+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
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- * Lesser General Public License for more details.
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- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
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- */
-#ifndef _GEMINATE_H
-#define _GEMINATE_H
-
-#include <stddef.h>
-
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/real.h"
-
-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.
- */
-
-/* This first part is derived from complex.c which I recieved from Omer Markowitch.
- * - Erik Marklund
- *
- * ------------- from complex.c ------------- */
-
-#include <math.h>
-/* definition of PI */
-#ifndef PI
-#define PI (acos(-1.0))
-#endif
-
-/* definition of the type complex */
-typedef struct
-{
- double r, i;
-} gem_complex;
-
-
-/* ------------ end of complex.c ------------ */
-
-/* This next part was derived from cerror.c and rerror.c,
- * also received from Omer Markovitch.
- * ------------- from [cr]error.c ------------- */
-
-#ifndef sPI
-#define sPI (sqrt(PI))
-#endif
-
-/* ------------ end of [cr]error.c ------------ */
-
-/* ///////////////// REVERSIBLE GEMINATE RECOMBINATION ///////////////////
- * Here follow routines and structs for reversible geminate recombination.
- */
-
-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) */
-/* 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
- **/
-/* #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. */
-} 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;
-} gemFitData;
-
-extern void takeAwayBallistic(double *ct, double *t,
- 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);
-
-/* 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);
-
-extern void dumpN(const real *e, const int nn, char *fn);
-
-/* Fix NaN that might appear in the theoretical acf. */
-extern void fixGemACF(double *ct, int len);
-
-#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff