src/gromacs/correlationfunctions/expfit.h

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  35 /*! \libinternal
  36  * \file
  37  * \brief
  38  * Declares routine for fitting a data set to a curve
  39  *
  40  * \author David van der Spoel <david.vanderspoel@icm.uu.se>
  41  * \inlibraryapi
  42  * \ingroup module_correlationfunctions
  43  */
  44 #ifndef GMX_EXPFIT_H
  45 #define GMX_EXPFIT_H
  46
  47 #include "gromacs/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49
  50 #ifdef __cplusplus
  51 extern "C" {
  52 #endif
  53
  54 struct gmx_output_env_t;
  55
  56 /*! \brief
  57  * Enum to select fitting functions
  58  */
  59 enum {
  60     effnNONE, effnEXP1, effnEXP2, effnEXPEXP,
  61     effnEXP5, effnEXP7, effnEXP9,
  62     effnVAC,  effnERF,  effnERREST, effnPRES, effnNR
  63 };
  64
  65 /*! \brief
  66  * Short name of each function type.
  67  * This is exported for now in order to use when
  68  * calling parse_common_args.
  69  */
  70 extern const char *s_ffn[effnNR+2];
  71
  72 /*! \brief
  73  * Returns  description corresponding to the enum above, or NULL if out of range
  74  * \param[in] effn Index
  75  * \return Description or NULL
  76  */
  77 const char *effnDescription(int effn);
  78
  79 /*! \brief
  80  * Returns  number of function parameters associated with a fitting function.
  81  * \param[in] effn Index
  82  * \return number or -1 if index out of range
  83  */
  84 int effnNparams(int effn);
  85
  86 /*! \brief
  87  * Returns  corresponding to the selected enum option in sffn
  88  * \param[in] sffn Two dimensional string array coming from parse_common_args
  89  * \return the ffn enum
  90  */
  91 int sffn2effn(const char **sffn);
  92
  93 /*! \brief
  94  * Returns the value of fit function eFitFn at x
  95  * \param[in] eFitFn the index to the fitting function (0 .. effnNR)
  96  * \param[in] parm Array of parameters, the length of which depends on eFitFn
  97  * \param[in] x The value of x
  98  * \return the value of the fit
  99  */
 100 double fit_function(const int eFitFn, const double parm[], const double x);
 101
 102 /*! \brief
 103  * Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential
 104  * or to a transverse current autocorrelation function.
 105  *
 106  * If x == NULL, the timestep dt will be used to create a time axis.
 107  * \param[in] ndata Number of data points
 108  * \param[in] c1 The data points
 109  * \param[in] sig The standard deviation in the points (can be NULL)
 110  * \param[in] dt The time step
 111  * \param[in] x0 The X-axis (may be NULL, see above)
 112  * \param[in] begintimefit Starting time for fitting
 113  * \param[in] endtimefit Ending time for fitting
 114  * \param[in] oenv Output formatting information
 115  * \param[in] bVerbose Should the routine write to console?
 116  * \param[in] eFitFn Fitting function (0 .. effnNR)
 117  * \param[inout] fitparms[] Fitting parameters, see printed manual for a
 118  * detailed description. Note that in all implemented cases the parameters
 119  * corresponding to time constants will be generated with increasing values.
 120  * Such input parameters should therefore be provided in increasing order.
 121  * If this is not the case or if subsequent time parameters differ by less than
 122  * a factor of 2, they will be modified to ensure tau_i+1 >= 2 tau_i.
 123  * \param[in] fix Constrains fit parameter i at it's starting value, when the i'th bit
 124  * of fix is set. This works only when the N last parameters are fixed
 125  * but not when a parameter somewhere in the middle needs to be fixed.
 126  * \param[in] fn_fitted If not NULL file to print the data and fitted curve to
 127  * \return integral.
 128  */
 129 real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x0,
 130               real begintimefit, real endtimefit, const gmx_output_env_t *oenv,
 131               gmx_bool bVerbose, int eFitFn, double fitparms[], int fix,
 132               const char *fn_fitted);
 133
 134 /*! \brief
 135  * Fit an autocorrelation function to a pre-defined functional form
 136  *
 137  * \todo check parameters
 138  * \param[in] ncorr
 139  * \param[in] fitfn Fitting function (0 .. effnNR)
 140  * \param[in] oenv Output formatting information
 141  * \param[in] bVerbose Should the routine write to console?
 142  * \param[in] tbeginfit Starting time for fitting
 143  * \param[in] tendfit Ending time for fitting
 144  * \param[in] dt The time step
 145  * \param[in] c1 The data points
 146  * \param[inout] fit The fitting parameters
 147  * \return the integral over the autocorrelation function?
 148  */
 149 real fit_acf(int ncorr, int fitfn, const gmx_output_env_t *oenv, gmx_bool bVerbose,
 150              real tbeginfit, real tendfit, real dt, real c1[], real *fit);
 151
 152 #ifdef __cplusplus
 153 }
 154 #endif
 155
 156 #endif