From 189da15810deabd739d7c11c6e95fea55739fe60 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Sat, 1 Aug 2020 15:13:49 +0200
Subject: Initial import from archive

---
 src/refine-rns.c | 122 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100644 src/refine-rns.c

(limited to 'src/refine-rns.c')

diff --git a/src/refine-rns.c b/src/refine-rns.c
new file mode 100644
index 0000000..3bfcd21
--- /dev/null
+++ b/src/refine-rns.c
@@ -0,0 +1,122 @@
+/*
+ * refine-rns.c
+ *
+ * Refinement by Random Neighbour Search
+ *
+ * (c) 2006-2009 Thomas White <taw27@cam.ac.uk>
+ *
+ *  synth2d - Two-Dimensional Crystallographic Fourier Synthesis
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "refine.h"
+#include "model.h"
+#include "reflist.h"
+#include "statistics.h"
+
+void refine_neighboursearch(AtomicModel *model, ReflectionList *reflections,
+			    RefinementSpec spec, double shift)
+{
+	unsigned int iterations_without_change;
+	double min_r;
+	ReflectionList *model_reflections;
+
+	model_reflections = model_calculate_f(reflections, model, 69);
+	if ( spec & REFINE_SPEC_INTENSITIES ) {
+		/* stat_r2(Fobs, Fcalc) */
+		min_r = stat_r2(reflections, model_reflections);
+	} else {
+		/* stat_r(Fobs, Fcalc) */
+		min_r = stat_r(reflections, model_reflections);
+	}
+
+	iterations_without_change = 0;
+	while ( (model->refine_window->run_semaphore)
+	     && (iterations_without_change < MAX_REFINEMENT_ITERATIONS) ) {
+
+		unsigned int i;
+		double x, y, z;
+		double new_r;
+		AtomicModel *copy;
+
+		/* Copy the structure */
+		copy = model_copy(model);
+
+		/* 'Jiggle' the atoms */
+		for ( i=1; i<model->n_atoms; i++ ) {
+
+			if ( model->atoms[i].refine ) {
+
+				x = model->atoms[i].x;
+				y = model->atoms[i].y;
+				z = model->atoms[i].z;
+
+				if ( spec & REFINE_SPEC_X ) {
+					if ( random() > (0.9*RAND_MAX) )
+						x += shift;
+					if ( random() > (0.9*RAND_MAX) )
+						x -= shift;
+					if ( x<0 ) x = 1+x;
+					if ( x>1 ) x = x-1;
+					model->atoms[i].x = x;
+				}
+
+				if ( spec & REFINE_SPEC_Y ) {
+					if ( random() > (0.9*RAND_MAX) )
+						y += shift;
+					if ( random() > (0.9*RAND_MAX) )
+						y -= shift;
+					if ( y<0 ) y = 1+y;
+					if ( y>1 ) y = y-1;
+					model->atoms[i].y = y;
+				}
+
+				if ( spec & REFINE_SPEC_Z ) {
+					if ( random() > (0.9*RAND_MAX) )
+						z += shift;
+					if ( random() > (0.9*RAND_MAX) )
+						z -= shift;
+					if ( z<0 ) z = 1+z;
+					if ( z>1 ) z = z-1;
+					model->atoms[i].z = z;
+				}
+
+			}
+
+		}
+
+		/* Recalculate structure factors and check for improvement */
+		model_reflections = model_calculate_f(reflections, model, 69);
+		if ( spec & REFINE_SPEC_INTENSITIES ) {
+			/* stat_r(Fobs, Fcalc) */
+			new_r = stat_r2(reflections, model_reflections);
+		} else {
+			/* stat_r(Fobs, Fcalc) */
+			new_r = stat_r(reflections, model_reflections);
+		}
+		if ( new_r < min_r ) {
+
+			min_r = new_r;
+			refine_schedule_update(model);
+			iterations_without_change = 0;
+
+			model_free(copy);
+
+		} else {
+
+			model_move(model, copy);
+			model_free(copy);
+			iterations_without_change++;
+
+		}
+		free(model_reflections);
+
+	}
+}
-- 
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