From: hackbard <hackbard>
Date: Sun, 10 Dec 2006 04:06:24 +0000 (+0000)
Subject: nearly finished 3bp tersoff routine (2bp post needs to be done after
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=8bb8358a7dca3d77f5c504f9da57002d2cf30303;p=physik%2Fposic.git

nearly finished 3bp tersoff routine (2bp post needs to be done after
that!)
---

diff --git a/moldyn.c b/moldyn.c
index 880e56c..8d1cb23 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1084,17 +1084,16 @@ int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
 	 *         their right values
 	 */
 
-	exchange->beta=&(params->beta[num]);
-	exchange->n=&(params->n[num]);
-	exchange->c=&(params->c[num]);
-	exchange->d=&(params->d[num]);
-	exchange->h=&(params->h[num]);
-
-	exchange->betan=pow(*(exchange->beta),*(exchange->n));
-	exchange->n_betan=*(exchange->n)*exchange->betan;
-	exchange->c2=params->c[num]*params->c[num];
-	exchange->d2=params->d[num]*params->d[num];
-	exchange->c2d2=exchange->c2/exchange->d2;
+	exchange->beta_i=&(params->beta[num]);
+	exchange->n_i=&(params->n[num]);
+	exchange->c_i=&(params->c[num]);
+	exchange->d_i=&(params->d[num]);
+	exchange->h_i=&(params->h[num]);
+
+	exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
+	exchange->ci2=params->c[num]*params->c[num];
+	exchange->di2=params->d[num]*params->d[num];
+	exchange->ci2di2=exchange->ci2/exchange->di2;
 
 	return 0;
 }
@@ -1115,22 +1114,33 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	double scale;
 
 	params=moldyn->pot2b_params;
-	num=ai->bnum;
+	num=aj->bnum;
 	exchange=&(params->exchange);
 
-	exchange->run3bp=0;
-	exchange->run2bp_post=0;
+	/* 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;
 	
 	/*
-	 * we need: f_c, df_c, f_r, df_r
+	 * calc of 2bp contribution of V_ij and dV_ij/ji
+	 *
+	 * for Vij and dV_ij we need:
+	 * - f_c_ij, df_c_ij
+	 * - f_r_ij, df_r_ij
+	 *
+	 * for dV_ji we need:
+	 * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+	 * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
 	 *
-	 * therefore we need: R, S, A, lambda
 	 */
 
+	/* dist_ij, d_ij */
 	v3_sub(&dist_ij,&(aj->r),&(ai->r));
-
 	if(bc) check_per_bound(moldyn,&dist_ij);
-
 	d_ij=v3_norm(&dist_ij);
 
 	/* save for use in 3bp */
@@ -1138,14 +1148,14 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	exchange->dist_ij=dist_ij;
 
 	/* constants */
-	if(num==aj->bnum) {
+	if(num==ai->bnum) {
 		S=params->S[num];
 		R=params->R[num];
 		A=params->A[num];
 		B=params->B[num];
 		lambda=params->lambda[num];
 		mu=params->mu[num];
-		params->exchange.chi=1.0;
+		exchange->chi=1.0;
 	}
 	else {
 		S=params->Smixed;
@@ -1156,34 +1166,60 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 		mu=params->mu_m;
 		params->exchange.chi=params->chi;
 	}
+
+	/* if d_ij > S => no force & potential energy contribution */
 	if(d_ij>S)
 		return 0;
 
+	/* more constants */
+	exchange->beta_j=&(params->beta[num]);
+	exchange->n_j=&(params->n[num]);
+	exchange->c_j=&(params->c[num]);
+	exchange->d_j=&(params->d[num]);
+	exchange->h_j=&(params->h[num]);
+	if(num==ai->bnum) {
+		exchange->betajnj=exchange->betaini;
+		exchange->cj2=exchange->ci2;
+		exchange->dj2=exchange->di2;
+		exchange->cj2dj2=exchange->ci2di2;
+	}
+	else {
+		exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
+		exchange->cj2=params->c[num]*params->c[num];
+		exchange->dj2=params->d[num]*params->d[num];
+		exchange->cj2dj2=exchange->cj2/exchange->dj2;
+	}
+
+	/* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
 	f_r=A*exp(-lambda*d_ij);
 	df_r=-lambda*f_r/d_ij;
 
-	/* f_a, df_a calc + save for later use */
+	/* f_a, df_a calc (again, same for ij and ji) | save for later use! */
 	exchange->f_a=-B*exp(-mu*d_ij);
 	exchange->df_a=-mu*exchange->f_a/d_ij;
 
+	/* f_c, df_c calc (again, same for ij and ji) */
 	if(d_ij<R) {
 		/* f_c = 1, df_c = 0 */
 		f_c=1.0;
 		df_c=0.0;
-		v3_scale(&force,&dist_ij,df_r);
+		/* two body contribution (ij, ji) */
+		v3_scale(&force,&dist_ij,-df_r);
 	}
 	else {
 		s_r=S-R;
 		arg=M_PI*(d_ij-R)/s_r;
 		f_c=0.5+0.5*cos(arg);
 		df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
-		scale=df_c*f_r+df_r*f_c;
-		v3_scale(&force,&dist_ij,scale);
+		/* two body contribution (ij, ji) */
+		v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
 	}
 
-	/* add forces */
+	/* add forces of 2bp (ij, ji) contribution
+	 * dVij = dVji and we sum up both: no 1/2) */
 	v3_add(&(ai->f),&(ai->f),&force);
-	/* energy is 0.5 f_r f_c ... */
+
+	/* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
 	moldyn->energy+=(0.5*f_r*f_c);
 
 	/* save for use in 3bp */
@@ -1195,8 +1231,12 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	exchange->run2bp_post=1;
 
 	/* reset 3bp sums */
-	exchange->zeta=0.0;
+	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));
 
 	return 0;
 }
@@ -1272,11 +1312,11 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 
 	t_tersoff_mult_params *params;
 	t_tersoff_exchange *exchange;
-	t_3dvec dist_ij,dist_ik;
-	t_3dvec temp,force;
+	t_3dvec dist_ij,dist_ik,dist_jk;
+	t_3dvec temp1,temp2;
 	double R,S,s_r;
-	double d_ij,d_ik;
-	double rijrik,dijdik;
+	double d_ij,d_ik,d_jk;
+	double rxxryy,dxxdyy;
 	double f_c,df_c,f_a,df_a;
 	double f_c_ik,df_c_ik,arg;
 	double n,c,d,h;
@@ -1288,43 +1328,56 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 	int num;
 
 	params=moldyn->pot3b_params;
-	num=ai->bnum;
 	exchange=&(params->exchange);
 
 	if(!(exchange->run3bp))
 		return 0;
 
 	/*
-	 * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+	 * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+	 * 2bp contribution of dV_jk
+	 *
+	 * for Vij and dV_ij we still need:
+	 * - b_ij, db_ij (zeta_ij)
+	 *   - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
+	 *
+	 * for dV_ji we still need:
+	 * - b_ji, db_ji (zeta_ji)
+	 *   - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+	 *
+	 * for dV_jk we need:
+	 * - f_c_jk
+	 * - f_a_jk
+	 * - db_jk (zeta_jk)
+	 *   - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
 	 *
-	 * we got f_c, df_c, f_a, df_a from 2bp calculation
 	 */
 
-	d_ij=exchange->d_ij;
-	dist_ij=exchange->dist_ij;
+	/*
+	 * get exchange data 
+	 */
 
-	f_a=params->exchange.f_a;
-	df_a=params->exchange.df_a;
+	/* dist_ij, d_ij - this is < S_ij ! */
+	dist_ij=exchange->dist_ij;
+	d_ij=exchange->d_ij;
 
+	/* f_c_ij, df_c_ij (same for ji) */
 	f_c=exchange->f_c;
 	df_c=exchange->df_c;
-	
-	/* d_ij is <= S, as we didn't return so far! */
 
 	/*
-	 * calc of b_ij (scalar) and db_ij (vector)
-	 *
-	 * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
-	 *
-	 * - for db_ij: d_costheta, cos_theta, f_c_ik, df_c_ik, w_ik
-	 *
+	 * calculate unknown values now ...
 	 */
 
+	/* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+
+	/* dist_ik, d_ik */
 	v3_sub(&dist_ik,&(ak->r),&(ai->r));
 	if(bc) check_per_bound(moldyn,&dist_ik);
 	d_ik=v3_norm(&dist_ik);
 
-	/* constants */
+	/* ik constants */
+	num=ai->bnum;
 	if(num==ak->bnum) {
 		R=params->R[num];
 		S=params->S[num];
@@ -1334,84 +1387,166 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 		S=params->Smixed;
 	}
 
-	/* there is no contribution if f_c_ik = 0 */
-	if(d_ik>S)
-		return 0;
-
-	/* get exchange data */
-	n=*(exchange->n);
-	c=*(exchange->c);
-	d=*(exchange->d);
-	h=*(exchange->h);
-	c2=exchange->c2;
-	d2=exchange->d2;
-	c2d2=exchange->c2d2;
-
-	/* cosine of theta by scalaproduct */
-	rijrik=v3_scalar_product(&dist_ij,&dist_ik);
-	dijdik=d_ij*d_ik;
-	cos_theta=rijrik/dijdik;
-
-	/* hack - cos theta machine accuracy problems! */
-	if(cos_theta>1.0||cos_theta<-1.0) {
-		printf("THETA CORRECTION\n");
-		moldyn->debug++;
-		if(fabs(cos_theta)>1.0+ACCEPTABLE_ERROR)
-			printf("[moldyn] WARNING: cos theta failure!\n");
-		if(cos_theta<0) {
-			cos_theta=-1.0;
+	/* zeta_ij/dzeta_ij contribution only for d_ik < S */
+	if(d_ik<S) {
+
+		/* get constants_i from exchange data */
+		n=*(exchange->n_i);
+		c=*(exchange->c_i);
+		d=*(exchange->d_i);
+		h=*(exchange->h_i);
+		c2=exchange->ci2;
+		d2=exchange->di2;
+		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;
+
+		/* d_costheta */
+		tmp=1.0/dijdik;
+		d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
+		d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+
+		/* some usefull values */
+		h_cos=(h-cos_theta);
+		d2_h_cos2=d2+(h_cos*h_cos);
+		frac=c2/(d2_h_cos2);
+
+		/* g(cos_theta) */
+		g=1.0+c2d2-frac;
+
+		/* d_costheta_ij and dg(cos_theta) - needed in any case! */
+		v3_scale(&temp1,&dist_ij,d_costheta1);
+		v3_scale(&temp2,&dist_ik,d_costheta2);
+		v3_add(&temp1,&temp1,&temp2);
+		v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+		/* f_c_ik & df_c_ik + {d,}zeta contribution */
+		if(d_ik<R) {
+			/* {d,}f_c_ik */
+			// => f_c_ik=1.0;
+			// => df_c_ik=0.0; of course we do not set this!
+
+			/* zeta_ij */
+			exchange->zeta_ij+=g;
+
+			/* dzeta_ij */
+			v3_add(dzeta_ij,dzeta_ij,&temp1);
 		}
 		else {
-			cos_theta=1.0;
+			/* {d,}f_c_ik */
+			s_r=S-R;
+			arg=M_PI*(d_ik-R)/s_r;
+			f_c_ik=0.5+0.5*cos(arg);
+			df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
+
+			/* zeta_ij */
+			exchange->zeta_ij+=f_c_ik*g;
+
+			/* dzeta_ij */
+			v3_scale(&temp1,&temp1,f_c_ik);
+			v3_scale(&temp2,&dist_ik,g*df_c_ik);
+			v3_add(dzeta_ij,&temp2,&temp1);
 		}
 	}
 
-	d_costheta1=dijdik-rijrik*d_ik/d_ij;
-	d_costheta2=dijdik-rijrik*d_ij/d_ik;
+	/* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+
+	/* dist_jk, d_jk */
+	v3_sub(&dist_jk,&(ak->r),&(aj->r));
+	if(bc) check_per_bound(moldyn,&dist_jk);
+	d_jk=v3_norm(&dist_jk);
 
-	h_cos=(h-cos_theta);
-	d2_h_cos2=d2+(h_cos*h_cos);
+	/* jk constants */
+	num=aj->bnum;
+	if(num==ak->bnum) {
+		R=params->R[num];
+		S=params->S[num];
+	}
+	else {
+		R=params->Rmixed;
+		S=params->Smixed;
+	}
 
-	frac=c2/(d2_h_cos2);
-	g=1.0+c2d2-frac;
+	/* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+	if(d_jk<S) {
+
+		/* constants_j from exchange data */
+		n=*(exchange->n_j);
+		c=*(exchange->c_j);
+		d=*(exchange->d_j);
+		h=*(exchange->h_j);
+		c2=exchange->cj2;
+		d2=exchange->dj2;
+		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;
+
+		/* d_costheta */
+		d_costheta1=1.0/(d_jk*d_ij);
+		d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+
+		/* some usefull values */
+		h_cos=(h-cos_theta);
+		d2_h_cos2=d2+(h_cos*h_cos);
+		frac=c2/(d2_h_cos2);
+
+		/* g(cos_theta) */
+		g=1.0+c2d2-frac;
+
+		/* d_costheta_ij and dg(cos_theta) - needed in any case! */
+		v3_scale(&temp1,&dist_jk,d_costheta1);
+		v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
+		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 !!! */
+		}
 
-	/* d_costheta contrib to db_ij (needed in all remaining cases) */
-	v3_scale(&temp,&dist_ij,d_costheta1);
-	v3_scale(&force,&dist_ik,d_costheta2);
-	v3_add(&force,&force,&temp);
-	v3_scale(&force,&force,-2.0*frac*h_cos/d2_h_cos2); /* f_c_ik missing */
+		/* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+		if(d_jk<R) {
+			/* f_c_jk */
+			// f_c_jk=1.0; again, we do not set this!
 
-	if(d_ik<R) {
-		/* f_c_ik = 1, df_c_ik = 0 */	
-		/* => only d_costheta contrib to db_ij */
-		// => do nothing ...
+			/* zeta_ji */
+			exchange->zeta_ji+=g;
 
-		/* zeta, f_c_ik = 1 */
-		exchange->zeta+=g;
-	}
-	else {
-		s_r=S-R;
-		arg=M_PI*(d_ik-R)/s_r;
-		f_c_ik=0.5+0.5*cos(arg);
-		df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
 
-		/* scale d_costheta contrib with f_c_ik */
-		v3_scale(&force,&force,f_c_ik);
+			/* dzeta_ji */
+			v3_add(dzeta_ji,dzeta_ji,&temp1);
+		}
+		else {
+			/* f_c_jk */
+			s_r=S-R;
+			arg=M_PI*(d_jk-R)/s_r;
+			f_c_jk=0.5+0.5*cos(arg);
 
-		/* df_c_ik contrib to db_ij */
-		v3_scale(&temp,&dist_ik,df_c_ik*g);
+			/* zeta_ji */
+			exchange->zeta_ji+=f_c_jk*g;
 
-		/* sum up both parts */
-		v3_add(&force,&force,&temp);
-		
-		/* zeta */
-		exchange->zeta+=f_c_ik*g;
+			/* dzeta_ij */
+			v3_scale(&temp1,&temp1,f_c_jk);
+			v3_add(dzeta_ji,dzeta_ji,&temp1);
+		}
 	}
-printf("%.30f\n",exchange->zeta);
-	
-	/* add to db_ij */
-	v3_add(&(exchange->db_ij),&(exchange->db_ij),&force);
-				
+
 	return 0;
 }
 
diff --git a/moldyn.h b/moldyn.h
index 32025fd..d62ec47 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -183,23 +183,34 @@ typedef struct s_tersoff_exchange {
 
 	double chi;
 
-	double *beta;
-	double *n;
-	double *c;
-	double *d;
-	double *h;
-
-	double c2;
-	double d2;
-	double c2d2;
-	double betan;
-	double n_betan;
+	double *beta_i;
+	double *beta_j;
+	double *n_i;
+	double *n_j;
+	double *c_i;
+	double *c_j;
+	double *d_i;
+	double *d_j;
+	double *h_i;
+	double *h_j;
+
+	double ci2;
+	double cj2;
+	double di2;
+	double dj2;
+	double ci2di2;
+	double cj2dj2;
+	double betaini;
+	double betajnj;
 
 	u8 run3bp;
 	u8 run2bp_post;
+	u8 d_ij_between_rs;
 
-	t_3dvec db_ij;
-	double zeta;
+	double zeta_ij;
+	double zeta_ji;
+	t_3dvec dzeta_ij;
+	t_3dvec dzeta_ji;
 } t_tersoff_exchange;
 
 /* tersoff multi (2!) potential parameters */