From 40dd7ff04a44688544e22cc3a0384bef808abc64 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 18 Nov 2015 17:07:32 +0100
Subject: Move B factor limit to general rejection function

---
 src/partialator.c | 7 +++----
 src/rejection.c   | 6 +++++-
 src/rejection.h   | 3 ++-
 src/scaling.c     | 9 +--------
 src/scaling.h     | 2 +-
 5 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/src/partialator.c b/src/partialator.c
index 6de69cd2..23f0c089 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -1009,7 +1009,7 @@ int main(int argc, char *argv[])
 	/* Initial rejection, figures of merit etc */
 	full = merge_intensities(crystals, n_crystals, nthreads, pmodel,
 	                         min_measurements, push_res, 1);
-	check_rejection(crystals, n_crystals, full);
+	check_rejection(crystals, n_crystals, full, max_B);
 	show_all_residuals(crystals, n_crystals, full);
 	write_pgraph(full, crystals, n_crystals, 0);
 
@@ -1019,8 +1019,7 @@ int main(int argc, char *argv[])
 		STATUS("Scaling and refinement cycle %i of %i\n", i+1, n_iter);
 
 		if ( !no_scale ) {
-			scale_all(crystals, n_crystals, nthreads, pmodel,
-			          max_B);
+			scale_all(crystals, n_crystals, nthreads, pmodel);
 			reflist_free(full);
 			full = merge_intensities(crystals, n_crystals, nthreads,
 			                         pmodel, min_measurements,
@@ -1036,7 +1035,7 @@ int main(int argc, char *argv[])
 			                         push_res, 1);
 		}
 
-		check_rejection(crystals, n_crystals, full);
+		check_rejection(crystals, n_crystals, full, max_B);
 		reflist_free(full);
 		full = merge_intensities(crystals, n_crystals, nthreads,
 		                         pmodel, min_measurements,
diff --git a/src/rejection.c b/src/rejection.c
index e9496932..441a83e6 100644
--- a/src/rejection.c
+++ b/src/rejection.c
@@ -192,7 +192,7 @@ static void show_duds(Crystal **crystals, int n_crystals)
 }
 
 
-void check_rejection(Crystal **crystals, int n, RefList *full)
+void check_rejection(Crystal **crystals, int n, RefList *full, double max_B)
 {
 	int i;
 	int n_acc = 0;
@@ -200,7 +200,11 @@ void check_rejection(Crystal **crystals, int n, RefList *full)
 	/* Check according to CCs FIXME: Disabled */
 	//if ( full != NULL ) check_ccs(crystals, n, full);
 
+
 	for ( i=0; i<n; i++ ) {
+		if ( fabs(crystal_get_Bfac(crystals[i])) > max_B ) {
+			crystal_set_user_flag(crystals[i], PRFLAG_BIGB);
+		}
 		if ( crystal_get_user_flag(crystals[i]) == 0 ) n_acc++;
 	}
 
diff --git a/src/rejection.h b/src/rejection.h
index ec529941..8979313b 100644
--- a/src/rejection.h
+++ b/src/rejection.h
@@ -38,6 +38,7 @@
 #include "crystal.h"
 
 extern void early_rejection(Crystal **crystals, int n);
-extern void check_rejection(Crystal **crystals, int n, RefList *full);
+extern void check_rejection(Crystal **crystals, int n, RefList *full,
+                            double max_B);
 
 #endif	/* REJECTION_H */
diff --git a/src/scaling.c b/src/scaling.c
index b3b9137e..5bfba451 100644
--- a/src/scaling.c
+++ b/src/scaling.c
@@ -317,7 +317,6 @@ struct scale_args
 	RefList *full;
 	Crystal *crystal;
 	PartialityModel pmodel;
-	double max_B;
 };
 
 
@@ -335,11 +334,6 @@ static void scale_crystal(void *task, int id)
 {
 	struct scale_args *pargs = task;
 	do_scale_refine(pargs->crystal, pargs->full, pargs->pmodel);
-
-	/* Reject if B factor modulus is very large */
-	if ( fabs(crystal_get_Bfac(pargs->crystal)) > pargs->max_B ) {
-		crystal_set_user_flag(pargs->crystal, PRFLAG_BIGB);
-	}
 }
 
 
@@ -395,7 +389,7 @@ static double total_log_r(Crystal **crystals, int n_crystals, RefList *full,
 
 /* Perform iterative scaling, all the way to convergence */
 void scale_all(Crystal **crystals, int n_crystals, int nthreads,
-               PartialityModel pmodel, double max_B)
+               PartialityModel pmodel)
 {
 	struct scale_args task_defaults;
 	struct queue_args qargs;
@@ -403,7 +397,6 @@ void scale_all(Crystal **crystals, int n_crystals, int nthreads,
 
 	task_defaults.crystal = NULL;
 	task_defaults.pmodel = pmodel;
-	task_defaults.max_B = max_B;
 
 	qargs.task_defaults = task_defaults;
 	qargs.n_crystals = n_crystals;
diff --git a/src/scaling.h b/src/scaling.h
index f8eb4e9e..534043d9 100644
--- a/src/scaling.h
+++ b/src/scaling.h
@@ -42,6 +42,6 @@ extern double log_residual(Crystal *cr, const RefList *full, int free,
                            int *pn_used, const char *filename);
 
 extern void scale_all(Crystal **crystals, int n_crystals, int nthreads,
-                      PartialityModel pmodel, double max_B);
+                      PartialityModel pmodel);
 
 #endif	/* SCALING_H */
-- 
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