X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=57f76c433ae7d431fc860dc51ddc21b6982a6d29;hb=06912ca45b46de412570a4bd5b5484aa9e8d6e6b;hp=e02557c38f78d57e3336fff421697de55c571de1;hpb=dc70c570abec4596355df26ff19756658e33e762;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index e02557c..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);
@@ -457,7 +444,7 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	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]));
 
  	link_cell_update(moldyn);
 	
@@ -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,
@@ -681,10 +666,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 	}
 
 	/* neighbour list update */
+printf("list update ...\n");
 	link_cell_update(moldyn);
+printf("done\n");
 
 	/* forces depending on chosen potential */
-	moldyn->potential_force_function(moldyn);
+printf("calc potential/force ...\n");
+	potential_force_calc(moldyn);
+	//moldyn->potential_force_function(moldyn);
+printf("done\n");
 
 	for(i=0;i<count;i++) {
 		/* again velocities */
@@ -702,6 +692,100 @@ int velocity_verlet(t_moldyn *moldyn) {
  * 
  */
 
+/* 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) {
@@ -861,7 +945,7 @@ int lennard_jones(t_moldyn *moldyn) {
 			d=v3_absolute_square(&distance);	/* 1/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);
@@ -869,7 +953,7 @@ 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),&force);
@@ -888,7 +972,7 @@ int lennard_jones(t_moldyn *moldyn) {
 				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);
@@ -896,7 +980,7 @@ 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),
@@ -920,7 +1004,7 @@ int lennard_jones(t_moldyn *moldyn) {
 				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);
@@ -928,7 +1012,7 @@ 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),
@@ -945,3 +1029,362 @@ int lennard_jones(t_moldyn *moldyn) {
 	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 energy 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 */
+
+			/* 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) {
+
+				/* determine the tersoff parameters */
+				if(atom[i].element!=btom->element) {
+				S=sqrt(TERSOFF_S[e1]*TERSOFF_S[e2]);
+				R=R_m;
+				A=;
+				lambda=;
+				B=;
+				mu=;
+				chi=;
+				beta=;
+				betaN=;
+
+				if(d_ij<=R) {
+					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;
+					arg1=PI*(d_ij-R)/s_r;
+					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);
+					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 
+				continue;		
+
+			
+			/* end 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);
+
+			/* go for zeta - 3 body stuff! */
+			zeta=0.0;
+			d_ij2=d_ij*d_ij;
+
+			/* 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) */
+				
+				v3_sub(&dist_ik,ktom,&(atom[i]));
+				d_ik=v3_norm(&dist_ik);
+				if(d_ik<=Sik) {
+
+				Rik=;
+				Sik=;
+				Aik=;
+				lambda_ik=;
+				Bik=;
+				mu_ik=;
+				omega_ik=;
+				c_i=;
+				d_i=;
+				h_i=;
+			
+
+					if(d_ik<=Rik) {
+						f_cik=1.0;
+						df_cik=0.0;
+					}
+					else {
+						sik_rik=Sik-Rik;
+						arg1ik=PI*(d_ik-Rik)/sik_rik;
+						f_cik=0.5+0.5*cos(arg1ik);
+						df_cik=-0.5*sin(arg1ik)* \
+						       (PI/(sik_rik*d_ik));
+						f_rik=Aik*exp(-lambda_ik*d_ik);
+						f_aik=-Bik*exp(-mu_ik*d_ik);
+					}
+			
+					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);
+
+					
+				}
+				else
+					continue;
+
+				/* end 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;
+}
+