src/tools/geminate.h

   1 #ifndef _GEMINATE_H
   2 #define _GEMINATE_H
   3
   4 enum { gemNULL, gemNONE, gemDD, gemAD, gemAA, gemA4, gemNR};
   5 static const char *gemType[] = {NULL, "none", "dd", "ad", "aa", "a4", NULL};
   6
   7 /* The first few sections of this file contain functions that were adopted,
   8  * and to some extent modified, by Erik Marklund (erikm[aT]xray.bmc.uu.se,
   9  * http://folding.bmc.uu.se) from code written by Omer Markovitch (email, url).
  10  * This is also the case with the function eq10v2() in geminate.c.
  11  *
  12  * The parts menetioned in the previous paragraph were contributed under a BSD license.
  13  */
  14
  15 /* This first part is derived from complex.c which I recieved from Omer Markowitch.
  16  * - Erik Marklund
  17  *
  18  * ------------- from complex.c ------------- */
  19
  20 #include <math.h>
  21 /* definition of PI */
  22 #ifndef PI
  23 #define PI (acos(-1.0))
  24 #endif
  25
  26 /* definition of the type complex */
  27 typedef struct
  28 {
  29   double r,i;
  30 } gem_complex;
  31
  32
  33 /* ------------ end of complex.c ------------ */
  34
  35 /* This next part was derived from cerror.c and rerror.c,
  36  * also received from Omer Markovitch.
  37  * ------------- from [cr]error.c ------------- */
  38
  39 #ifndef sPI
  40 #define sPI (sqrt(PI))
  41 #endif
  42
  43 /* ------------ end of [cr]error.c ------------ */
  44
  45 /* ///////////////// REVERSIBLE GEMINATE RECOMBINATION ///////////////////
  46  * Here follow routines and structs for reversible geminate recombination.
  47  */
  48
  49 typedef struct{
  50   size_t n;
  51   double *y;
  52   double tDelta;
  53   int nexp;
  54 } balData;
  55
  56
  57 typedef struct {
  58   /* Used in the rewritten version of Omer's gem. recomb. analysis */
  59   double ka, kd;                 /* -- || -- results[]  */
  60   double sigma;                  /* -- || -- sigma      */
  61   double D;                      /* The diffusion coefficient */
  62   double kD;                     /* Replaces kD in analyse_corr_gem3d() */
  63
  64   /* The following members are for calcsquare() and takeAwayBallistic() */
  65   double tDelta;              /* Time between frames */
  66   /* double logAfterTime;        /\* Time after which we do the lsq calculations on a logarithmic timescale. *\/ */
  67   int nFitPoints;             /* Number of points to take from the ACF for fitting */
  68   double begFit;              /* Fit from this time (ps) */
  69   double endFit;              /* Fit up to this time (ps) */
  70 /*   double logDelta; */
  71 /*   double logPF; */
  72   /* To get an equal number of points in the lin and log regime,
  73    * we'll use logDelta to calculate where to sample the ACF.
  74    * if i and j are indices in the linear and log regime, then:
  75    *   j = Cexp(A(i+nLin)),
  76    * where C = (nLin**2 / len) and A = log(len/nLin) / nLin.
  77    * This expands to j = (nLin**2 / len) * exp((i+nLin) * log(len/nLin) / nLin).
  78    * We'll save part of our brains and some computing time if we pre-calculate
  79    *  1) logDelta = log(len/nLin) / nLin
  80    *  2) logPF    = nLin**2 / len
  81    * and get j = logPF * exp((i+nLin) * logDelta). */
  82
  83   /* I will redo this for a fit done entirely in log-log.
  84    *  j' = j+1
  85    *  nFitPoints' = nFitPoints-1
  86    *
  87    *  j' = Cexp(Ai)
  88    *  (j'= 1 <=> i=0)
  89    *     => C=1
  90    *  (j'=len <=> i=nFitPoints')
  91    *     => A=log(len)/nFitPoints'
  92    *     => j = exp(i*log(len)/(nFitPoints-1)) -1
  93    **/
  94 /* #define GETLOGINDEX(i,params) (params)->logPF * exp(((i)+(params)->nLin) * (params)->logDelta)
  95  */
  96   double logQuota;
  97   int nLin;                 /* Number of timepoints in the linear regime */
  98   int len;                  /* Length of time and ct arrays */
  99   int nExpFit;              /* Number of exponentials to fit */
 100   real ballistic;           /* Time before which the ballistic term should be fitted */
 101   gmx_bool bDt;                 /* TRUE =>  use time derivative at time 0
 102                              *          to find fastest component.
 103                              * FALSE => use coefficient in exponenetial
 104                              *          to find fastest component. */
 105 } t_gemParams;
 106
 107
 108 typedef struct{
 109   size_t n;         /* Number of data points (lin-log) */
 110   double *y;        /* The datapoints */
 111   double *ctTheory; /* The theoretical ct which will be built by gemFunc_f. */
 112   double *LinLog;
 113   double *time;
 114   double ka;
 115   double kd;
 116   double tDelta;    /* time difference between subsequent datapoints */
 117   size_t nData;     /* real size of the data */
 118   int    *logtime;
 119   double *doubleLogTime;
 120   t_gemParams *params;
 121 } gemFitData;
 122
 123 extern void takeAwayBallistic(double *ct, double *t,
 124                               int len, real tMax,
 125                               int nexp, gmx_bool bDerivative);
 126
 127
 128 extern t_gemParams *init_gemParams(const double sigma, const double D,
 129                                    const real *t, const int len, const int nFitPoints,
 130                                    const real begFit, const real endFit,
 131                                    const real ballistic, const int nBalExp, const gmx_bool bDt);
 132
 133 /* Fit to geminate recombination model.
 134    Returns root mean square error of fit. */
 135 extern real fitGemRecomb(double *ct, double *time, double **ctFit,
 136                          const int nData, t_gemParams *params);
 137
 138 extern void dumpN(const real *e, const int nn, char *fn);
 139
 140 #endif