X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=57f76c433ae7d431fc860dc51ddc21b6982a6d29;hb=06912ca45b46de412570a4bd5b5484aa9e8d6e6b;hp=ad0f9a383ea7ae3e01a5a7c3ebc67de518756dc6;hpb=e763f6e3072fbbbc5ecf7345b989d7d29929a38f;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index ad0f9a3..57f76c4 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -58,6 +58,7 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 	int i;
 	t_ho_params hop;
 	t_lj_params ljp;
+	t_tersoff_params tp;
 	double s,e;
 
 	memset(moldyn,0,sizeof(t_moldyn));
@@ -81,10 +82,6 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 					moldyn->mwrite=atoi(argv[++i]);
 					strncpy(moldyn->mfb,argv[++i],64);
 					break;
-				case 'D':
-					moldyn->dwrite=atoi(argv[++i]);
-					strncpy(moldyn->dfb,argv[++i],64);
-					break;
 				case 'S':
 					moldyn->swrite=atoi(argv[++i]);
 					strncpy(moldyn->sfb,argv[++i],64);
@@ -187,16 +184,6 @@ int moldyn_log_init(t_moldyn *moldyn) {
 	if(moldyn->swrite)
 		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
 
-	if(moldyn->dwrite) {
-		moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
-                if(moldyn->dfd<0) {
-			perror("[moldyn] dfd open");
-			return moldyn->dfd;
-		}
-		write(moldyn->dfd,moldyn,sizeof(t_moldyn));
-		moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
-	}
-
 	if((moldyn->vwrite)&&(vis)) {
 		moldyn->visual=vis;
 		visual_init(vis,moldyn->vfb);
@@ -481,7 +468,7 @@ int link_cell_update(t_moldyn *moldyn) {
 	for(i=0;i<lc->cells;i++)
 		list_destroy(&(moldyn->lc.subcell[i]));
 	
-	for(count=0;count<moldyn->count;count++) {
+	for(count=0;count<moedyn->count;count++) {
 		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
@@ -544,6 +531,9 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
 		}
 	}
 
+	lc->dnlc=count2;
+	lc->countn=27;
+
 	return count2;
 }
 
@@ -632,14 +622,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 					write(fd,moldyn->atom,
 					      moldyn->count*sizeof(t_atom));
 				}
+				close(fd);
 			}	
 		}
-		if(d) {
-			if(!(i%d))
-				write(moldyn->dfd,moldyn->atom,
-				      moldyn->count*sizeof(t_atom));
-
-		}
 		if(v) {
 			if(!(i%v)) {
 				visual_atoms(moldyn->visual,i*moldyn->tau,
@@ -687,7 +672,8 @@ printf("done\n");
 
 	/* forces depending on chosen potential */
 printf("calc potential/force ...\n");
-	moldyn->potential_force_function(moldyn);
+	potential_force_calc(moldyn);
+	//moldyn->potential_force_function(moldyn);
 printf("done\n");
 
 	for(i=0;i<count;i++) {
@@ -706,6 +692,100 @@ 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;
+	t_atom *atom;
+	t_linkcell *lc;
+	t_list neighbour[27];
+	t_list *this;
+	double u;
+
+	count=moldyn->count;
+	atom=moldyn->atom;
+	lc=&(moldyn->lc);
+
+	/* reset energy */
+	u=0.0;
+
+	for(i=0;i<count;i++) {
+	
+		/* reset force */
+		v3_zero(&(atom[i].f));
+
+		/* single particle potential/force */
+		if(moldyn->status&MOLDYN_STAT_1BP)
+			moldyn->pf_func1b(moldyn,&(atom[i]));
+
+		/* 2 body pair potential/force */
+		if(moldyn->status&MOLDYN_STAT_2BP) {
+		
+			CREATE_CELL_LIST(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]))
+					moldyn->pf_func2b(moldyn,
+					                  &(atom[i]),btom);
+			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+			/*
+			 * 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;
+						moldyn->pf_func2b(moldyn,
+						                  &(atom[i]),
+						                  btom);
+
+			}
+
+		}
+
+	return 0;
+}
+
+
 /* harmonic oscillator potential and force */
 
 int harmonic_oscillator(t_moldyn *moldyn) {
@@ -995,12 +1075,16 @@ int tersoff(t_moldyn *moldyn) {
 
 			/* 2 body stuff */
 
+			/* we need: f_c, df_c, f_r, df_r */
+
 			v3_sub(&dist_ij,btom,&(atom[i]));
 			d_ij=v3_norm(&dist_ij);
 			if(d_ij<=S) {
 
-				S=;
-				R=;
+				/* determine the tersoff parameters */
+				if(atom[i].element!=btom->element) {
+				S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
+				R=R_m;
 				A=;
 				lambda=;
 				B=;
@@ -1010,8 +1094,10 @@ int tersoff(t_moldyn *moldyn) {
 				betaN=;
 
 				if(d_ij<=R) {
-					f_c=1.0;
-					df_c=0.0;
+					df_r=-lambda*A*exp(-lambda*d_ij)/d_ij;
+					v3_scale(&force,&dist_ij,df_r);
+					v3_add(&(atom[i].f),&(atom[i].f),
+						&force);
 				}
 				else {
 					s_r=S-R;
@@ -1019,7 +1105,11 @@ int tersoff(t_moldyn *moldyn) {
 					f_c=0.5+0.5*cos(arg1);
 					df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
 					f_r=A*exp(-lambda*d_ij);
-					f_a=-B*exp(-mu*d_ij);
+					df_r=-lambda*f_r/d_ij;
+					scale=df_c*f_r+df_r*f_c;
+					v3_scale(&force,&dist_ij,scale);
+					v3_add(&(atom[i].f),&(atom[i].f),
+					       &force);
 				}
 			}
 			else 
@@ -1084,6 +1174,8 @@ int tersoff(t_moldyn *moldyn) {
 					v3_sub(&distance_jk,ktom,btom);
 					cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/\
 					          (2*d_ij*d_ik);
+					sin_theta=sqrt(1.0/\
+					          (cos_theta*cos_theta));
 					theta=arccos(cos_theta);