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/*
* refine-brent.c
*
* Refinement by Sequential Brent Minimisation
*
* (c) 2006-2007 Thomas White <taw27@cam.ac.uk>
*
* synth2d - Two-Dimensional Crystallographic Fourier Synthesis
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <gsl/gsl_errno.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_min.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_linalg.h>
#include "refine.h"
#include "model.h"
#include "reflist.h"
#include "statistics.h"
/* For the purposes of GSL */
static double refine_calc_r(double loc, void *params) {
double r;
ReflectionList *model_reflections;
RefinementPair *pair = params;
AtomicModel *model;
model = model_copy(pair->model);
switch ( pair->cur_mod_coor ) {
case COORDINATE_X : model->atoms[pair->cur_mod_atom].x = loc; break;
case COORDINATE_Y : model->atoms[pair->cur_mod_atom].y = loc; break;
case COORDINATE_Z : model->atoms[pair->cur_mod_atom].z = loc; break;
}
model_reflections = model_calculate_f(pair->reflections, model, 69);
if ( pair->spec & REFINE_SPEC_INTENSITIES ) {
r = stat_r2(pair->reflections, model_reflections); /* stat_r(Fobs, Fcalc) */
} else {
r = stat_r(pair->reflections, model_reflections); /* stat_r(Fobs, Fcalc) */
}
free(model_reflections);
model_free(model);
return r;
}
void refine_brent(AtomicModel *model, ReflectionList *reflections, RefinementSpec spec) {
gsl_function F;
gsl_min_fminimizer *s;
int status;
RefinementPair pair;
pair.reflections = reflections;
pair.model = model;
pair.cur_mod_coor = COORDINATE_X;
pair.cur_mod_atom = 1;
F.function = &refine_calc_r;
F.params = &pair;
s = gsl_min_fminimizer_alloc(gsl_min_fminimizer_brent);
while ( model->refine_window->run_semaphore ) {
double loc_cur;
unsigned int iter = 0;
/* Select the next thing to refine */
pair.cur_mod_coor++;
if ( pair.cur_mod_coor > COORDINATE_Z ) {
pair.cur_mod_coor = COORDINATE_X;
pair.cur_mod_atom++;
if ( pair.cur_mod_atom >= pair.model->n_atoms ) pair.cur_mod_atom = 1;
}
// if ( random() < (0.3333*RAND_MAX) ) pair.cur_mod_coor = COORDINATE_Y;
// if ( random() > (0.6666*RAND_MAX) ) pair.cur_mod_coor = COORDINATE_Z;
// atom = 1 + (random()*(double)(pair.model->n_atoms-1))/RAND_MAX;
// pair.cur_mod_atom = atom;
loc_cur = 0;
switch ( pair.cur_mod_coor ) {
case COORDINATE_X : loc_cur = pair.model->atoms[pair.cur_mod_atom].x; break;
case COORDINATE_Y : loc_cur = pair.model->atoms[pair.cur_mod_atom].y; break;
case COORDINATE_Z : loc_cur = pair.model->atoms[pair.cur_mod_atom].z; break;
}
gsl_min_fminimizer_set(s, &F, loc_cur, loc_cur-0.1, loc_cur+0.1);
do {
double lo, up;
/* Iterate */
gsl_min_fminimizer_iterate(s);
iter++;
/* Get the current estimate */
loc_cur = gsl_min_fminimizer_x_minimum(s);
lo = gsl_min_fminimizer_x_lower(s);
up = gsl_min_fminimizer_x_upper(s);
/* Check for convergence */
status = gsl_min_test_interval(lo, up, 0.001, 0.0);
} while ( status == GSL_CONTINUE );
if (status == GSL_SUCCESS) {
if ( loc_cur < 0 ) loc_cur = 1+loc_cur;
if ( loc_cur >= 1 ) loc_cur = loc_cur-1;
switch ( pair.cur_mod_coor ) {
case COORDINATE_X : pair.model->atoms[pair.cur_mod_atom].x = loc_cur; break;
case COORDINATE_Y : pair.model->atoms[pair.cur_mod_atom].y = loc_cur; break;
case COORDINATE_Z : pair.model->atoms[pair.cur_mod_atom].z = loc_cur; break;
}
refine_schedule_update(model);
}
}
gsl_min_fminimizer_free(s);
}
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