2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
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, effnEXP3, effnVAC,
59 effnEXP5, effnEXP7, effnEXP9, effnERF, effnERREST, effnPRES, effnNR
63 * Short name of each function type.
64 * This is exported for now in order to use when
65 * calling parse_common_args.
67 extern const char *s_ffn[effnNR+2];
70 * Returns description corresponding to the enum above, or NULL if out of range
71 * \param[in] effn Index
72 * \return Description or NULL
74 const char *effnDescription(int effn);
77 * Returns number of function parameters associated with a fitting function.
78 * \param[in] effn Index
79 * \return number or -1 if index out of range
81 int effnNparams(int effn);
84 * Returns corresponding to the selected enum option in sffn
85 * \param[in] sffn Two dimensional string array coming from parse_common_args
86 * \return the ffn enum
88 int sffn2effn(const char **sffn);
91 * Returns the value of fit function eFitFn at x
92 * \param[in] eFitFn the index to the fitting function (0 .. effnNR)
93 * \param[in] parm Array of parameters, the length of which depends on eFitFn
94 * \param[in] x The value of x
95 * \return the value of the fit
97 double fit_function(int eFitFn, double *parm, double x);
100 * Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential
101 * or to a transverse current autocorrelation function.
103 * If x == NULL, the timestep dt will be used to create a time axis.
104 * \param[in] ndata Number of data points
105 * \param[in] c1 The data points
106 * \param[in] sig The standard deviation in the points
107 * \param[in] dt The time step
108 * \param[in] x The X-axis (may be NULL, see above)
109 * \param[in] begintimefit Starting time for fitting
110 * \param[in] endtimefit Ending time for fitting
111 * \param[in] oenv Output formatting information
112 * \param[in] bVerbose Should the routine write to console?
113 * \param[in] eFitFn Fitting function (0 .. effnNR)
114 * \param[out] fitparms[]
115 * \param[in] fix Constrains fit parameter i at it's starting value, when the i'th bit
119 real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x,
120 real begintimefit, real endtimefit, const output_env_t oenv,
121 gmx_bool bVerbose, int eFitFn, double fitparms[], int fix);
124 * Fit an autocorrelation function to a pre-defined functional form
126 * \todo check parameters
128 * \param[in] fitfn Fitting function (0 .. effnNR)
129 * \param[in] oenv Output formatting information
130 * \param[in] bVerbose Should the routine write to console?
131 * \param[in] tbeginfit Starting time for fitting
132 * \param[in] tendfit Ending time for fitting
133 * \param[in] dt The time step
134 * \param[in] c1 The data points
135 * \param[out] fit The fitting parameters
136 * \return the integral over the autocorrelation function?
138 real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
139 real tbeginfit, real tendfit, real dt, real c1[], real *fit);