X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=80f4fa1b7f8cbff28fdb05b3a6e2c4f17c78faaa;hb=4bf9958c9ed62371b6d620c7ca167bd9993d2148;hp=ed831aed93ec4861c71a383033af863ef1378074;hpb=dece53fc37f9ebb52b33c9743333c213be2d6f26;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index ed831ae..80f4fa1 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -72,7 +72,7 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 }
 
 int set_temperature(t_moldyn *moldyn,double t) {
-	
+
 	moldyn->t=t;
 
 	return 0;
@@ -331,6 +331,7 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	int i;
 	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
@@ -339,13 +340,29 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	 */
 
 	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+	count=0;
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].attr&ATOM_ATTR_HB) {
+			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+
+	/* temporary hack for e,t = 0 */
+	if(e==0.0) {
+		if(moldyn->t!=0.0)
+			thermal_init(moldyn);
+		else
+			return 0;
+	}
+
+	/* direct scaling */
+	scale=(1.5*count*K_BOLTZMANN*moldyn->t)/e;
 	if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
 	scale=sqrt(scale);
 	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),scale);
+		if(atom[i].attr&ATOM_ATTR_HB)
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
@@ -497,7 +514,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 	count2=27;
 	a=nx*ny;
 
-
 	cell[0]=lc->subcell[i+j*nx+k*a];
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
@@ -636,7 +652,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* zero absolute time */
 	moldyn->time=0.0;
-
 	for(sched=0;sched<moldyn->schedule.content_count;sched++) {
 
 		/* setting amount of runs and finite time step size */
@@ -760,15 +775,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 int potential_force_calc(t_moldyn *moldyn) {
 
 	int i,j,k,count;
-	t_atom *atom,*btom,*ktom;
+	t_atom *itom,*jtom,*ktom;
 	t_linkcell *lc;
-	t_list neighbour[27];
-	t_list *this,*thisk,*neighbourk;
-	u8 bc,bck;
+	t_list neighbour_i[27],neighbour_j[27];
+	t_list *this,*that;
+	u8 bc_ij,bc_ijk;
 	int countn,dnlc;
 
 	count=moldyn->count;
-	atom=moldyn->atom;
+	itom=moldyn->atom;
 	lc=&(moldyn->lc);
 
 	/* reset energy */
@@ -777,87 +792,117 @@ int potential_force_calc(t_moldyn *moldyn) {
 	for(i=0;i<count;i++) {
 
 		/* reset force */
-		v3_zero(&(atom[i].f));
+		v3_zero(&(itom[i].f));
 
 		/* single particle potential/force */
-		if(atom[i].attr&ATOM_ATTR_1BP)
-			moldyn->func1b(moldyn,&(atom[i]));
+		if(itom[i].attr&ATOM_ATTR_1BP)
+			moldyn->func1b(moldyn,&(itom[i]));
 
 		/* 2 body pair potential/force */
-		if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
+		if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
 	
 			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);
+				(itom[i].r.x+moldyn->dim.x/2)/lc->x,
+				(itom[i].r.y+moldyn->dim.y/2)/lc->y,
+				(itom[i].r.z+moldyn->dim.z/2)/lc->z,
+				neighbour_i);
 
 			countn=lc->countn;
 			dnlc=lc->dnlc;
 
 			for(j=0;j<countn;j++) {
 
-				this=&(neighbour[j]);
+				this=&(neighbour_i[j]);
 				list_reset(this);
 
 				if(this->start==NULL)
 					continue;
 
-				bc=(j<dnlc)?0:1;
+				bc_ij=(j<dnlc)?0:1;
 
 				do {
-					btom=this->current->data;
+					jtom=this->current->data;
 
-					if(btom==&(atom[i]))
+					if(jtom==&(itom[i]))
 						continue;
 
-					if((btom->attr&ATOM_ATTR_2BP)&
-					   (atom[i].attr&ATOM_ATTR_2BP))
+					if((jtom->attr&ATOM_ATTR_2BP)&
+					   (itom[i].attr&ATOM_ATTR_2BP))
 						moldyn->func2b(moldyn,
-						               &(atom[i]),
-						               btom,
-						               bc);
+						               &(itom[i]),
+						               jtom,
+						               bc_ij);
 
 					/* 3 body potential/force */
 
-					if(!(atom[i].attr&ATOM_ATTR_3BP)||
-					   !(btom->attr&ATOM_ATTR_3BP))
+					if(!(itom[i].attr&ATOM_ATTR_3BP)||
+					   !(jtom->attr&ATOM_ATTR_3BP))
 						continue;
 
-printf("DEBUG: problem exists here ...\n");
 					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);
-printf("DEBUG: as you won't see that!\n");
+					   (jtom->r.x+moldyn->dim.x/2)/lc->x,
+					   (jtom->r.y+moldyn->dim.y/2)/lc->y,
+					   (jtom->r.z+moldyn->dim.z/2)/lc->z,
+					   neighbour_j);
 
+					/* neighbours of j */
 					for(k=0;k<lc->countn;k++) {
 
-						thisk=&(neighbourk[k]);
-						list_reset(thisk);
+						that=&(neighbour_j[k]);
+						list_reset(that);
+					
+						if(that->start==NULL)
+							continue;
+
+						bc_ijk=(k<lc->dnlc)?0:1;
+
+						do {
+
+			ktom=that->current->data;
+
+			if(!(ktom->attr&ATOM_ATTR_3BP))
+				continue;
+
+			if(ktom==jtom)
+				continue;
+
+			if(ktom==&(itom[i]))
+				continue;
+
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+
+						} while(list_next(that)!=\
+						        L_NO_NEXT_ELEMENT);
+
+					}
+					
+					/* neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i[k]);
+						list_reset(that);
 					
-						if(thisk->start==NULL)
+						if(that->start==NULL)
 							continue;
 
-						bck=(k<lc->dnlc)?0:1;
+						bc_ijk=(k<dnlc)?0:1;
 
 						do {
 
-			ktom=thisk->current->data;
+			ktom=that->current->data;
 
 			if(!(ktom->attr&ATOM_ATTR_3BP))
 				continue;
 
-			if(ktom==btom)
+			if(ktom==jtom)
 				continue;
 
-			if(ktom==&(atom[i]))
+			if(ktom==&(itom[i]))
 				continue;
 
-			moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
 
-						} while(list_next(thisk)!=\
+						} while(list_next(that)!=\
 						        L_NO_NEXT_ELEMENT);
 
 					}