#ifndef _GEMINATE_H
#define _GEMINATE_H
-enum { gemNULL, gemNONE, gemDD, gemAD, gemAA, gemA4, gemNR};
+enum {
+ gemNULL, gemNONE, gemDD, gemAD, gemAA, gemA4, gemNR
+};
static const char *gemType[] = {NULL, "none", "dd", "ad", "aa", "a4", NULL};
/* The first few sections of this file contain functions that were adopted,
* and to some extent modified, by Erik Marklund (erikm[aT]xray.bmc.uu.se,
* http://folding.bmc.uu.se) from code written by Omer Markovitch (email, url).
* This is also the case with the function eq10v2() in geminate.c.
- *
+ *
* The parts menetioned in the previous paragraph were contributed under a BSD license.
*/
/* definition of the type complex */
typedef struct
{
- double r,i;
+ double r, i;
} gem_complex;
* Here follow routines and structs for reversible geminate recombination.
*/
-typedef struct{
- size_t n;
- double *y;
- double tDelta;
- int nexp;
+typedef struct {
+ size_t n;
+ double *y;
+ double tDelta;
+ int nexp;
} balData;
typedef struct {
- /* Used in the rewritten version of Omer's gem. recomb. analysis */
- double ka, kd; /* -- || -- results[] */
- double sigma; /* -- || -- sigma */
- double D; /* The diffusion coefficient */
- double kD; /* Replaces kD in analyse_corr_gem3d() */
-
- /* The following members are for calcsquare() and takeAwayBallistic() */
- double tDelta; /* Time between frames */
- /* double logAfterTime; /\* Time after which we do the lsq calculations on a logarithmic timescale. *\/ */
- int nFitPoints; /* Number of points to take from the ACF for fitting */
- double begFit; /* Fit from this time (ps) */
- double endFit; /* Fit up to this time (ps) */
+ /* Used in the rewritten version of Omer's gem. recomb. analysis */
+ double ka, kd; /* -- || -- results[] */
+ double sigma; /* -- || -- sigma */
+ double D; /* The diffusion coefficient */
+ double kD; /* Replaces kD in analyse_corr_gem3d() */
+
+ /* The following members are for calcsquare() and takeAwayBallistic() */
+ double tDelta; /* Time between frames */
+ /* double logAfterTime; /\* Time after which we do the lsq calculations on a logarithmic timescale. *\/ */
+ int nFitPoints; /* Number of points to take from the ACF for fitting */
+ double begFit; /* Fit from this time (ps) */
+ double endFit; /* Fit up to this time (ps) */
/* double logDelta; */
/* double logPF; */
- /* To get an equal number of points in the lin and log regime,
- * we'll use logDelta to calculate where to sample the ACF.
- * if i and j are indices in the linear and log regime, then:
- * j = Cexp(A(i+nLin)),
- * where C = (nLin**2 / len) and A = log(len/nLin) / nLin.
- * This expands to j = (nLin**2 / len) * exp((i+nLin) * log(len/nLin) / nLin).
- * We'll save part of our brains and some computing time if we pre-calculate
- * 1) logDelta = log(len/nLin) / nLin
- * 2) logPF = nLin**2 / len
- * and get j = logPF * exp((i+nLin) * logDelta). */
-
- /* I will redo this for a fit done entirely in log-log.
- * j' = j+1
- * nFitPoints' = nFitPoints-1
- *
- * j' = Cexp(Ai)
- * (j'= 1 <=> i=0)
- * => C=1
- * (j'=len <=> i=nFitPoints')
- * => A=log(len)/nFitPoints'
- * => j = exp(i*log(len)/(nFitPoints-1)) -1
- **/
+/* To get an equal number of points in the lin and log regime,
+ * we'll use logDelta to calculate where to sample the ACF.
+ * if i and j are indices in the linear and log regime, then:
+ * j = Cexp(A(i+nLin)),
+ * where C = (nLin**2 / len) and A = log(len/nLin) / nLin.
+ * This expands to j = (nLin**2 / len) * exp((i+nLin) * log(len/nLin) / nLin).
+ * We'll save part of our brains and some computing time if we pre-calculate
+ * 1) logDelta = log(len/nLin) / nLin
+ * 2) logPF = nLin**2 / len
+ * and get j = logPF * exp((i+nLin) * logDelta). */
+
+ /* I will redo this for a fit done entirely in log-log.
+ * j' = j+1
+ * nFitPoints' = nFitPoints-1
+ *
+ * j' = Cexp(Ai)
+ * (j'= 1 <=> i=0)
+ * => C=1
+ * (j'=len <=> i=nFitPoints')
+ * => A=log(len)/nFitPoints'
+ * => j = exp(i*log(len)/(nFitPoints-1)) -1
+ **/
/* #define GETLOGINDEX(i,params) (params)->logPF * exp(((i)+(params)->nLin) * (params)->logDelta)
*/
- double logQuota;
- int nLin; /* Number of timepoints in the linear regime */
- int len; /* Length of time and ct arrays */
- int nExpFit; /* Number of exponentials to fit */
- real ballistic; /* Time before which the ballistic term should be fitted */
- gmx_bool bDt; /* TRUE => use time derivative at time 0
- * to find fastest component.
- * FALSE => use coefficient in exponenetial
- * to find fastest component. */
+ double logQuota;
+ int nLin; /* Number of timepoints in the linear regime */
+ int len; /* Length of time and ct arrays */
+ int nExpFit; /* Number of exponentials to fit */
+ real ballistic; /* Time before which the ballistic term should be fitted */
+ gmx_bool bDt; /* TRUE => use time derivative at time 0
+ * to find fastest component.
+ * FALSE => use coefficient in exponenetial
+ * to find fastest component. */
} t_gemParams;
-typedef struct{
- size_t n; /* Number of data points (lin-log) */
- double *y; /* The datapoints */
- double *ctTheory; /* The theoretical ct which will be built by gemFunc_f. */
- double *LinLog;
- double *time;
- double ka;
- double kd;
- double tDelta; /* time difference between subsequent datapoints */
- size_t nData; /* real size of the data */
- int *logtime;
- double *doubleLogTime;
- t_gemParams *params;
+typedef struct {
+ size_t n; /* Number of data points (lin-log) */
+ double *y; /* The datapoints */
+ double *ctTheory; /* The theoretical ct which will be built by gemFunc_f. */
+ double *LinLog;
+ double *time;
+ double ka;
+ double kd;
+ double tDelta; /* time difference between subsequent datapoints */
+ size_t nData; /* real size of the data */
+ int *logtime;
+ double *doubleLogTime;
+ t_gemParams *params;
} gemFitData;
extern void takeAwayBallistic(double *ct, double *t,
- int len, real tMax,
- int nexp, gmx_bool bDerivative);
+ int len, real tMax,
+ int nexp, gmx_bool bDerivative);
extern t_gemParams *init_gemParams(const double sigma, const double D,
- const real *t, const int len, const int nFitPoints,
- const real begFit, const real endFit,
- const real ballistic, const int nBalExp, const gmx_bool bDt);
+ const real *t, const int len, const int nFitPoints,
+ const real begFit, const real endFit,
+ const real ballistic, const int nBalExp, const gmx_bool bDt);
/* Fit to geminate recombination model.
Returns root mean square error of fit. */
extern real fitGemRecomb(double *ct, double *time, double **ctFit,
- const int nData, t_gemParams *params);
+ const int nData, t_gemParams *params);
extern void dumpN(const real *e, const int nn, char *fn);
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