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