X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=26f298fbb58f2488f048d04dd4fbaad550e9563e;hb=a33fe7f5d4d7e09b5b52f5f4dadd462cf868ec2f;hp=d52fcd3868c2481e70cbc804b5a9cdf92542708d;hpb=180ff86ae35ca0ea6ee857e92e56120e65315d17;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index d52fcd3..26f298f 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -231,13 +231,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	printf("[moldyn] created lattice with %d atoms\n",count);
 
 	while(count) {
-		moldyn->atom[count-1].element=element;
-		moldyn->atom[count-1].mass=mass;
-		moldyn->atom[count-1].attr=attr;
-		moldyn->atom[count-1].bnum=bnum;
 		count-=1;
+		moldyn->atom[count].element=element;
+		moldyn->atom[count].mass=mass;
+		moldyn->atom[count].attr=attr;
+		moldyn->atom[count].bnum=bnum;
+		check_per_bound(moldyn,&(moldyn->atom[count].r));
 	}
 
+
 	return ret;
 }
 
@@ -495,7 +497,6 @@ 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;
@@ -529,7 +530,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
-	lc->dnlc=count2;
+	lc->dnlc=count1;
 	lc->countn=27;
 
 	return count2;
@@ -618,7 +619,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* sqaure of some variables */
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
-
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
 
@@ -635,7 +635,6 @@ 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 */
@@ -759,102 +758,134 @@ 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 */
 	moldyn->energy=0.0;
 
 	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;
 
 					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);
+					   (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);
 
 					}
@@ -971,6 +1002,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
  * tersoff potential & force for 2 sorts of atoms
  */
 
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+	printf("[moldyn] tersoff parameter completion\n");
+	p->Smixed=sqrt(p->S[0]*p->S[1]);
+	p->Rmixed=sqrt(p->R[0]*p->R[1]);
+	p->Amixed=sqrt(p->A[0]*p->A[1]);
+	p->Bmixed=sqrt(p->B[0]*p->B[1]);
+	p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+	p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+	return 0;
+}
+
 /* tersoff 1 body part */
 int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {