From: hackbard <hackbard>
Date: Wed, 22 Nov 2006 10:40:07 +0000 (+0000)
Subject: security ci
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=0656efc2936da55ecf0b818fe33bb2acebc689c6;p=physik%2Fposic.git

security ci
---

diff --git a/moldyn.c b/moldyn.c
index 57f76c4..d74b391 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -694,14 +694,6 @@ printf("done\n");
 
 /* generic potential and force calculation */
 
-#define		CREATE_CELL_LIST(nb_list) \
-	link_cell_neighbour_index(moldyn,\
-	                          (atom[i].r.x+moldyn->dim.x/2)/lc->x,\
-	                          (atom[i].r.y+moldyn->dim.y/2)/lc->y,\
-	                          (atom[i].r.z+moldyn->dim.z/2)/lc->z,\
-	                          nb_list);
-
-
 int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,count;
@@ -710,13 +702,15 @@ int potential_force_calc(t_moldyn *moldyn) {
 	t_list neighbour[27];
 	t_list *this;
 	double u;
+	unsigned char bc,bc3;
+	int countn,dnlc;
 
 	count=moldyn->count;
 	atom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	/* reset energy */
-	u=0.0;
+	moldyn->energy=0.0;
 
 	for(i=0;i<count;i++) {
 	
@@ -724,71 +718,99 @@ int potential_force_calc(t_moldyn *moldyn) {
 		v3_zero(&(atom[i].f));
 
 		/* single particle potential/force */
-		if(moldyn->status&MOLDYN_STAT_1BP)
+		if(atom[i].attr&ATOM_ATTR_1BP)
 			moldyn->pf_func1b(moldyn,&(atom[i]));
 
 		/* 2 body pair potential/force */
-		if(moldyn->status&MOLDYN_STAT_2BP) {
+		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 		
-			CREATE_CELL_LIST(neighbour);
+			link_cell_neighbour_index(moldyn,
+				(atom[i].r.x+moldyn->dim.x/2)/lc->x,
+				(atom[i].r.y+moldyn->dim.y/2)/lc->y,
+				(atom[i].r.z+moldyn->dim.z/2)/lc->z,
+				neighbour);
 
-			/*
-			 * processing cell of atom i
-			 * => no need to check for empty list
-			 *    (1 element at minimum)
-			 */
+			countn=lc->countn;
+			dnlc=lc->dnlc;
 
-			this=&(neighbour[0]);
-			list_reset(this);
-			do {
-				btom=this->current->data;
-				if(btom!=&(atom[i]))
-					moldyn->pf_func2b(moldyn,
-					                  &(atom[i]),btom);
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			for(j=0;j<countn;j++) {
 
-			/*
-			 * direct neighbour cells
-			 * => no boundary condition check necessary
-			 */
-			for(j=0;j<lc->dnlc;j++) {
 				this=&(neighbour[j]);
 				list_reset(this);
-				if(this->start!=NULL) {
-					do {
-						btom=this->current->data;
-						moldyn->pf_func2b(moldyn,
-						                  &(atom[i]),
-						                  btom);
-					} while(list_next(this)!=\
-					        L_NO_NEXT_ELEMENT);
-			}
 
-			/*
-			 * neighbour cells due to periodic bc
-			 * => check boundary conditions
-			 */
-			for(j=lc->dnlc;j<lc->countn;j++) {
-				this=&(neighbour[j]);
-				list_reset(this);
-				if(this->start!=NULL) {
-					do {
-						btom=this->current->data;
+				if(this->start==NULL)
+					continue;
+
+				bc=(j<dnlc)?0:1;
+
+				do {
+					btom=this->current->data;
+
+					if(btom==&(atom[i]))
+						continue;
+
+					if((btom->attr&ATOM_ATTR_2BP)&
+					   (atom[i].attr&ATOM_ATTR_2BP))
 						moldyn->pf_func2b(moldyn,
 						                  &(atom[i]),
-						                  btom);
+						                  btom,
+						                  bc);
 
-			}
+					/* 3 body potential/force */
 
+					if(!(atom[i].attr&ATOM_ATTR_3BP)||
+					   !(btom->attr&ATOM_ATTR_3BP))
+						continue;
+
+					link_cell_neighbour_index(moldyn,
+					   (btom->r.x+moldyn->dim.x/2)/lc->x,
+					   (btom->r.y+moldyn->dim.y/2)/lc->y,
+					   (btom->r.z+moldyn->dim.z/2)/lc->z,
+					   neighbourk);
+
+					for(k=0;k<lc->countn;k++) {
+
+						thisk=&(neighbourk[k]);
+						list_reset(thisk);
+					
+						if(thisk->start==NULL)
+							continue;
+
+						bck=(k<lc->dnlc)?0:1;
+
+						do {
+
+			ktom=thisk->current->data;
+
+			if(!(ktom->attr&ATOM_ATTR_3BP))
+				continue;
+
+			if(ktom==btom)
+				continue;
+
+			if(ktom==&(atom[i]))
+				continue;
+
+			moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
+
+						} while(list_next(thisk)!=\
+						        L_NO_NEXT_ELEMENT);
+					
+				} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			}
 		}
+	}
 
 	return 0;
 }
 
+/*
+ * example potentials
+ */
 
 /* harmonic oscillator potential and force */
 
-int harmonic_oscillator(t_moldyn *moldyn) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,unsigned char bc)) {
 
 	t_ho_params *params;
 	t_atom *atom,*btom;
diff --git a/moldyn.h b/moldyn.h
index 717388a..66f774e 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -15,6 +15,7 @@
 
 /* datatypes */
 
+typedef unsigned char u8;
 
 /* the atom of the md simulation */
 
@@ -30,6 +31,10 @@ typedef struct s_atom {
 #define ATOM_ATTR_FP	0x01	/* fixed position (bulk material) */
 #define ATOM_ATTR_HB	0x02	/* coupled to heat bath (velocity scaling) */
 
+#define ATOM_ATTR_1BP	0x10	/* single paricle potential */
+#define ATOM_ATTR_2BP	0x20	/* pair potential */
+#define ATOM_ATTR_3BP	0x40	/* 3 body potential */ 
+
 /* cell lists */
 
 typedef struct s_linkcell {
@@ -99,9 +104,6 @@ typedef struct s_moldyn {
 #define MOLDYN_LVSTAT_VISUAL		0x08
 #define MOLDYN_LVSTAT_INITIALIZED	0x10
 
-#define MOLDYN_STAT_1BP			0x01
-#define MOLDYN_STAT_2BP			0x02	/* define for pair potentials */
-#define MOLDYN_STAT_3BP			0x04	/* define for 3 body pot */ 
 #define MOLDYN_STAT_PBX			0x08	/* periodic boudaries in x */
 #define MOLDYN_STAT_PBY			0x10	/* y */
 #define MOLDYN_STAT_PBZ			0x20	/* and z direction */