X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=3424d4946b18e4f74185554bb71cb9c7e58893c3;hb=2a902b8d09fd57bc20681448774e2f93894f10aa;hp=707fe032e2e51f87a13800e717f33a461f5e85b7;hpb=c38fe34069adb9697683235f8b1e2311a3122e8f;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 707fe03..3424d49 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -456,8 +456,8 @@ int link_cell_init(t_moldyn *moldyn) {
 	printf("initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		list_init(&(lc->subcell[i]),1);
-		//list_init(&(lc->subcell[i]),lc->listfd);
+		//list_init(&(lc->subcell[i]),1);
+		list_init(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -512,7 +512,6 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 
 
 	cell[0]=lc->subcell[i+j*nx+k*a];
-	printf("%d\n",i+j*nx+k*a);
 	for(ci=-1;ci<=1;ci++) {
 		bx=0;
 		x=i+ci;
@@ -535,16 +534,11 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 					bz=1;
 				}
 				if(!(ci|cj|ck)) continue;
-				printf(" %d %d %d \n",x,y,z);
 				if(bx|by|bz) {
 					cell[--count2]=lc->subcell[x+y*nx+z*a];
-					printf("%d\n",x+y*nx+z*a);
-					printf("--- %d\n",count2);
 				}
 				else {
 					cell[count1++]=lc->subcell[x+y*nx+z*a];
-					printf("%d\n",x+y*nx+z*a);
-					printf("--- %d\n",count1);
 				}
 			}
 		}
@@ -585,6 +579,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	int fd;
 	char fb[128];
 
+	/* initialize linked cell method */
+	link_cell_init(moldyn);
+
 	/* logging & visualization */
 	e=moldyn->ewrite;
 	m=moldyn->mwrite;
@@ -606,9 +603,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	for(i=0;i<moldyn->time_steps;i++) {
 
-		/* neighbour list update */
-		link_cell_update(moldyn);
-
 		/* integration step */
 		moldyn->integrate(moldyn);
 
@@ -686,8 +680,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
+	/* neighbour list update */
+printf("list update ...\n");
+	link_cell_update(moldyn);
+printf("done\n");
+
 	/* forces depending on chosen potential */
+printf("calc potential/force ...\n");
 	moldyn->potential_force_function(moldyn);
+printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -727,30 +728,43 @@ int harmonic_oscillator(t_moldyn *moldyn) {
 	equi_dist=params->equilibrium_distance;
 	count=moldyn->count;
 
+	/* reset energy counter */
 	u=0.0;
+
 	for(i=0;i<count;i++) {
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
 		/* determine cell + neighbours */
 		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
 		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
 		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-		printf("%d %d %d\n",ni,nj,nk);
 		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
 
-		/* processing cell of atom i */
+		/*
+		 * processing cell of atom i
+		 * => no need to check for empty list (1 element at minimum)
+		 */
 		this=&(neighbour[0]);
-		list_reset(this); /* list has 1 element at minimum */
+		list_reset(this);
 		do {
 			btom=this->current->data;
 			if(btom==&(atom[i]))
 				continue;
 			v3_sub(&distance,&(atom[i].r),&(btom->r));
 			d=v3_norm(&distance);
-			u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
-			v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
-			v3_add(&(atom[i].f),&(atom[i].f),&force);
+			if(d<=moldyn->cutoff) {
+				u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+				v3_scale(&force,&distance,
+				         -sc*(1.0-(equi_dist/d)));
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+			}
 		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
-		/* neighbours not doing boundary condition overflow */
+		/*
+		 * direct neighbour cells
+		 * => no boundary condition check necessary
+		 */
 		for(j=1;j<c;j++) {
 			this=&(neighbour[j]);
 			list_reset(this); /* there might not be a single atom */
@@ -772,7 +786,10 @@ int harmonic_oscillator(t_moldyn *moldyn) {
 			}
 		}
 
-		/* neighbours due to boundary conditions */
+		/*
+		 * indirect neighbour cells
+		 * => check boundary conditions
+		 */
 		for(j=c;j<27;j++) {
 			this=&(neighbour[j]);
 			list_reset(this); /* check boundary conditions */
@@ -796,7 +813,7 @@ int harmonic_oscillator(t_moldyn *moldyn) {
 		}
 	}
 
-	moldyn->energy=u;
+	moldyn->energy=0.5*u;
 
 	return 0;
 }
@@ -824,18 +841,18 @@ int lennard_jones(t_moldyn *moldyn) {
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
+	/* reset energy counter */
 	u=0.0;
+
 	for(i=0;i<count;i++) {
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
 		/* determine cell + neighbours */
 		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
 		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
 		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
-			printf("hier atom = %08x\n",&(atom[i]));
 		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-			printf("da atom = %08x\n",&(atom[i]));
-			printf("da atom = %08x\n",&(moldyn->atom[i]));
-
-		printf("c = %d (%d %d %d)\n",c,ni,nj,nk);
 
 		/* processing cell of atom i */
 		this=&(neighbour[0]);
@@ -844,23 +861,23 @@ int lennard_jones(t_moldyn *moldyn) {
 			btom=this->current->data;
 			if(btom==&(atom[i]))
 				continue;
-		puts("foo");
 			v3_sub(&distance,&(atom[i].r),&(btom->r));
-		puts("foo");
-			d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
-			h1=d*d; 	/* 1/r^4 */
-			h2*=d;	 	/* 1/r^6 */
-			h1=h2*h2; 	/* 1/r^12 */
-			u+=eps*(sig12*h1-sig6*h2);
-			h2*=d;		/* 1/r^8 */
-			h1*=d;		/* 1/r^14 */
-			h2*=6*sig6;
-			h1*=12*sig12;
-			d=-h1+h2;
-			d*=eps;
-			v3_scale(&force,&distance,d);
-			v3_add(&(atom[i].f),&(atom[i].f),&force);
-			printf("test!!\n");
+			d=v3_absolute_square(&distance);	/* 1/r^2 */
+			if(d<=moldyn->cutoff_square) {
+				d=1.0/d;	/* 1/r^2 */
+				h2=d*d; 	/* 1/r^4 */
+				h2*=d;	 	/* 1/r^6 */
+				h1=h2*h2; 	/* 1/r^12 */
+				u+=eps*(sig12*h1-sig6*h2);
+				h2*=d;		/* 1/r^8 */
+				h1*=d;		/* 1/r^14 */
+				h2*=6*sig6;
+				h1*=12*sig12;
+				d=+h1-h2;
+				d*=eps;
+				v3_scale(&force,&distance,d);
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+			}
 		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
 
 		/* neighbours not doing boundary condition overflow */
@@ -870,13 +887,12 @@ int lennard_jones(t_moldyn *moldyn) {
 			if(this->start!=NULL) {
 
 			do {
-				printf("in bound: %d\n",j);
 				btom=this->current->data;
 				v3_sub(&distance,&(atom[i].r),&(btom->r));
 				d=v3_absolute_square(&distance); /* r^2 */
 				if(d<=moldyn->cutoff_square) {
 					d=1.0/d;	/* 1/r^2 */
-					h1=d*d; 	/* 1/r^4 */
+					h2=d*d; 	/* 1/r^4 */
 					h2*=d;	 	/* 1/r^6 */
 					h1=h2*h2; 	/* 1/r^12 */
 					u+=eps*(sig12*h1-sig6*h2);
@@ -884,7 +900,7 @@ int lennard_jones(t_moldyn *moldyn) {
 					h1*=d;		/* 1/r^14 */
 					h2*=6*sig6;
 					h1*=12*sig12;
-					d=-h1+h2;
+					d=+h1-h2;
 					d*=eps;
 					v3_scale(&force,&distance,d);
 					v3_add(&(atom[i].f),&(atom[i].f),
@@ -902,14 +918,13 @@ int lennard_jones(t_moldyn *moldyn) {
 			if(this->start!=NULL) {
 
 			do {
-				printf("out bound: %d\n",j);
 				btom=this->current->data;
 				v3_sub(&distance,&(atom[i].r),&(btom->r));
 				v3_per_bound(&distance,&(moldyn->dim));
 				d=v3_absolute_square(&distance); /* r^2 */
 				if(d<=moldyn->cutoff_square) {
 					d=1.0/d;	/* 1/r^2 */
-					h1=d*d; 	/* 1/r^4 */
+					h2=d*d; 	/* 1/r^4 */
 					h2*=d; 		/* 1/r^6 */
 					h1=h2*h2; 	/* 1/r^12 */
 					u+=eps*(sig12*h1-sig6*h2);
@@ -917,7 +932,7 @@ int lennard_jones(t_moldyn *moldyn) {
 					h1*=d;		/* 1/r^14 */
 					h2*=6*sig6;
 					h1*=12*sig12;
-					d=-h1+h2;
+					d=+h1-h2;
 					d*=eps;
 					v3_scale(&force,&distance,d);
 					v3_add(&(atom[i].f),&(atom[i].f),
@@ -929,8 +944,275 @@ int lennard_jones(t_moldyn *moldyn) {
 		}
 	}
 
-	moldyn->energy=u;
+	moldyn->energy=0.5*u;
 	
 	return 0;
 }
 
+/* tersoff potential & force for 2 sorts of atoms */
+
+int tersoff(t_moldyn *moldyn) {
+
+	t_tersoff_params *params;
+	t_atom *atom,*btom,*ktom;
+	t_linkcell *lc;
+	t_list *this,*thisk,neighbour[27],neighbourk[27];
+	int i,j,k,c,ck;
+	int count;
+	double u;
+	int ni,nj,nk;
+	int ki,kj,kk;
+	
+
+	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+	count=moldyn->count;
+	
+	/* reset enrgy counter */
+	u=0.0;
+
+	for(i=0;i<count;i++) {
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* determin cell neighbours */
+		ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
+		nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
+		nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
+		c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+		/*
+		 * processing cell of atom i
+		 * => no need to check for empty list (1 element at minimum)
+		 */
+		this=&(neighbour[0]);
+		list_reset(this);
+		do {
+			btom=this->current->data;
+			if(btom==&(atom[i]))
+				continue;
+
+			/* 2 body stuff */
+
+			/* determine cell neighbours of btom */
+			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+			                             neighbourk);
+
+			/* cell of btom */
+			thisk=&(neighbourk[0]);
+			list_reset(thisk);
+			do {
+				ktom=thisk->current->data;
+				if(ktom==btom)
+					continue;
+				if(ktom==&(atom[i]))
+					continue;
+				
+				/* 3 body stuff (1) */
+
+			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+			/* direct neighbours of btom cell */
+			for(k=1;k<ck;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (2) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+			/* indirect neighbours of btom cell */
+			for(k=ck;k<27;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+
+		} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+		/*
+		 * direct neighbour cells of atom i
+		 */
+		for(j=1;j<c;j++) {
+			this=&(neighbour[j]);
+			list_reset(this);
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+
+				/* 2 body stuff */
+
+
+			/* determine cell neighbours of btom */
+			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+			                             neighbourk);
+
+			/* cell of btom */
+			thisk=&(neighbourk[0]);
+			list_reset(thisk);
+			do {
+				ktom=thisk->current->data;
+				if(ktom==btom)
+					continue;
+				if(ktom==&(atom[i]))
+					continue;
+				
+				/* 3 body stuff (1) */
+
+			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+			/* direct neighbours of btom cell */
+			for(k=1;k<ck;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (2) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+			/* indirect neighbours of btom cell */
+			for(k=ck;k<27;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (3) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			}
+		}
+
+		/*
+		 * indirect neighbour cells of atom i
+		 */
+		for(j=c;j<27;j++) {
+			this=&(neighbour[j]);
+			list_reset(this);
+			if(this->start!=NULL) {
+
+			do {
+				btom=this->current->data;
+
+				/* 2 body stuff */
+
+
+			/* determine cell neighbours of btom */
+			ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
+			kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
+			kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
+			ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
+			                             neighbourk);
+
+			/* cell of btom */
+			thisk=&(neighbourk[0]);
+			list_reset(thisk);
+			do {
+				ktom=thisk->current->data;
+				if(ktom==btom)
+					continue;
+				if(ktom==&(atom[i]))
+					continue;
+				
+				/* 3 body stuff (1) */
+
+			} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+			/* direct neighbours of btom cell */
+			for(k=1;k<ck;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (2) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+			/* indirect neighbours of btom cell */
+			for(k=ck;k<27;k++) {
+				thisk=&(neighbourk[k]);
+				list_reset(thisk);
+				if(thisk->start!=NULL) {
+
+				do {
+					ktom=thisk->current->data;
+					if(ktom==&(atom[i]))
+						continue;
+
+				/* 3 body stuff (3) */
+
+				} while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+
+				}
+			}
+
+
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			}
+		}
+		
+	}
+
+	moldyn->energy=0.5*u;
+
+	return 0;
+}
+