X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=af0132dff157564f46f593c3280700b045a1810c;hb=a9fbc66448c52bc4138176739b33d17ba86b7eae;hp=d52fcd3868c2481e70cbc804b5a9cdf92542708d;hpb=180ff86ae35ca0ea6ee857e92e56120e65315d17;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index d52fcd3..af0132d 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -71,9 +71,18 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 	return 0;
 }
 
-int set_temperature(t_moldyn *moldyn,double t) {
-	
-	moldyn->t=t;
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+	moldyn->t_ref=t_ref;
+
+	return 0;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+	moldyn->pt_scale=(ptype|ttype);
+	moldyn->t_tc=ttc;
+	moldyn->p_tc=ptc;
 
 	return 0;
 }
@@ -231,13 +240,15 @@ 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;
 }
 
@@ -276,7 +287,7 @@ int destroy_atoms(t_moldyn *moldyn) {
 	return 0;
 }
 
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -296,7 +307,7 @@ int thermal_init(t_moldyn *moldyn) {
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<moldyn->count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
 		atom[i].v.x=v;
@@ -319,16 +330,17 @@ int thermal_init(t_moldyn *moldyn) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(moldyn,VSCALE_INIT_EQUI);
+	scale_velocity(moldyn,equi_init);
 
 	return 0;
 }
 
-int scale_velocity(t_moldyn *moldyn,u8 type) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
 	int i;
 	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
@@ -336,14 +348,41 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 	 */
 
+	/* get kinetic energy / temperature & count involved atoms */
 	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
-	if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
+	count=0;
+	for(i=0;i<moldyn->count;i++) {
+		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+	if(count!=0) moldyn->t=(2.0*e)/(3.0*count*K_BOLTZMANN);
+	else return 0;	/* no atoms involved in scaling! */
+	
+	/* (temporary) hack for e,t = 0 */
+	if(e==0.0) {
+	moldyn->t=0.0;
+		if(moldyn->t_ref!=0.0)
+			thermal_init(moldyn,equi_init);
+		else
+			return 0; /* no scaling needed */
+	}
+
+
+	/* get scaling factor */
+	scale=moldyn->t_ref/moldyn->t;
+	if(equi_init&TRUE)
+		scale*=2.0;
+	else
+		if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+			scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
 	scale=sqrt(scale);
+
+	/* velocity scaling */
 	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),scale);
+		if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
@@ -495,7 +534,6 @@ 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 +567,7 @@ 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 +656,6 @@ 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 +672,6 @@ 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 */
@@ -650,6 +686,10 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		/* integration step */
 		moldyn->integrate(moldyn);
 
+		/* p/t scaling */
+		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+			scale_velocity(moldyn,FALSE);
+
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
 
@@ -759,102 +799,152 @@ 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];
+	t_list neighbour_i2[27];
+	//t_list 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);
-
-					for(k=0;k<lc->countn;k++) {
-
-						thisk=&(neighbourk[k]);
-						list_reset(thisk);
+			/*
+			 * according to mr. nordlund, we dont need to take the 
+			 * sum over all atoms now, as 'this is centered' around
+			 * atom i ...
+			 * i am not quite sure though! there is a not vanishing
+			 * part even if f_c_ik is zero ...
+			 * this analytical potentials suck!
+			 * switching from mc to md to dft soon!
+			 */
+
+			//		link_cell_neighbour_index(moldyn,
+			//		   (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++) {
+//
+//						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);
+//
+//					}
+			
+					/* copy the neighbour lists */
+					memcpy(neighbour_i2,neighbour_i,
+					       27*sizeof(t_list));
+
+					/* get neighbours of i */
+					for(k=0;k<countn;k++) {
+
+						that=&(neighbour_i2[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);
+printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+			moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
+printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
 
-						} while(list_next(thisk)!=\
+						} while(list_next(that)!=\
 						        L_NO_NEXT_ELEMENT);
 
 					}
@@ -971,6 +1061,20 @@ 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) {
 
@@ -1032,8 +1136,11 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	if(bc) check_per_bound(moldyn,&dist_ij);
 
-	/* save for use in 3bp */ /* REALLY ?!?!?! */
-	exchange->dist_ij=dist_ij;
+	d_ij=v3_norm(&dist_ij);
+
+	/* save for use in 3bp */
+	exchange->dist_ij=dist_ij; /* <- needed ? */
+	exchange->d_ij=d_ij;
 
 	/* constants */
 	if(num==aj->bnum) {
@@ -1059,11 +1166,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		params->exchange.chi=params->chi;
 	}
 
-	d_ij=v3_norm(&dist_ij);
-
-	/* save for use in 3bp */
-	exchange->d_ij=d_ij;
-
 	if(d_ij>S)
 		return 0;
 
@@ -1091,8 +1193,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	/* add forces */
 	v3_add(&(ai->f),&(ai->f),&force);
-	/* energy is 0.5 f_r f_c, but we will sum it up twice ... */
-	moldyn->energy+=(0.25*f_r*f_c);
+	/* energy is 0.5 f_r f_c ... */
+	moldyn->energy+=(0.5*f_r*f_c);
 
 	/* save for use in 3bp */
 	exchange->f_c=f_c;