X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=80f4fa1b7f8cbff28fdb05b3a6e2c4f17c78faaa;hb=4bf9958c9ed62371b6d620c7ca167bd9993d2148;hp=de7bbbf2a99df465459ee11ac6993c0b6fea58e1;hpb=d0b3c58c84496f5a031f6121f54e2a3d00075b63;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index de7bbbf..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;
@@ -93,6 +93,13 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
 	return 0;
 }
 
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+	moldyn->nnd=dist;
+
+	return 0;
+}
+
 int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
 
 	if(x)
@@ -221,15 +228,18 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	}
 
 	moldyn->count=count;
+	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;
 }
 
@@ -311,16 +321,17 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn);
+	scale_velocity(moldyn,VSCALE_INIT_EQUI);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 type) {
 
 	int i;
-	double e,c;
+	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
@@ -328,17 +339,30 @@ int scale_velocity(t_moldyn *moldyn) {
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
 
-	if(moldyn->t==0.0) {
-		printf("[moldyn] no velocity scaling for T = 0 K\n");
-		return -1;
+	e=0.0;
+	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;
+		}
 	}
 
-	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+	/* 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),(1.0/c));
+		if(atom[i].attr&ATOM_ATTR_HB)
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
@@ -490,7 +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;
@@ -524,7 +547,7 @@ 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;
@@ -594,9 +617,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	t_3dvec p;
 	t_moldyn_schedule *schedule;
 	t_atom *atom;
-
 	int fd;
 	char fb[128];
+	double ds;
 
 	schedule=&(moldyn->schedule);
 	atom=moldyn->atom;
@@ -613,13 +636,22 @@ 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);
 
+	/* do some checks before we actually start calculating bullshit */
+	if(moldyn->cutoff>0.5*moldyn->dim.x)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.y)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+	if(moldyn->cutoff>0.5*moldyn->dim.z)
+		printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+	if(ds>0.05*moldyn->nnd)
+		printf("[moldyn] warning: forces too high / tau too small!\n");
+
 	/* 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 */
@@ -743,103 +775,134 @@ 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++) {
-printf("BAR %d %d\n",i,count);
-	
+
 		/* 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(thisk->start==NULL)
+						if(that->start==NULL)
 							continue;
 
-						bck=(k<lc->dnlc)?0:1;
+						bc_ijk=(k<lc->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);
+
+					}
+					
+					/* neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i[k]);
+						list_reset(that);
+					
+						if(that->start==NULL)
+							continue;
+
+						bc_ijk=(k<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);
 
 					}
@@ -956,6 +1019,20 @@ 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) {