/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
*
***********************************************/
-real LegendreP(real x,unsigned long m);
+real LegendreP(real x, unsigned long m);
#define eacNormal (1<<0)
#define eacCos (1<<1)
#define eacIden (1<<9)
enum {
- effnNONE, effnEXP1, effnEXP2, effnEXP3, effnVAC,
- effnEXP5, effnEXP7, effnEXP9, effnERF, effnERREST, effnNR
+ effnNONE, effnEXP1, effnEXP2, effnEXP3, effnVAC,
+ effnEXP5, effnEXP7, effnEXP9, effnERF, effnERREST, effnNR
};
/* must correspond with 'leg' g_chi.c:727 */
-enum { edPhi=0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax };
+enum {
+ edPhi = 0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax
+};
-enum { edPrintST=0,edPrintRO } ;
+enum {
+ edPrintST = 0, edPrintRO
+};
#define NHISTO 360
#define NONCHI 3
#define MAXCHI edMax-NONCHI
-#define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
+#define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
typedef struct {
- int minO,minC,H,N,C,O,Cn[MAXCHI+3];
+ int minO, minC, H, N, C, O, Cn[MAXCHI+3];
} t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
typedef struct {
- char name[12];
- int resnr;
- int index; /* Index for amino acids (histograms) */
- int j0[edMax]; /* Index in dih array (phi angle is first...) */
- t_dihatms atm;
- int b[edMax];
- int ntr[edMax];
- real S2[edMax];
- real rot_occ[edMax][NROT];
+ char name[12];
+ int resnr;
+ int index; /* Index for amino acids (histograms) */
+ int j0[edMax]; /* Index in dih array (phi angle is first...) */
+ t_dihatms atm;
+ int b[edMax];
+ int ntr[edMax];
+ real S2[edMax];
+ real rot_occ[edMax][NROT];
} t_dlist;
-extern const int nfp_ffn[effnNR];
+extern const int nfp_ffn[effnNR];
extern const char *s_ffn[effnNR+2];
int sffn2effn(const char **sffn);
/* Returns the ffn enum corresponding to the selected enum option in sffn */
-t_pargs *add_acf_pargs(int *npargs,t_pargs *pa);
+t_pargs *add_acf_pargs(int *npargs, t_pargs *pa);
/* Add options for autocorr to the current set of options.
* *npargs must be initialised to the number of elements in pa,
* it will be incremented appropriately.
*/
-void cross_corr(int n,real f[],real g[],real corr[]);
+void cross_corr(int n, real f[], real g[], real corr[]);
/* Simple minded cross correlation algorithm */
-
-real fit_acf(int ncorr,int fitfn,const output_env_t oenv,gmx_bool bVerbose,
- real tbeginfit,real tendfit,real dt,real c1[],real *fit);
- /* Fit an ACF to a given function */
-
-void do_autocorr(const char *fn,const output_env_t oenv,
- const char *title,
- int nframes,int nitem,real **c1,
- real dt,unsigned long mode,gmx_bool bAver);
+
+real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
+ real tbeginfit, real tendfit, real dt, real c1[], real *fit);
+/* Fit an ACF to a given function */
+
+void do_autocorr(const char *fn, const output_env_t oenv,
+ const char *title,
+ int nframes, int nitem, real **c1,
+ real dt, unsigned long mode, gmx_bool bAver);
/* Calls low_do_autocorr (see below). After calling add_acf_pargs */
-void low_do_autocorr(const char *fn,const output_env_t oenv,
- const char *title, int nframes,int nitem,
- int nout,real **c1, real dt,unsigned long mode,
- int nrestart, gmx_bool bAver,gmx_bool bNormalize,
- gmx_bool bVerbose,real tbeginfit,real tendfit,
- int nfitparm,int nskip);
-/*
+void low_do_autocorr(const char *fn, const output_env_t oenv,
+ const char *title, int nframes, int nitem,
+ int nout, real **c1, real dt, unsigned long mode,
+ int nrestart, gmx_bool bAver, gmx_bool bNormalize,
+ gmx_bool bVerbose, real tbeginfit, real tendfit,
+ int nfitparm, int nskip);
+/*
* do_autocorr calculates autocorrelation functions for many things.
* It takes a 2 d array containing nitem arrays of length nframes
* for each item the ACF is calculated.
* C(t) = < ( X(tau) * X(tau+t) )^2 >
* }
*
- * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
+ * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
* 3 x nframes long, where each triplet is taken as a 3D vector
*
* For mode eacCos inputdata must be in radians, not degrees!
* title is the title in the output file
* nframes is the number of frames in the time series
* nitem is the number of items
- * c1 is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
- * on output, this array is filled with the correlation function
- * to reduce storage
- * nrestart is the number of steps between restarts for direct ACFs
+ * c1 is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
+ * on output, this array is filled with the correlation function
+ * to reduce storage
+ * nrestart is the number of steps between restarts for direct ACFs
* (i.e. without FFT) When set to 1 all points are used as
* time origin for averaging
- * dt is the time between frames
- * bAver If set, all ndih C(t) functions are averaged into a single
- * C(t)
- * (bFour If set, will use fast fourier transform (FFT) for evaluating
- * the ACF: removed option, now on the command line only)
- * bNormalize If set, all ACFs will be normalized to start at 0
- * nskip Determines whether steps a re skipped in the output
+ * dt is the time between frames
+ * bAver If set, all ndih C(t) functions are averaged into a single
+ * C(t)
+ * (bFour If set, will use fast fourier transform (FFT) for evaluating
+ * the ACF: removed option, now on the command line only)
+ * bNormalize If set, all ACFs will be normalized to start at 0
+ * nskip Determines whether steps a re skipped in the output
*/
-
+
typedef struct {
- const char *name; /* Description of the J coupling constant */
- real A,B,C; /* Karplus coefficients */
- real offset; /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
- real Jc; /* Resulting Jcoupling */
- real Jcsig; /* Standard deviation in Jc */
+ const char *name; /* Description of the J coupling constant */
+ real A, B, C; /* Karplus coefficients */
+ real offset; /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
+ real Jc; /* Resulting Jcoupling */
+ real Jcsig; /* Standard deviation in Jc */
} t_karplus;
-void calc_distribution_props(int nh,int histo[],
- real start,int nkkk, t_karplus kkk[],
- real *S2);
+void calc_distribution_props(int nh, int histo[],
+ real start, int nkkk, t_karplus kkk[],
+ real *S2);
/* This routine takes a dihedral distribution and calculates
* coupling constants and dihedral order parameters of it.
*
* histo is the array of datapoints which is assumed to span
* 2 M_PI radians
* start is the starting angle of the histogram, this can be either 0
- * or -M_PI
+ * or -M_PI
* nkkk is the number of karplus sets (multiple coupling constants may be
* derived from a single angle)
* kkk are the constants for calculating J coupling constants using a
* S2 is the resulting dihedral order parameter
*
*/
-
-
+
+
/***********************************************
*
* F I T R O U T I N E S
*
***********************************************/
-void do_expfit(int ndata,real c1[],real dt,
- real begintimefit,real endtimefit);
+void do_expfit(int ndata, real c1[], real dt,
+ real begintimefit, real endtimefit);
-void expfit(int n, real x[], real y[], real Dy[],
- real *a, real *sa,
- real *b, real *sb);
+void expfit(int n, real x[], real y[], real Dy[],
+ real *a, real *sa,
+ real *b, real *sb);
/* This procedure fits y=exp(a+bx) for n (x,y) pairs to determine a and b.
* The uncertainties in the y values must be in the vector Dy.
* The standard deviations of a and b, sa and sb, are also calculated.
* Routine from Computers in physics, 7(3) (1993), p. 280-285.
*/
-void ana_dih_trans(const char *fn_trans,const char *fn_histo,
- real **dih,int nframes,int nangles,
- const char *grpname,real *time,gmx_bool bRb,
- const output_env_t oenv);
+void ana_dih_trans(const char *fn_trans, const char *fn_histo,
+ real **dih, int nframes, int nangles,
+ const char *grpname, real *time, gmx_bool bRb,
+ const output_env_t oenv);
/*
* Analyse dihedral transitions, by counting transitions per dihedral
* and per frame. The total number of transitions is printed to
* stderr, as well as the average time between transitions.
*
- * is wrapper to low_ana_dih_trans, which also passes in and out the
- number of transitions per dihedral per residue. that uses struc dlist
- which is not external, so pp2shift.h must be included.
+ * is wrapper to low_ana_dih_trans, which also passes in and out the
+ number of transitions per dihedral per residue. that uses struc dlist
+ which is not external, so pp2shift.h must be included.
* Dihedrals are supposed to be in either of three minima,
* (trans, gauche+, gauche-)
- *
+ *
* fn_trans output file name for #transitions per timeframe
* fn_histo output file name for transition time histogram
* dih the actual dihedral angles
*/
void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
- gmx_bool bHisto, const char *fn_histo, int maxchi,
- real **dih, int nlist, t_dlist dlist[],
- int nframes, int nangles, const char *grpname,
- int multiplicity[], real *time, gmx_bool bRb,
- real core_frac, const output_env_t oenv);
- /* as above but passes dlist so can copy occupancies into it, and multiplicity[]
- * (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
- * rotamers. Also production of xvg output files is conditional
- * and the fractional width of each rotamer can be set ie for a 3 fold
- * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
- * to each rotamer, the rest goes to rotamer zero */
+ gmx_bool bHisto, const char *fn_histo, int maxchi,
+ real **dih, int nlist, t_dlist dlist[],
+ int nframes, int nangles, const char *grpname,
+ int multiplicity[], real *time, gmx_bool bRb,
+ real core_frac, const output_env_t oenv);
+/* as above but passes dlist so can copy occupancies into it, and multiplicity[]
+ * (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
+ * rotamers. Also production of xvg output files is conditional
+ * and the fractional width of each rotamer can be set ie for a 3 fold
+ * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
+ * to each rotamer, the rest goes to rotamer zero */
void read_ang_dih(const char *trj_fn,
- gmx_bool bAngles,gmx_bool bSaveAll,gmx_bool bRb,gmx_bool bPBC,
- int maxangstat,int angstat[],
- int *nframes,real **time,
- int isize,atom_id index[],
- real **trans_frac,
- real **aver_angle,
- real *dih[],
- const output_env_t oenv);
-/*
+ gmx_bool bAngles, gmx_bool bSaveAll, gmx_bool bRb, gmx_bool bPBC,
+ int maxangstat, int angstat[],
+ int *nframes, real **time,
+ int isize, atom_id index[],
+ real **trans_frac,
+ real **aver_angle,
+ real *dih[],
+ const output_env_t oenv);
+/*
* Read a trajectory and calculate angles and dihedrals.
*
* trj_fn file name of trajectory
* aver_angle average angle at each time frame
* dih all angles at each time frame
*/
-
+
void make_histo(FILE *log,
- int ndata,real data[],int npoints,int histo[],
- real minx,real maxx);
-/*
+ int ndata, real data[], int npoints, int histo[],
+ real minx, real maxx);
+/*
* Make a histogram from data. The min and max of the data array can
* be determined (if minx == 0 and maxx == 0)
* and the index in the histogram is computed from
* if both are 0, these values are computed by the routine itself
*/
-void normalize_histo(int npoints,int histo[],real dx,real normhisto[]);
-/*
- * Normalize a histogram so that the integral over the histo is 1
+void normalize_histo(int npoints, int histo[], real dx, real normhisto[]);
+/*
+ * Normalize a histogram so that the integral over the histo is 1
*
* npoints number of points in the histo array
* histo input histogram
* normhisto normalized output histogram
*/
-real fit_function(int eFitFn,real *parm,real x);
+real fit_function(int eFitFn, real *parm, real x);
/* Returns the value of fit function eFitFn at x */
/* Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential */
/* or to a transverse current autocorrelation function */
/* Or: "There is no KILL like OVERKILL", Dr. Ir. D. van der Spoel */
-real do_lmfit(int ndata,real c1[],real sig[],real dt,real *x,
- real begintimefit,real endtimefit,const output_env_t oenv,
- gmx_bool bVerbose, int eFitFn,real fitparms[],int fix);
+real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x,
+ real begintimefit, real endtimefit, const output_env_t oenv,
+ gmx_bool bVerbose, int eFitFn, real fitparms[], int fix);
/* Returns integral.
* If x == NULL, the timestep dt will be used to create a time axis.
* fix fixes fit parameter i at it's starting value, when the i'th bit
- * of fix is set.
+ * of fix is set.
*/
-real evaluate_integral(int n,real x[],real y[],real dy[],
- real aver_start,real *stddev);
-/* Integrate data in y, and, if given, use dy as weighting
- * aver_start should be set to a value where the function has
+real evaluate_integral(int n, real x[], real y[], real dy[],
+ real aver_start, real *stddev);
+/* Integrate data in y, and, if given, use dy as weighting
+ * aver_start should be set to a value where the function has
* converged to 0.
*/
-real print_and_integrate(FILE *fp,int n,real dt,
- real c[],real *fit,int nskip);
+real print_and_integrate(FILE *fp, int n, real dt,
+ real c[], real *fit, int nskip);
/* Integrate the data in c[] from 0 to n using trapezium rule.
* If fp != NULL output is written to it
* nskip determines whether all elements are written to the output file
* (written when i % nskip == 0)
* If fit != NULL the fit is also written.
*/
-
+
int get_acfnout(void);
-/* Return the output length for the correlation function
+/* Return the output length for the correlation function
* Works only AFTER do_auto_corr has been called!
*/
/* Return the fit function type.
* Works only AFTER do_auto_corr has been called!
*/
-
- /* Routines from pp2shift (anadih.c etc.) */
-void do_pp2shifts(FILE *fp,int nframes,
- int nlist,t_dlist dlist[],real **dih);
+/* Routines from pp2shift (anadih.c etc.) */
+
+void do_pp2shifts(FILE *fp, int nframes,
+ int nlist, t_dlist dlist[], real **dih);
-gmx_bool has_dihedral(int Dih,t_dlist *dl);
+gmx_bool has_dihedral(int Dih, t_dlist *dl);
-t_dlist *mk_dlist(FILE *log,
- t_atoms *atoms, int *nlist,
- gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi, int r0, gmx_residuetype_t rt);
-
-void pr_dlist(FILE *fp,int nl,t_dlist dl[],real dt, int printtype,
- gmx_bool bPhi, gmx_bool bPsi,gmx_bool bChi,gmx_bool bOmega, int maxchi);
+t_dlist *mk_dlist(FILE *log,
+ t_atoms *atoms, int *nlist,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
+ int maxchi, int r0, gmx_residuetype_t rt);
-int pr_trans(FILE *fp,int nl,t_dlist dl[],real dt,int Xi);
+void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt, int printtype,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi);
-void mk_chi_lookup (int **lookup, int maxchi, real **dih,
- int nlist, t_dlist dlist[]) ;
+int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi);
-void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
- int nlist, t_dlist dlist[],int nangle) ;
+void mk_chi_lookup (int **lookup, int maxchi, real **dih,
+ int nlist, t_dlist dlist[]);
-void get_chi_product_traj (real **dih,int nframes,int nangles,
- int nlist,int maxchi, t_dlist dlist[],
- real time[], int **lookup,int *multiplicity,
- gmx_bool bRb,gmx_bool bNormalize,
- real core_frac,gmx_bool bAll,const char *fnall,
- const output_env_t oenv);
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
+ int nlist, t_dlist dlist[], int nangle);
+
+void get_chi_product_traj (real **dih, int nframes, int nangles,
+ int nlist, int maxchi, t_dlist dlist[],
+ real time[], int **lookup, int *multiplicity,
+ gmx_bool bRb, gmx_bool bNormalize,
+ real core_frac, gmx_bool bAll, const char *fnall,
+ const output_env_t oenv);
void print_one (const output_env_t oenv, const char *base,
- const char *name,
- const char *title, const char *ylabel,int nf,
- real time[],real data[]);
-
+ const char *name,
+ const char *title, const char *ylabel, int nf,
+ real time[], real data[]);
+
/* Routines from g_hbond */
-void analyse_corr(int n,real t[],real ct[],real nt[],real kt[],
- real sigma_ct[],real sigma_nt[],real sigma_kt[],
- real fit_start,real temp,real smooth_tail_start,
- const output_env_t oenv);
+void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
+ real sigma_ct[], real sigma_nt[], real sigma_kt[],
+ real fit_start, real temp, real smooth_tail_start,
+ const output_env_t oenv);
-void compute_derivative(int nn,real x[],real y[],real dydx[]);
+void compute_derivative(int nn, real x[], real y[], real dydx[]);
#ifdef __cplusplus
- }
+}
#endif
-
-#endif
-
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff