From: hackbard <hackbard>
Date: Sun, 10 Dec 2006 22:44:50 +0000 (+0000)
Subject: mods to corect 3bp derivative, still segfaulting ...
X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=b30d3d558354102cf5d0c06392961032b21bf9a9;p=physik%2Fposic.git

mods to corect 3bp derivative, still segfaulting ...
---

diff --git a/moldyn.c b/moldyn.c
index 8d1cb23..6736e45 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -697,7 +697,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	for(i=0;i<moldyn->time_steps;i++) {
 
 		/* integration step */
-printf("MOVE\n");
 		moldyn->integrate(moldyn);
 
 		/* p/t scaling */
@@ -921,14 +920,15 @@ int potential_force_calc(t_moldyn *moldyn) {
 		
 				/* 2bp post function */
 				if(moldyn->func2b_post) {
+printf("DEBUG: vor 2bp post\n");
 					moldyn->func2b_post(moldyn,
 					                    &(itom[i]),
 					                    jtom,bc_ij);
+printf("DEBUG: nach 2bp post\n");
 				}
 
 			}
 		}
-printf("debug atom %d: %.15f %.15f %.15f\n",i,itom[i].r.x,itom[i].v.x,itom[i].f.x);
 	}
 
 	return 0;
@@ -1111,19 +1111,14 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	int num;
 	double s_r;
 	double arg;
-	double scale;
 
 	params=moldyn->pot2b_params;
 	num=aj->bnum;
 	exchange=&(params->exchange);
 
 	/* clear 3bp and 2bp post run */
-	exchange->run3bp_ij=0;
-	exchange->run3bp_ji=0;
-	exchange->run3bp_jk=0;
-	exchange->run2bp_post_ij=0;
-	exchange->run2bp_post_ji=0;
-	exchange->run2bp_post_jk=0;
+	exchange->run3bp=0;
+	exchange->run2bp_post=0;
 	
 	/*
 	 * calc of 2bp contribution of V_ij and dV_ij/ji
@@ -1233,10 +1228,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	/* reset 3bp sums */
 	exchange->zeta_ij=0.0;
 	exchange->zeta_ji=0.0;
-	exchange->zeta_kl=0.0;
-	v3_zero(&(exchange->db_ij));
-	v3_zero(&(exchange->db_ji));
-	v3_zero(&(exchange->db_jk));
+	v3_zero(&(exchange->dzeta_ij));
+	v3_zero(&(exchange->dzeta_ji));
 
 	return 0;
 }
@@ -1245,16 +1238,27 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-	/* here we have to allow for the 3bp sums */
+	/*
+	 * here we have to allow for the 3bp sums
+	 *
+	 * that is:
+	 * - zeta_ij, dzeta_ij
+	 * - zeta_ji, dzeta_ji
+	 *
+	 * to compute the 3bp contribution to:
+	 * - Vij, dVij
+	 * - dVji
+	 *
+	 */
 
 	t_tersoff_mult_params *params;
 	t_tersoff_exchange *exchange;
 
-	t_3dvec force,temp,*db_ij,*dist_ij;
-	double db_ij_scale1,db_ij_scale2;
-	double b_ij;
+	t_3dvec force,temp;
+	t_3dvec *dist_ij;
+	double b,db,tmp;
 	double f_c,df_c,f_a,df_a;
-	double chi,n,n_betan;
+	double chi,ni,betaini,nj,betajnj;
 	double zeta;
 
 	params=moldyn->pot2b_params;
@@ -1264,44 +1268,53 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	if(!(exchange->run2bp_post))
 		return 0;
 
-	db_ij=&(exchange->db_ij);
 	f_c=exchange->f_c;
 	df_c=exchange->df_c;
 	f_a=exchange->f_a;
 	df_a=exchange->df_a;
-	n_betan=exchange->n_betan;
-	n=*(exchange->n);
+	betaini=exchange->betaini;
+	betajnj=exchange->betajnj;
+	ni=*(exchange->n_i);
+	nj=*(exchange->n_j);
 	chi=exchange->chi;
 	dist_ij=&(exchange->dist_ij);
-	zeta=exchange->zeta;
-
-	db_ij_scale2=pow(zeta,n-1.0);
-printf("DEBUG: %.15f %.15f\n",zeta,db_ij_scale2);
-	db_ij_scale1=db_ij_scale2*zeta;
-	db_ij_scale2*=n_betan;
-	db_ij_scale1=pow((1.0+n_betan*db_ij_scale1),-1.0/(2*n)-1);
-	b_ij=chi*db_ij_scale1*(1.0+n_betan*db_ij_scale1);
-	db_ij_scale1*=(-1.0*chi/(2*n));
-
-	/* db_ij part */
-	v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
-	v3_scale(db_ij,db_ij,f_a);
-
-	/* df_a part */
-	v3_scale(&temp,dist_ij,b_ij*df_a);
-
-	/* db_ij + df_a part */
-	v3_add(&force,&temp,db_ij);
+	
+	/* Vij and dVij */
+	zeta=exchange->zeta_ij;
+	tmp=betaini*pow(zeta,ni-1.0);		/* beta^n * zeta^n-1 */
+	b=(1+zeta*tmp);				/* 1 + beta^n * zeta^n */
+	db=chi*pow(b,-1.0/(2*ni)-1);		/* chi * (...)^(-1/2n - 1) */
+	b=db*b;					/* b_ij */
+	db*=-0.5*tmp;				/* db_ij */
+	v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+	v3_scale(&temp,dist_ij,df_a*b);
+	v3_add(&force,&force,&temp);
 	v3_scale(&force,&force,f_c);
-
-	/* df_c part */
-	v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
+	v3_scale(&temp,dist_ij,df_c*b*f_a);
+	v3_add(&force,&force,&temp);
 
 	/* add energy of 3bp sum */
-	moldyn->energy+=(0.5*f_c*b_ij*f_a);
+	moldyn->energy+=(0.5*f_c*b*f_a);
+
+	/* add force (sub, as F = - dVij) */
+	v3_sub(&(ai->f),&(ai->f),&force);
+
+	/* dVji */
+	zeta=exchange->zeta_ji;
+	tmp=betajnj*pow(zeta,nj-1.0);		/* beta^n * zeta^n-1 */
+	b=(1+zeta*tmp);				/* 1 + beta^n * zeta^n */
+	db=chi*pow(b,-1.0/(2*nj)-1);		/* chi * (...)^(-1/2n - 1) */
+	b=db*b;					/* b_ij */
+	db*=-0.5*tmp;				/* db_ij */
+	v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+	v3_scale(&temp,dist_ij,df_a*b);
+	v3_add(&force,&force,&temp);
+	v3_scale(&force,&force,f_c);
+	v3_scale(&temp,dist_ij,df_c*b*f_a);
+	v3_add(&force,&force,&temp);
 
-	/* add force of 3bp calculation (all three parts) */
-	v3_add(&(ai->f),&temp,&force);
+	/* add force (sub, as F = - dVji) */
+	v3_sub(&(ai->f),&(ai->f),&force);
 
 	return 0;
 }
@@ -1314,17 +1327,20 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	t_tersoff_exchange *exchange;
 	t_3dvec dist_ij,dist_ik,dist_jk;
 	t_3dvec temp1,temp2;
+	t_3dvec *dzeta;
 	double R,S,s_r;
+	double B,mu;
 	double d_ij,d_ik,d_jk;
-	double rxxryy,dxxdyy;
-	double f_c,df_c,f_a,df_a;
+	double rr,dd;
+	double f_c,df_c;
 	double f_c_ik,df_c_ik,arg;
+	double f_c_jk;
 	double n,c,d,h;
 	double c2,d2,c2d2;
 	double cos_theta,d_costheta1,d_costheta2;
 	double h_cos,d2_h_cos2;
-	double frac;
-	double g;
+	double frac,g,zeta,chi;
+	double tmp;
 	int num;
 
 	params=moldyn->pot3b_params;
@@ -1400,12 +1416,12 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		c2d2=exchange->ci2di2;
 
 		/* cosine of theta_ijk by scalaproduct */
-		rijrik=v3_scalar_product(&dist_ij,&dist_ik);
-		dijdik=d_ij*d_ik;
-		cos_theta=rijrik/dijdik;
+		rr=v3_scalar_product(&dist_ij,&dist_ik);
+		dd=d_ij*d_ik;
+		cos_theta=rr/dd;
 
 		/* d_costheta */
-		tmp=1.0/dijdik;
+		tmp=1.0/dd;
 		d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
 		d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
 
@@ -1424,6 +1440,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
 
 		/* f_c_ik & df_c_ik + {d,}zeta contribution */
+		dzeta=&(exchange->dzeta_ij);
 		if(d_ik<R) {
 			/* {d,}f_c_ik */
 			// => f_c_ik=1.0;
@@ -1433,7 +1450,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			exchange->zeta_ij+=g;
 
 			/* dzeta_ij */
-			v3_add(dzeta_ij,dzeta_ij,&temp1);
+			v3_add(dzeta,dzeta,&temp1);
 		}
 		else {
 			/* {d,}f_c_ik */
@@ -1448,7 +1465,8 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 			/* dzeta_ij */
 			v3_scale(&temp1,&temp1,f_c_ik);
 			v3_scale(&temp2,&dist_ik,g*df_c_ik);
-			v3_add(dzeta_ij,&temp2,&temp1);
+			v3_add(&temp1,&temp1,&temp2);
+			v3_add(dzeta,dzeta,&temp1);
 		}
 	}
 
@@ -1464,10 +1482,16 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	if(num==ak->bnum) {
 		R=params->R[num];
 		S=params->S[num];
+		B=params->B[num];
+		mu=params->mu[num];
+		chi=1.0;
 	}
 	else {
 		R=params->Rmixed;
 		S=params->Smixed;
+		B=params->Bmixed;
+		mu=params->mu_m;
+		chi=params->chi;
 	}
 
 	/* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
@@ -1483,9 +1507,9 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		c2d2=exchange->cj2dj2;
 
 		/* cosine of theta_jik by scalaproduct */
-		rxxryy=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
-		dxxdyy=d_ij*d_jk;
-		cos_theta=rxxryy/dxxdyy;
+		rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+		dd=d_ij*d_jk;
+		cos_theta=rr/dd;
 
 		/* d_costheta */
 		d_costheta1=1.0/(d_jk*d_ij);
@@ -1505,32 +1529,17 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		v3_add(&temp1,&temp1,&temp2);
 		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
 
-		/* dV_jk stuff | add force contribution on atom i immediately */
-		if(exchange->d_ij_between_rs) {
-			tmp=pow(f_c_ij*g,(n_j-1.0)); /* zeta_jk ^ n_j-1 */
-			v3_scale(&temp2,&temp1,f_c_ij)
-			v3_scale(&temp3,&dist_ij,df_c_ij);
-			v3_add(&temp3,&temp3,&temp2); /* dzeta_jk */
-		}
-		else {
-			/* f_c_ij = 1, df_c_ij = 0 */
-			tmp=pow(g,(n_j-1.0)); /* zeta_jk ^ n_j-1 */
-			tmp
-			/* dzeta_jk in temp1 */
-			/* HIER WEITER !!! */
-		}
-
 		/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+		dzeta=&(exchange->dzeta_ji);
 		if(d_jk<R) {
 			/* f_c_jk */
-			// f_c_jk=1.0; again, we do not set this!
+			f_c_jk=1.0;
 
 			/* zeta_ji */
 			exchange->zeta_ji+=g;
 
-
 			/* dzeta_ji */
-			v3_add(dzeta_ji,dzeta_ji,&temp1);
+			v3_add(dzeta,dzeta,&temp1);
 		}
 		else {
 			/* f_c_jk */
@@ -1543,8 +1552,25 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
 			/* dzeta_ij */
 			v3_scale(&temp1,&temp1,f_c_jk);
-			v3_add(dzeta_ji,dzeta_ji,&temp1);
+			v3_add(dzeta,dzeta,&temp1);
+		}
+
+		/* dV_jk stuff | add force contribution on atom i immediately */
+		if(exchange->d_ij_between_rs) {
+			zeta=f_c*g;
+			v3_scale(&temp1,&temp1,f_c);
+			v3_scale(&temp2,&dist_ij,df_c);
+			v3_add(&temp1,&temp1,&temp2);
+		}
+		else {
+			zeta=g;
+			// dzeta_jk is simply dg, which is temp1
 		}
+		/* betajnj * zeta_jk ^ nj-1 */
+		tmp=exchange->betajnj*pow(zeta,(n-1.0));
+		tmp=-chi/2.0*pow(1+tmp*zeta,-1.0/(2.0*n)-1)*tmp;
+		v3_scale(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk);
+		v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
 	}
 
 	return 0;
diff --git a/sic.c b/sic.c
index 8073559..d141782 100644
--- a/sic.c
+++ b/sic.c
@@ -96,7 +96,7 @@ int main(int argc,char **argv) {
 
 	/* set (initial) dimensions of simulation volume */
 	printf("[sic] setting dimensions\n");
-	set_dim(&md,5*LC_SI,5*LC_SI,5*LC_SI,TRUE);
+	set_dim(&md,2*LC_SI,2*LC_SI,2*LC_SI,TRUE);
 
 	/* set periodic boundary conditions in all directions */
 	printf("[sic] setting periodic boundary conditions\n");
@@ -107,7 +107,7 @@ int main(int argc,char **argv) {
 	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
 	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
 	               //ATOM_ATTR_2BP|ATOM_ATTR_HB,
-	               0,5,5,5);
+	               0,2,2,2);
 
 	/* setting a nearest neighbour distance for the moldyn checks */
 	set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */