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