include/gstat.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
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  35
  36 #ifndef _gstat_h
  37 #define _gstat_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "typedefs.h"
  44 #include "statutil.h"
  45 #include "mshift.h"
  46 #include "rmpbc.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 /***********************************************
  53  *
  54  *     A U T O C O R R E L A T I O N
  55  *
  56  ***********************************************/
  57
  58 extern real LegendreP(real x,unsigned long m);
  59
  60 #define eacNormal (1<<0)
  61 #define eacCos    (1<<1)
  62 #define eacVector (1<<2)
  63 #define eacRcross (1<<3  | eacVector)
  64 #define eacP0     (1<<4  | eacVector)
  65 #define eacP1     (1<<5  | eacVector)
  66 #define eacP2     (1<<6  | eacVector)
  67 #define eacP3     (1<<7  | eacVector)
  68 #define eacP4     (1<<8  | eacVector)
  69 #define eacIden   (1<<9)
  70
  71 enum {
  72   effnNONE, effnEXP1, effnEXP2, effnEXP3,   effnVAC,
  73   effnEXP5, effnEXP7, effnEXP9, effnERREST, effnNR
  74 };
  75
  76 /* must correspond with 'leg' g_chi.c:727 */
  77 enum { edPhi=0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax };
  78
  79 enum { edPrintST=0,edPrintRO } ;
  80
  81 #define NHISTO 360
  82 #define NONCHI 3
  83 #define MAXCHI edMax-NONCHI
  84 #define NROT 4  /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
  85
  86 typedef struct {
  87   int minO,minC,H,N,C,O,Cn[MAXCHI+3];
  88 } t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
  89
  90 typedef struct {
  91   char name[12];
  92   int  resnr;
  93   int  index;       /* Index for amino acids (histograms) */
  94   int  j0[edMax];   /* Index in dih array (phi angle is first...) */
  95   t_dihatms  atm;
  96   int  b[edMax];
  97   int  ntr[edMax];
  98   real S2[edMax];
  99   real rot_occ[edMax][NROT];
 100
 101 } t_dlist;
 102
 103 extern int  nfp_ffn[effnNR];
 104
 105 extern const char *s_ffn[effnNR+2];
 106
 107 extern const char *longs_ffn[effnNR];
 108
 109 int sffn2effn(const char **sffn);
 110 /* Returns the ffn enum corresponding to the selected enum option in sffn */
 111
 112 extern t_pargs *add_acf_pargs(int *npargs,t_pargs *pa);
 113 /* Add options for autocorr to the current set of options.
 114  * *npargs must be initialised to the number of elements in pa,
 115  * it will be incremented appropriately.
 116  */
 117
 118 extern void cross_corr(int n,real f[],real g[],real corr[]);
 119 /* Simple minded cross correlation algorithm */
 120
 121 extern real fit_acf(int ncorr,int fitfn,const output_env_t oenv,bool bVerbose,
 122                     real tbeginfit,real tendfit,real dt,real c1[],real *fit);
 123   /* Fit an ACF to a given function */
 124
 125 extern void do_autocorr(const char *fn,const output_env_t oenv,
 126                         const char *title,
 127                         int nframes,int nitem,real **c1,
 128                         real dt,unsigned long mode,bool bAver);
 129 /* Calls low_do_autocorr (see below). After calling add_acf_pargs */
 130
 131 extern void low_do_autocorr(const char *fn,const output_env_t oenv,
 132                             const char *title, int  nframes,int nitem,
 133                             int nout,real **c1, real dt,unsigned long mode,
 134                             int nrestart, bool bAver,bool bNormalize,
 135                             bool bVerbose,real tbeginfit,real tendfit,
 136                             int nfitparm,int nskip);
 137 /*
 138  * do_autocorr calculates autocorrelation functions for many things.
 139  * It takes a 2 d array containing nitem arrays of length nframes
 140  * for each item the ACF is calculated.
 141  *
 142  * A number of "modes" exist for computation of the ACF
 143  *
 144  * if (mode == eacNormal) {
 145  *   C(t) = < X (tau) * X (tau+t) >
 146  * }
 147  * else if (mode == eacCos) {
 148  *   C(t) = < cos (X(tau) - X(tau+t)) >
 149  * }
 150  * else if (mode == eacIden) { **not fully supported yet**
 151  *   C(t) = < (X(tau) == X(tau+t)) >
 152  * }
 153  * else if (mode == eacVector) {
 154  *   C(t) = < X(tau) * X(tau+t)
 155  * }
 156  * else if (mode == eacP1) {
 157  *   C(t) = < cos (X(tau) * X(tau+t) >
 158  * }
 159  * else if (mode == eacP2) {
 160  *   C(t) = 1/2 * < 3 cos (X(tau) * X(tau+t) - 1 >
 161  * }
 162  * else if (mode == eacRcross) {
 163  *   C(t) = < ( X(tau) * X(tau+t) )^2 >
 164  * }
 165  *
 166  * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
 167  * 3 x nframes long, where each triplet is taken as a 3D vector
 168  *
 169  * For mode eacCos inputdata must be in radians, not degrees!
 170  *
 171  * Other parameters are:
 172  *
 173  * fn is output filename (.xvg) where the correlation function(s) are printed
 174  * title is the title in the output file
 175  * nframes is the number of frames in the time series
 176  * nitem is the number of items
 177  * c1           is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
 178  *              on output, this array is filled with the correlation function
 179  *              to reduce storage
 180  * nrestart     is the number of steps between restarts for direct ACFs
 181  *              (i.e. without FFT) When set to 1 all points are used as
 182  *              time origin for averaging
 183  * dt           is the time between frames
 184  * bAver        If set, all ndih C(t) functions are averaged into a single
 185  *              C(t)
 186  * (bFour       If set, will use fast fourier transform (FFT) for evaluating
 187  *              the ACF: removed option, now on the command line only)
 188  * bNormalize   If set, all ACFs will be normalized to start at 0
 189  * nskip        Determines whether steps a re skipped in the output
 190  */
 191
 192 typedef struct {
 193   const char *name; /* Description of the J coupling constant */
 194   real A,B,C;   /* Karplus coefficients */
 195   real offset;  /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
 196   real Jc;      /* Resulting Jcoupling */
 197   real Jcsig;   /* Standard deviation in Jc */
 198 } t_karplus;
 199
 200 extern void calc_distribution_props(int nh,int histo[],
 201                                     real start,int  nkkk, t_karplus kkk[],
 202                                     real *S2);
 203 /* This routine takes a dihedral distribution and calculates
 204  * coupling constants and dihedral order parameters of it.
 205  *
 206  * nh      is the number of points
 207  * histo   is the array of datapoints which is assumed to span
 208  *         2 M_PI radians
 209  * start   is the starting angle of the histogram, this can be either 0
 210  *         or -M_PI
 211  * nkkk    is the number of karplus sets (multiple coupling constants may be
 212  *         derived from a single angle)
 213  * kkk     are the constants for calculating J coupling constants using a
 214  *         Karplus equation according to
 215  *
 216  *                  2
 217  *         J = A cos theta + B cos theta + C
 218  *
 219  *         where theta is phi - offset (phi is the angle in the histogram)
 220  * offset  is subtracted from phi before substitution in the Karplus
 221  *         equation
 222  * S2      is the resulting dihedral order parameter
 223  *
 224  */
 225
 226
 227 /***********************************************
 228  *
 229  *     F I T   R O U T I N E S
 230  *
 231  ***********************************************/
 232 extern void do_expfit(int ndata,real c1[],real dt,
 233                       real begintimefit,real endtimefit);
 234
 235 extern void expfit(int n, real x[], real y[], real Dy[],
 236                    real *a, real *sa,
 237                    real *b, real *sb);
 238 /* This procedure fits y=exp(a+bx) for n (x,y) pairs to determine a and b.
 239  * The uncertainties in the y values must be in the vector Dy.
 240  * The standard deviations of a and b, sa and sb, are also calculated.
 241  *
 242  * Routine from Computers in physics, 7(3) (1993), p. 280-285.
 243  */
 244
 245 extern void ana_dih_trans(const char *fn_trans,const char *fn_histo,
 246                           real **dih,int nframes,int nangles,
 247                           const char *grpname,real t0,real dt,bool bRb,
 248                           const output_env_t oenv);
 249 /*
 250  * Analyse dihedral transitions, by counting transitions per dihedral
 251  * and per frame. The total number of transitions is printed to
 252  * stderr, as well as the average time between transitions.
 253  *
 254  * is wrapper to low_ana_dih_trans, which also passes in and out the
 255      number of transitions per dihedral per residue. that uses struc dlist
 256      which is not external, so pp2shift.h must be included.
 257
 258  * Dihedrals are supposed to be in either of three minima,
 259  * (trans, gauche+, gauche-)
 260  *
 261  * fn_trans  output file name for #transitions per timeframe
 262  * fn_histo  output file name for transition time histogram
 263  * dih       the actual dihedral angles
 264  * nframes   number of times frames
 265  * nangles   number of angles
 266  * grpname   a string for the header of plots
 267  * t0,dt     starting time resp. time between time frames
 268  * bRb       determines whether the polymer convention is used
 269  *           (trans = 0)
 270  */
 271
 272 extern void low_ana_dih_trans(bool bTrans, const char *fn_trans,
 273                               bool bHisto, const char *fn_histo, int maxchi,
 274                               real **dih, int nlist, t_dlist dlist[],
 275                               int nframes, int nangles, const char *grpname,
 276                               int xity[], real t0, real dt, bool bRb,
 277                               real core_frac, const output_env_t oenv);
 278   /* as above but passes dlist so can copy occupancies into it, and xity[]
 279    *  (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
 280    * rotamers. Also production of xvg output files is conditional
 281    * and the fractional width of each rotamer can be set ie for a 3 fold
 282    * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
 283    * to each rotamer, the rest goes to rotamer zero */
 284
 285
 286
 287 extern void read_ang_dih(const char *trj_fn,
 288                          bool bAngles,bool bSaveAll,bool bRb,bool bPBC,
 289                          int maxangstat,int angstat[],
 290                          int *nframes,real **time,
 291                          int isize,atom_id index[],
 292                          real **trans_frac,
 293                          real **aver_angle,
 294                          real *dih[],
 295                          const output_env_t oenv);
 296 /*
 297  * Read a trajectory and calculate angles and dihedrals.
 298  *
 299  * trj_fn      file name of trajectory
 300  * tpb_fn      file name of tpb file
 301  * bAngles     do we have to read angles or dihedrals
 302  * bSaveAll    do we have to store all in the dih array
 303  * bRb         do we have Ryckaert-Bellemans dihedrals (trans = 0)
 304  * bPBC        compute angles module 2 Pi
 305  * maxangstat  number of entries in distribution array
 306  * angstat     angle distribution
 307  * *nframes    number of frames read
 308  * time        simulation time at each time frame
 309  * isize       number of entries in the index, when angles 3*number of angles
 310  *             else 4*number of angles
 311  * index       atom numbers that define the angles or dihedrals
 312  *             (i,j,k) resp (i,j,k,l)
 313  * trans_frac  number of dihedrals in trans
 314  * aver_angle  average angle at each time frame
 315  * dih         all angles at each time frame
 316  */
 317
 318 extern void make_histo(FILE *log,
 319                        int ndata,real data[],int npoints,int histo[],
 320                        real minx,real maxx);
 321 /*
 322  * Make a histogram from data. The min and max of the data array can
 323  * be determined (if minx == 0 and maxx == 0)
 324  * and the index in the histogram is computed from
 325  * ind = npoints/(max(data) - min(data))
 326  *
 327  * log       write error output to this file
 328  * ndata     number of points in data
 329  * data      data points
 330  * npoints   number of points in histogram
 331  * histo     histogram array. This is NOT set to zero, to allow you
 332  *           to add multiple histograms
 333  * minx      start of the histogram
 334  * maxx      end of the histogram
 335  *           if both are 0, these values are computed by the routine itself
 336  */
 337
 338 extern void normalize_histo(int npoints,int histo[],real dx,real normhisto[]);
 339 /*
 340  * Normalize a histogram so that the integral over the histo is 1
 341  *
 342  * npoints    number of points in the histo array
 343  * histo      input histogram
 344  * dx         distance between points on the X-axis
 345  * normhisto  normalized output histogram
 346  */
 347
 348 extern real fit_function(int eFitFn,real *parm,real x);
 349 /* Returns the value of fit function eFitFn at x */
 350
 351 /* Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential */
 352 /* or to a transverse current autocorrelation function */
 353 /* Or: "There is no KILL like OVERKILL", Dr. Ir. D. van der Spoel */
 354 extern real do_lmfit(int ndata,real c1[],real sig[],real dt,real *x,
 355                      real begintimefit,real endtimefit,const output_env_t oenv,
 356                      bool bVerbose, int eFitFn,real fitparms[],int fix);
 357 /* Returns integral.
 358  * If x == NULL, the timestep dt will be used to create a time axis.
 359  * fix fixes fit parameter i at it's starting value, when the i'th bit
 360  * of fix is set.
 361  */
 362
 363 extern real evaluate_integral(int n,real x[],real y[],real dy[],
 364                               real aver_start,real *stddev);
 365 /* Integrate data in y, and, if given, use dy as weighting
 366  * aver_start should be set to a value where the function has
 367  * converged to 0.
 368  */
 369
 370 extern real print_and_integrate(FILE *fp,int n,real dt,
 371                                 real c[],real *fit,int nskip);
 372 /* Integrate the data in c[] from 0 to n using trapezium rule.
 373  * If fp != NULL output is written to it
 374  * nskip determines whether all elements are written to the output file
 375  * (written when i % nskip == 0)
 376  * If fit != NULL the fit is also written.
 377  */
 378
 379 extern int get_acfnout(void);
 380 /* Return the output length for the correlation function
 381  * Works only AFTER do_auto_corr has been called!
 382  */
 383
 384 extern int get_acffitfn(void);
 385 /* Return the fit function type.
 386  * Works only AFTER do_auto_corr has been called!
 387  */
 388
 389   /* Routines from pp2shift (anadih.c etc.) */
 390
 391 extern void do_pp2shifts(FILE *fp,int nframes,
 392                          int nlist,t_dlist dlist[],real **dih);
 393
 394 extern bool has_dihedral(int Dih,t_dlist *dl);
 395
 396 extern t_dlist *mk_dlist(FILE *log,
 397                          t_atoms *atoms, int *nlist,
 398                          bool bPhi, bool bPsi, bool bChi, bool bHChi,
 399                          int maxchi,int r0,int naa,char **aa);
 400
 401 extern void pr_dlist(FILE *fp,int nl,t_dlist dl[],real dt,  int printtype,
 402                      bool bPhi, bool bPsi,bool bChi,bool bOmega, int maxchi);
 403
 404 extern int pr_trans(FILE *fp,int nl,t_dlist dl[],real dt,int Xi);
 405
 406 extern void mk_chi_lookup (int **lookup, int maxchi, real **dih,
 407                            int nlist, t_dlist dlist[]) ;
 408
 409 extern void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
 410                                     int nlist, t_dlist dlist[],int nangle) ;
 411
 412 extern void get_chi_product_traj (real **dih,int nframes,int nangles,
 413                                   int nlist,int maxchi, t_dlist dlist[],
 414                                   real time[], int **lookup,int *xity,
 415                                   bool bRb,bool bNormalize,
 416                                   real core_frac,bool bAll,const char *fnall,
 417                                   const output_env_t oenv);
 418
 419 extern void print_one (const output_env_t oenv, const char *base,
 420                        const char *name,
 421                        const char *title, const char *ylabel,int nf,
 422                        real time[],real data[]);
 423
 424 /* Routines from g_hbond */
 425 extern void analyse_corr(int n,real t[],real ct[],real nt[],real kt[],
 426                          real sigma_ct[],real sigma_nt[],real sigma_kt[],
 427                          real fit_start,real temp,real smooth_tail_start,
 428                          const output_env_t oenv);
 429
 430 extern void compute_derivative(int nn,real x[],real y[],real dydx[]);
 431
 432 #ifdef __cplusplus
 433              }
 434 #endif
 435
 436 #endif
 437
 438