static void calc_either_side(Crystal *cr, double incr_val,
int *valid, long double *vals[3], int refine,
PartialityModel pmodel)
{
RefList *compare;
struct image *image = crystal_get_image(cr);
if ( (refine != REF_DIV) ) {
Crystal *cr_new;
/* Crystal properties */
cr_new = new_shifted_crystal(cr, refine, -incr_val);
compare = find_intersections(image, cr_new, pmodel);
scan_partialities(crystal_get_reflections(cr), compare, valid,
vals, 0, pmodel);
cell_free(crystal_get_cell(cr_new));
crystal_free(cr_new);
reflist_free(compare);
cr_new = new_shifted_crystal(cr, refine, +incr_val);
compare = find_intersections(image, cr_new, pmodel);
scan_partialities(crystal_get_reflections(cr), compare, valid,
vals, 2, pmodel);
cell_free(crystal_get_cell(cr_new));
crystal_free(cr_new);
reflist_free(compare);
} else {
struct image im_moved;
/* "Image" properties */
im_moved = *image;
shift_parameter(&im_moved, refine, -incr_val);
compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 0, pmodel);
reflist_free(compare);
im_moved = *image;
shift_parameter(&im_moved, refine, +incr_val);
compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 2, pmodel);
reflist_free(compare);
}
}
static Crystal *new_shifted_crystal(Crystal *cr, int refine, double incr_val)
{
Crystal *cr_new;
double r;
UnitCell *cell;
cr_new = crystal_copy(cr);
if ( cr_new == NULL ) {
ERROR("Failed to allocate crystal.\n");
return NULL;
}
crystal_set_image(cr_new, crystal_get_image(cr));
r = crystal_get_profile_radius(cr_new);
switch ( refine ) {
case REF_ASX :
case REF_ASY :
case REF_ASZ :
case REF_BSX :
case REF_BSY :
case REF_BSZ :
case REF_CSX :
case REF_CSY :
case REF_CSZ :
cell = new_shifted_cell(crystal_get_cell(cr), refine,
incr_val);
crystal_set_cell(cr_new, cell);
break;
case REF_R :
cell = cell_new_from_cell(crystal_get_cell(cr));
crystal_set_cell(cr_new, cell);
crystal_set_profile_radius(cr_new, r + incr_val);
break;
default :
ERROR("Can't shift %i\n", refine);
break;
}
return cr_new;
}
/* Return the gradient of partiality wrt parameter 'k' given the current status
* of 'image'. */
double p_gradient(Crystal *cr, int k, Reflection *refl, PartialityModel pmodel)
{
double glow, ghigh;
double rlow, rhigh, p;
struct image *image = crystal_get_image(cr);
double R = crystal_get_profile_radius(cr);
get_partial(refl, &rlow, &rhigh, &p);
if ( k == GPARAM_R ) {
double Rglow, Rghigh;
double D, psph;
D = rlow - rhigh;
psph = volume_fraction(rlow, rhigh, R, pmodel);
Rglow = volume_fraction_rgradient(rlow, R, pmodel);
Rghigh = volume_fraction_rgradient(rhigh, R, pmodel);
return 4.0*psph/(3.0*D) + (4.0*R/(3.0*D))*(Rglow - Rghigh);
}
/* Calculate the gradient of partiality wrt excitation error. */
glow = partiality_gradient(rlow, R, pmodel, rlow, rhigh);
ghigh = partiality_gradient(rhigh, R, pmodel, rlow, rhigh);
if ( k == GPARAM_DIV ) {
double D, psph, ds;
signed int hs, ks, ls;
D = rlow - rhigh;
psph = volume_fraction(rlow, rhigh, R, pmodel);
get_symmetric_indices(refl, &hs, &ks, &ls);
ds = 2.0 * resolution(crystal_get_cell(cr), hs, ks, ls);
return (ds/2.0)*(glow+ghigh) - 4.0*R*psph*ds/(3.0*D*D);
}
return r_gradient(crystal_get_cell(cr), k, refl, image) * (glow-ghigh);
}
/* Apply the given shift to the 'k'th parameter of 'image'. */
static void apply_shift(Crystal *cr, int k, double shift)
{
double t;
struct image *image = crystal_get_image(cr);
switch ( k ) {
case GPARAM_DIV :
if ( isnan(shift) ) {
ERROR("NaN divergence shift\n");
} else {
image->div += shift;
if ( image->div < 0.0 ) image->div = 0.0;
}
break;
case GPARAM_R :
t = crystal_get_profile_radius(cr);
t += shift;
crystal_set_profile_radius(cr, t);
break;
case GPARAM_ASX :
case GPARAM_ASY :
case GPARAM_ASZ :
case GPARAM_BSX :
case GPARAM_BSY :
case GPARAM_BSZ :
case GPARAM_CSX :
case GPARAM_CSY :
case GPARAM_CSZ :
apply_cell_shift(crystal_get_cell(cr), k, shift);
break;
default :
ERROR("No shift defined for parameter %i\n", k);
abort();
}
}
static void calc_either_side(Crystal *cr, double incr_val,
int *valid, long double *vals[3], int refine,
PartialityModel pmodel)
{
RefList *compare;
struct image *image = crystal_get_image(cr);
struct image im_moved;
im_moved = *image;
shift_parameter(&im_moved, refine, -incr_val);
compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 0);
reflist_free(compare);
im_moved = *image;
shift_parameter(&im_moved, refine, +incr_val);
compare = find_intersections(&im_moved, cr, pmodel);
scan_partialities(crystal_get_reflections(cr), compare,
valid, vals, 2);
reflist_free(compare);
}
static double test_gradients(Crystal *cr, double incr_val, int refine,
const char *str, const char *file,
PartialityModel pmodel, int quiet, int plot)
{
Reflection *refl;
RefListIterator *iter;
long double *vals[3];
int i;
int *valid;
int nref;
int n_good, n_invalid, n_small, n_nan, n_bad;
RefList *reflections;
FILE *fh = NULL;
int ntot = 0;
double total = 0.0;
char tmp[32];
double *vec1;
double *vec2;
int n_line;
double cc;
reflections = find_intersections(crystal_get_image(cr), cr, pmodel);
crystal_set_reflections(cr, reflections);
nref = num_reflections(reflections);
if ( nref < 10 ) {
ERROR("Too few reflections found. Failing test by default.\n");
return 0.0;
}
vals[0] = malloc(nref*sizeof(long double));
vals[1] = malloc(nref*sizeof(long double));
vals[2] = malloc(nref*sizeof(long double));
if ( (vals[0] == NULL) || (vals[1] == NULL) || (vals[2] == NULL) ) {
ERROR("Couldn't allocate memory.\n");
return 0.0;
}
valid = malloc(nref*sizeof(int));
if ( valid == NULL ) {
ERROR("Couldn't allocate memory.\n");
return 0.0;
}
for ( i=0; i<nref; i++ ) valid[i] = 1;
scan_partialities(reflections, reflections, valid, vals, 1, pmodel);
calc_either_side(cr, incr_val, valid, vals, refine, pmodel);
if ( plot ) {
snprintf(tmp, 32, "gradient-test-%s.dat", file);
fh = fopen(tmp, "w");
}
vec1 = malloc(nref*sizeof(double));
vec2 = malloc(nref*sizeof(double));
if ( (vec1 == NULL) || (vec2 == NULL) ) {
ERROR("Couldn't allocate memory.\n");
return 0.0;
}
n_invalid = 0; n_good = 0;
n_nan = 0; n_small = 0; n_bad = 0; n_line = 0;
i = 0;
for ( refl = first_refl(reflections, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
long double grad1, grad2, grad;
double cgrad;
signed int h, k, l;
get_indices(refl, &h, &k, &l);
if ( !valid[i] ) {
n_invalid++;
i++;
} else {
double r1, r2, p;
grad1 = (vals[1][i] - vals[0][i]) / incr_val;
grad2 = (vals[2][i] - vals[1][i]) / incr_val;
grad = (grad1 + grad2) / 2.0;
i++;
cgrad = p_gradient(cr, refine, refl, pmodel);
get_partial(refl, &r1, &r2, &p);
if ( isnan(cgrad) ) {
n_nan++;
continue;
}
if ( plot ) {
fprintf(fh, "%e %Le\n", cgrad, grad);
}
vec1[n_line] = cgrad;
vec2[n_line] = grad;
n_line++;
if ( (fabs(cgrad) < 5e-8) && (fabs(grad) < 5e-8) ) {
n_small++;
continue;
}
total += fabs(cgrad - grad);
ntot++;
if ( !within_tolerance(grad, cgrad, 5.0)
|| !within_tolerance(cgrad, grad, 5.0) )
{
if ( !quiet ) {
STATUS("!- %s %3i %3i %3i"
" %10.2Le %10.2e ratio = %5.2Lf"
" %10.2e %10.2e\n",
str, h, k, l, grad, cgrad,
cgrad/grad, r1, r2);
}
n_bad++;
} else {
//STATUS("OK %s %3i %3i %3i"
// " %10.2Le %10.2e ratio = %5.2Lf"
// " %10.2e %10.2e\n",
// str, h, k, l, grad, cgrad, cgrad/grad,
// r1, r2);
n_good++;
}
}
}
STATUS("%3s: %3i within 5%%, %3i outside, %3i nan, %3i invalid, "
"%3i small. ", str, n_good, n_bad, n_nan, n_invalid, n_small);
if ( plot ) {
fclose(fh);
}
cc = gsl_stats_correlation(vec1, 1, vec2, 1, n_line);
STATUS("CC = %+f\n", cc);
return cc;
}
static int write_crystal(Stream *st, Crystal *cr, int include_reflections)
{
UnitCell *cell;
RefList *reflist;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
double a, b, c, al, be, ga;
double rad;
int ret = 0;
fprintf(st->fh, CRYSTAL_START_MARKER"\n");
cell = crystal_get_cell(cr);
assert(cell != NULL);
cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga);
fprintf(st->fh, "Cell parameters %7.5f %7.5f %7.5f nm,"
" %7.5f %7.5f %7.5f deg\n",
a*1.0e9, b*1.0e9, c*1.0e9,
rad2deg(al), rad2deg(be), rad2deg(ga));
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
fprintf(st->fh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
asx/1e9, asy/1e9, asz/1e9);
fprintf(st->fh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
bsx/1e9, bsy/1e9, bsz/1e9);
fprintf(st->fh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
csx/1e9, csy/1e9, csz/1e9);
fprintf(st->fh, "lattice_type = %s\n",
str_lattice(cell_get_lattice_type(cell)));
fprintf(st->fh, "centering = %c\n", cell_get_centering(cell));
fprintf(st->fh, "unique_axis = %c\n", cell_get_unique_axis(cell));
rad = crystal_get_profile_radius(cr);
fprintf(st->fh, "profile_radius = %.5f nm^-1\n", rad/1e9);
if ( crystal_get_notes(cr) != NULL ) {
fprintf(st->fh, "%s\n", crystal_get_notes(cr));
}
reflist = crystal_get_reflections(cr);
if ( reflist != NULL ) {
fprintf(st->fh, "diffraction_resolution_limit"
" = %.2f nm^-1 or %.2f A\n",
crystal_get_resolution_limit(cr)/1e9,
1e10 / crystal_get_resolution_limit(cr));
fprintf(st->fh, "num_reflections = %i\n",
num_integrated_reflections(reflist));
fprintf(st->fh, "num_saturated_reflections = %lli\n",
crystal_get_num_saturated_reflections(cr));
fprintf(st->fh, "num_implausible_reflections = %lli\n",
crystal_get_num_implausible_reflections(cr));
}
if ( include_reflections ) {
if ( reflist != NULL ) {
struct image *image;
image = crystal_get_image(cr);
fprintf(st->fh, REFLECTION_START_MARKER"\n");
if ( AT_LEAST_VERSION(st, 2, 3) ) {
ret = write_stream_reflections_2_3(st->fh,
reflist,
image);
} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
ret = write_stream_reflections_2_2(st->fh,
reflist,
image);
} else {
/* This function writes like a normal reflection
* list was written in stream 2.1 */
ret = write_stream_reflections_2_1(st->fh,
reflist,
image);
}
fprintf(st->fh, REFLECTION_END_MARKER"\n");
} else {
fprintf(st->fh, "No integrated reflections.\n");
}
}
fprintf(st->fh, CRYSTAL_END_MARKER"\n");
return ret;
}
