getSoluteRadius(thee) ((thee)->soluteRadius)
00347 #   define Vpbe_getSoluteXlen(thee) ((thee)->soluteXlen)
00348 #   define Vpbe_getSoluteYlen(thee) ((thee)->soluteYlen)
00349 #   define Vpbe_getSoluteZlen(thee) ((thee)->soluteZlen)
00350 #   define Vpbe_getSoluteCharge(thee) ((thee)->soluteCharge)
00351 #   define Vpbe_getSolventDiel(thee) ((thee)->solventDiel)
00352 #   define Vpbe_getSolventRadius(thee) ((thee)->solventRadius)
00353 #   define Vpbe_getMaxIonRadius(thee) ((thee)->maxIonRadius)
00354 #   define Vpbe_getXkappa(thee) ((thee)->xkappa)
00355 #   define Vpbe_getDeblen(thee) ((thee)->deblen)
00356 #   define Vpbe_getZkappa2(thee) ((thee)->zkappa2)
00357 #   define Vpbe_getZmagic(thee) ((thee)->zmagic)
00358 
00359 /*------------------------------------------------------------*/
00360 /* Added by Michael Grabe                                     */
00361 /*------------------------------------------------------------*/
00362 
00363 #   define Vpbe_getzmem(thee) ((thee)->z_mem)
00364 #   define Vpbe_getLmem(thee) ((thee)->L)
00365 #   define Vpbe_getmembraneDiel(thee) ((thee)->membraneDiel)
00366 #   define Vpbe_getmemv(thee) ((thee)->V)
00367 
00368 /*------------------------------------------------------------*/
00369 
00370 
00371 #endif /* if !defined(VINLINE_VPBE) */
00372 
00373 /* ///////////////////////////////////////////////////////////////////////////
00374    // Class Vpbe: Non-Inlineable methods (vpbe.c)
00376 
00409 /*---------------------------------------------------------------*/
00410 /* Additions by Michael Grabe to Vpbe_ctor2 and Vpbe_ctor        */
00411 /*---------------------------------------------------------------*/
00412 
00413 Vpbe*   Vpbe_ctor(Valist *alist, int ionNum, double *ionConc, 
00414                                                    double *ionRadii, double *ionQ, double T, 
00415                                                    double soluteDiel, double solventDiel,  
00416                                                    double solventRadius, int focusFlag, double sdens,
00417                                                    double z_mem, double L, double membraneDiel, double V);
00418 
00451 int    Vpbe_ctor2(Vpbe *thee, Valist *alist, int ionNum, 
00452                                                    double *ionConc, double *ionRadii, double *ionQ, 
00453                                                    double T, double soluteDiel, 
00454                                                    double solventDiel, double solventRadius, int focusFlag,
00455                                                    double sdens, double z_mem, double L, double membraneDiel, 
00456                                                    double V);
00457 
00468 int     Vpbe_getIons(Vpbe *thee, int *nion, double ionConc[MAXION],
00469                                                           double ionRadii[MAXION], double ionQ[MAXION]);
00470 
00476 void    Vpbe_dtor(Vpbe **thee);
00477 
00483 void    Vpbe_dtor2(Vpbe *thee);
00484 
00499 double  Vpbe_getCoulombEnergy1(Vpbe *thee);
00500 
00508 unsigned long int Vpbe_memChk(Vpbe *thee);
00509 
00510 #endif /* ifndef _VPBE_H_ */
00511