Residual and scaling fixes

3 files changed, 16 insertions, 16 deletions

diff --git a/src/partialator.c b/src/partialator.c
index a72eda50..46a5a25f 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1236,6 +1236,13 @@ int main(int argc, char *argv[])
 
 		STATUS("Scaling and refinement cycle %i of %i\n", i+1, n_iter);
 
+		if ( !no_pr ) {
+
+			r = (reference != NULL) ? reference : full;
+			refine_all(crystals, n_crystals, r, nthreads, pmodel);
+
+		}
+
 		if ( !no_scale ) {
 
 			if ( reference == NULL ) {
@@ -1257,18 +1264,6 @@ int main(int argc, char *argv[])
 			}
 		}
 
-		if ( !no_pr ) {
-
-			r = (reference != NULL) ? reference : full;
-			refine_all(crystals, n_crystals, r, nthreads, pmodel);
-
-			reflist_free(full);
-			full = merge_intensities(crystals, n_crystals, nthreads,
-			                         pmodel, min_measurements,
-			                         push_res, 1);
-
-		}
-
 		check_rejection(crystals, n_crystals, full, max_B);
 		reflist_free(full);
 		full = merge_intensities(crystals, n_crystals, nthreads,
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 2eae8e91..e1a2e05a 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -92,6 +92,10 @@ double residual(Crystal *cr, const RefList *full, int free,
 	double B = crystal_get_Bfac(cr);
 	UnitCell *cell = crystal_get_cell(cr);
 
+	if ( linear_scale(crystal_get_reflections(cr), full, &G) ) {
+		return INFINITY;
+	}
+
 	for ( refl = first_refl(crystal_get_reflections(cr), &iter);
 	      refl != NULL;
 	      refl = next_refl(refl, iter) )
@@ -120,10 +124,9 @@ double residual(Crystal *cr, const RefList *full, int free,
 		int2 = p*I_full;
 		w = 1.0;
 
-		if ( int1 + int2 < 0.0 ) continue;
 
 		num += fabs(int1 - int2) * w;
-		den += (int1 + int2) * w/2.0;
+		den += fabs(int1 + int2) * w/2.0;
 
 		n_used++;
 
@@ -295,7 +298,7 @@ static double residual_f(const gsl_vector *v, void *pp)
 	crystal_set_image(cr, &im);
 	apply_parameters(v, pv->initial, pv->rv, cr);
 
-	if ( crystal_get_profile_radius(cr) < 0.0 ) {
+	if ( crystal_get_profile_radius(cr) <= 0.0 ) {
 		crystal_free(cr);
 		return INFINITY;
 	}
@@ -439,7 +442,7 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 			       res, size);
 		}
 
-		status = gsl_multimin_test_size(min->size, 0.1);
+		status = gsl_multimin_test_size(min->size, 0.005);
 
 	} while ( status == GSL_CONTINUE && n_iter < 1000 );
 
diff --git a/src/scaling.h b/src/scaling.h
index 7b055003..85e8c8ab 100644
--- a/src/scaling.h
+++ b/src/scaling.h
@@ -41,6 +41,8 @@
 extern double log_residual(Crystal *cr, const RefList *full, int free,
                            int *pn_used, const char *filename);
 
+extern int linear_scale(RefList *list1, const RefList *list2, double *G);
+
 extern void scale_all(Crystal **crystals, int n_crystals, int nthreads,
                       PartialityModel pmodel);