X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=potentials%2Ftersoff.c;h=4ca7141d4252c0aade8386eb4bb3319e1712f594;hb=0d2f9a11030dff3583104dac5d4dcb9f040a1327;hp=531d292131121ad5acb7b1ce2a4a0c551199b34a;hpb=0b96eb313c9bfec6272b1f8de0d99c4ce26d1686;p=physik%2Fposic.git

diff --git a/potentials/tersoff.c b/potentials/tersoff.c
index 531d292..4ca7141 100644
--- a/potentials/tersoff.c
+++ b/potentials/tersoff.c
@@ -20,20 +20,95 @@
 #include "tersoff.h"
 
 /* create mixed terms from parameters and set them */
-int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+int tersoff_mult_set_params(t_moldyn *moldyn,int element1,int element2) {
 
-	printf("[moldyn] tersoff parameter completion\n");
+	t_tersoff_mult_params *p;
+
+	// set cutoff before parameters (actually only necessary for some pots)
+	if(moldyn->cutoff==0.0) {
+		printf("[tersoff] WARNING: no cutoff!\n");
+		return -1;
+	}
+
+	/* alloc mem for potential parameters */
+	 moldyn->pot_params=malloc(sizeof(t_tersoff_mult_params));
+	 if(moldyn->pot_params==NULL) {
+	 	perror("[tersoff] pot params alloc");
+		return -1;
+	}
+
+	/* these are now tersoff parameters */
+	p=moldyn->pot_params;
+
+	// only 1 combination by now :p
+	switch(element1) {
+		case SI:
+			/* type: silicon */
+			p->S[0]=TM_S_SI;
+			p->R[0]=TM_R_SI;
+			p->A[0]=TM_A_SI;
+			p->B[0]=TM_B_SI;
+			p->lambda[0]=TM_LAMBDA_SI;
+			p->mu[0]=TM_MU_SI;
+			p->beta[0]=TM_BETA_SI;
+			p->n[0]=TM_N_SI;
+			p->c[0]=TM_C_SI;
+			p->d[0]=TM_D_SI;
+			p->h[0]=TM_H_SI;
+			switch(element2) {
+				case C:
+					p->chi=TM_CHI_SIC;
+					break;
+				default:
+					printf("[tersoff] WARNING: element2\n");
+					return -1;
+			}
+			break;
+		default:
+			printf("[tersoff] WARNING: element1\n");
+			return -1;
+	}
+
+	switch(element2) {
+		case C:
+			/* type carbon */
+			p->S[1]=TM_S_C;
+			p->R[1]=TM_R_C;
+			p->A[1]=TM_A_C;
+			p->B[1]=TM_B_C;
+			p->lambda[1]=TM_LAMBDA_C;
+			p->mu[1]=TM_MU_C;
+			p->beta[1]=TM_BETA_C;
+			p->n[1]=TM_N_C;
+			p->c[1]=TM_C_C;
+			p->d[1]=TM_D_C;
+			p->h[1]=TM_H_C;
+			break;
+		default:
+			printf("[tersoff] WARNING: element2\n");
+			return -1;
+	}
+
+	printf("[tersoff] parameter completion\n");
 	p->S2[0]=p->S[0]*p->S[0];
 	p->S2[1]=p->S[1]*p->S[1];
-	p->Smixed=sqrt(p->S[0]*p->S[1]);
-	p->S2mixed=p->Smixed*p->Smixed;
+	p->S2mixed=p->S[0]*p->S[1];
+	p->Smixed=sqrt(p->S2mixed);
 	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]);
-
-	printf("[moldyn] tersoff mult parameter info:\n");
+	p->betaini[0]=pow(p->beta[0],p->n[0]);
+	p->betaini[1]=pow(p->beta[1],p->n[1]);
+	p->ci2[0]=p->c[0]*p->c[0];
+	p->ci2[1]=p->c[1]*p->c[1];
+	p->di2[0]=p->d[0]*p->d[0];
+	p->di2[1]=p->d[1]*p->d[1];
+	p->ci2di2[0]=p->ci2[0]/p->di2[0];
+	p->ci2di2[1]=p->ci2[1]/p->di2[1];
+
+	printf("[tersoff] mult parameter info:\n");
 	printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
 	printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
 	printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
@@ -51,36 +126,6 @@ int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
 	return 0;
 }
 
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
-
-	int brand;
-	t_tersoff_mult_params *params;
-	t_tersoff_exchange *exchange;
-	
-	brand=ai->brand;
-	params=moldyn->pot_params;
-	exchange=&(params->exchange);
-
-	/*
-	 * simple: point constant parameters only depending on atom i to
-	 *         their right values
-	 */
-
-	exchange->beta_i=&(params->beta[brand]);
-	exchange->n_i=&(params->n[brand]);
-	exchange->c_i=&(params->c[brand]);
-	exchange->d_i=&(params->d[brand]);
-	exchange->h_i=&(params->h[brand]);
-
-	exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
-	exchange->ci2=params->c[brand]*params->c[brand];
-	exchange->di2=params->d[brand]*params->d[brand];
-	exchange->ci2di2=exchange->ci2/exchange->di2;
-
-	return 0;
-}
-	
 /* tersoff 2 body part */
 int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
@@ -93,6 +138,10 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	int brand;
 	double s_r;
 	double arg;
+	double energy;
+
+	printf("WARNING! - tersoff_mult_2bp is obsolete.\n");
+	printf("WARNING! - repulsive part handled in 3bp/j2 routine.\n");
 
 	/* use newtons third law */
 	if(ai<aj) return 0;
@@ -153,7 +202,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
 	/* add forces */
 	v3_add(&(ai->f),&(ai->f),&force);
-	v3_sub(&(aj->f),&(aj->f),&force);
+	v3_scale(&force,&force,-1.0); // reason: dri rij = - drj rij
+	v3_add(&(aj->f),&(aj->f),&force);
 
 #ifdef DEBUG
 	if((ai==&(moldyn->atom[0]))|(aj==&(moldyn->atom[0]))) {
@@ -167,17 +217,13 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 #endif
 
 	/* virial */
-	//virial_calc(ai,&force,&dist_ij);
-	//virial_calc(aj,&force,&dist_ij);
-	//ai->virial.xx-=force.x*dist_ij.x;
-	//ai->virial.yy-=force.y*dist_ij.y;
-	//ai->virial.zz-=force.z*dist_ij.z;
-	//ai->virial.xy-=force.x*dist_ij.y;
-	//ai->virial.xz-=force.x*dist_ij.z;
-	//ai->virial.yz-=force.y*dist_ij.z;
+	virial_calc(ai,&force,&dist_ij);
 
 	/* energy 2bp contribution */
-	moldyn->energy+=f_r*f_c;
+	energy=f_r*f_c;
+	moldyn->energy+=energy;
+	ai->e+=0.5*energy;
+	aj->e+=0.5*energy;
 
 	return 0;
 }
@@ -296,10 +342,10 @@ int tersoff_mult_3bp_k1(t_moldyn *moldyn,
 	cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
 
 	/* g_ijk */
-	h_cos=*(exchange->h_i)-cos_theta;
-	d2_h_cos2=exchange->di2+(h_cos*h_cos);
-	frac=exchange->ci2/d2_h_cos2;
-	g=1.0+exchange->ci2di2-frac;
+	h_cos=params->h[brand]-cos_theta;
+	d2_h_cos2=params->di2[brand]+(h_cos*h_cos);
+	frac=params->ci2[brand]/d2_h_cos2;
+	g=1.0+params->ci2di2[brand]-frac;
 	dg=-2.0*frac*h_cos/d2_h_cos2;
 
 	/* zeta sum += f_c_ik * g_ijk */
@@ -316,6 +362,11 @@ int tersoff_mult_3bp_k1(t_moldyn *moldyn,
 		exchange->zeta_ij+=f_c_ik*g;
 	}
 
+#ifdef DEBUG
+	if(ai==&(moldyn->atom[DATOM]))
+		printf("zeta_ij: %f %f %f %f\n",f_c_ik*g,f_c_ik,g,d_ik);
+#endif
+
 	/* store even more data for second k loop */
 	exchange->g[kcount]=g;
 	exchange->dg[kcount]=dg;
@@ -336,28 +387,36 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	t_tersoff_exchange *exchange;
 	t_3dvec force;
 	double f_a,df_a,b,db,f_c,df_c;
+	double f_r,df_r;
+	double scale;
 	double mu,B,chi;
+	double lambda,A;
 	double d_ij;
 	unsigned char brand;
 	double ni,tmp;
 	double S,R,s_r,arg;
+	double energy;
 
 	params=moldyn->pot_params;
 	exchange=&(params->exchange);
 
-	brand=aj->brand;
-	if(brand==ai->brand) {
+	brand=ai->brand;
+	if(brand==aj->brand) {
 		S=params->S[brand];
 		R=params->R[brand];
 		B=params->B[brand];
+		A=params->A[brand];
 		mu=params->mu[brand];
+		lambda=params->lambda[brand];
 		chi=1.0;
 	}
 	else {
 		S=params->Smixed;
 		R=params->Rmixed;
 		B=params->Bmixed;
+		A=params->Amixed;
 		mu=params->mu_m;
+		lambda=params->lambda_m;
 		chi=params->chi;
 	}
 
@@ -379,46 +438,55 @@ int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 	f_a=-B*exp(-mu*d_ij);
 	df_a=mu*f_a/d_ij;
 
+	/* f_r, df_r */
+	f_r=A*exp(-lambda*d_ij);
+	df_r=lambda*f_r/d_ij;
+
 	/* b, db */
 	if(exchange->zeta_ij==0.0) {
 		b=chi;
 		db=0.0;
 	}
 	else {
-		ni=*(exchange->n_i);
-		tmp=exchange->betaini*pow(exchange->zeta_ij,ni-1.0);
+		ni=params->n[brand];
+		tmp=params->betaini[brand]*pow(exchange->zeta_ij,ni-1.0);
 		b=(1.0+exchange->zeta_ij*tmp);
-		db=chi*pow(b,-1.0/(2*ni)-1.0);
+		db=chi*pow(b,-1.0/(2.0*ni)-1.0);
 		b=db*b;
 		db*=-0.5*tmp;
 	}
 
 	/* force contribution */
-	v3_scale(&force,&(exchange->dist_ij),df_a*f_c+f_a*df_c);
-	v3_scale(&force,&force,-0.5*b);
+	scale=-0.5*(f_c*(df_r+b*df_a)+df_c*(f_r+b*df_a));
+	v3_scale(&force,&(exchange->dist_ij),scale);
 	v3_add(&(ai->f),&(ai->f),&force);
-	v3_sub(&(aj->f),&(aj->f),&force);
+	v3_scale(&force,&force,-1.0); // dri rij = - drj rij
+	v3_add(&(aj->f),&(aj->f),&force);
 
 #ifdef DEBUG
-	if((ai==&(moldyn->atom[0]))|(aj==&(moldyn->atom[0]))) {
+	if((ai==&(moldyn->atom[DATOM]))|(aj==&(moldyn->atom[DATOM]))) {
 		printf("force 3bp (j2): [%d %d sum]\n",ai->tag,aj->tag);
 		printf("adding %f %f %f\n",force.x,force.y,force.z);
-		if(ai==&(moldyn->atom[0]))
+		if(ai==&(moldyn->atom[DATOM]))
 			printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
-		if(aj==&(moldyn->atom[0]))
+		if(aj==&(moldyn->atom[DATOM]))
 			printf("total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+		printf("energy: %f = %f %f %f %f\n",0.5*f_c*(b*f_a+f_r),
+		                                    f_c,b,f_a,f_r);
+		printf("        %f %f %f\n",exchange->zeta_ij,.0,.0);
 	}
 #endif
 
 	/* virial */
-	//virial_calc(ai,&force,&(exchange->dist_ij));
-	//virial_calc(aj,&force,&(exchange->dist_ij));
+	virial_calc(ai,&force,&(exchange->dist_ij));
 
 	/* dzeta prefactor = - 0.5 f_c f_a db */
 	exchange->pre_dzeta=-0.5*f_a*f_c*db;
 
 	/* energy contribution */
-	moldyn->energy+=0.5*f_c*b*f_a;
+	energy=0.5*f_c*(b*f_a+f_r);
+	moldyn->energy+=energy;
+	ai->e+=energy;
 
 	/* reset k counter for second k loop */
 	exchange->kcount=0;
@@ -441,7 +509,7 @@ int tersoff_mult_3bp_k2(t_moldyn *moldyn,
 	double pre_dzeta;
 	double f_c_ik,df_c_ik;
 	double dijdik_inv,fcdg,dfcg;
-	t_3dvec dcosdri,dcosdrj,dcosdrk;
+	t_3dvec dcosdrj,dcosdrk;
 	t_3dvec force,tmp;
 
 	params=moldyn->pot_params;
@@ -495,52 +563,36 @@ int tersoff_mult_3bp_k2(t_moldyn *moldyn,
 	v3_scale(&dcosdrk,&dist_ij,dijdik_inv);
 	v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
 	v3_add(&dcosdrk,&dcosdrk,&tmp);
-	v3_add(&dcosdri,&dcosdrj,&dcosdrk);
-	v3_scale(&dcosdri,&dcosdri,-1.0);
 
 	/* f_c_ik * dg, df_c_ik * g */
 	fcdg=f_c_ik*dg;
 	dfcg=df_c_ik*g;
 
-	/* derivative wrt i */
-	v3_scale(&force,&dist_ik,dfcg);
-	v3_scale(&tmp,&dcosdri,fcdg);
-	v3_add(&force,&force,&tmp);
-	v3_scale(&force,&force,pre_dzeta);
-
-	/* force contribution */
-	v3_add(&(ai->f),&(ai->f),&force);
-	
-#ifdef DEBUG
-	if(ai==&(moldyn->atom[0])) {
-		printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
-		printf("adding %f %f %f\n",force.x,force.y,force.z);
-		printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
-	}
-#endif
-
-	/* virial */
-	//virial_calc(ai,&force,&dist_ij);
-
-	/* derivatice wrt j */
+	/* derivative wrt j */
 	v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
 
 	/* force contribution */
 	v3_add(&(aj->f),&(aj->f),&force);
 
 #ifdef DEBUG
-	if(aj==&(moldyn->atom[0])) {
+	if(aj==&(moldyn->atom[DATOM])) {
 		printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
-		printf("adding %f %f %f\n",force.x,force.y,force.z);
-		printf("total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+		printf("  adding %f %f %f\n",force.x,force.y,force.z);
+		printf("  total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+		printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+		printf("    d ij ik = %f %f\n",d_ij,d_ik);
 	}
 #endif
 
 	/* virial */
-	//virial_calc(aj,&force,&dist_ij);
+	virial_calc(ai,&force,&dist_ij);
+
+	/* force contribution to atom i */
+	v3_scale(&force,&force,-1.0);
+	v3_add(&(ai->f),&(ai->f),&force);
 
 	/* derivative wrt k */
-	v3_scale(&force,&dist_ik,dfcg);
+	v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik
 	v3_scale(&tmp,&dcosdrk,fcdg);
 	v3_add(&force,&force,&tmp);
 	v3_scale(&force,&force,pre_dzeta);
@@ -549,19 +601,52 @@ int tersoff_mult_3bp_k2(t_moldyn *moldyn,
 	v3_add(&(ak->f),&(ak->f),&force);
 
 #ifdef DEBUG
-	if(ak==&(moldyn->atom[0])) {
+	if(ak==&(moldyn->atom[DATOM])) {
 		printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
-		printf("adding %f %f %f\n",force.x,force.y,force.z);
-		printf("total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z);
+		printf("  adding %f %f %f\n",force.x,force.y,force.z);
+		printf("  total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z);
+		printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+		printf("    d ij ik = %f %f\n",d_ij,d_ik);
 	}
 #endif
 
 	/* virial */
-	virial_calc(ak,&force,&dist_ik);
+	virial_calc(ai,&force,&dist_ik);
+
+	/* force contribution to atom i */
+	v3_scale(&force,&force,-1.0);
+	v3_add(&(ai->f),&(ai->f),&force);
 	
 	/* increase k counter */
-	exchange->kcount++;	
+	exchange->kcount++;
 
 	return 0;
 
 }
+
+int tersoff_mult_check_2b_bond(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+	t_tersoff_mult_params *params;
+	t_3dvec dist;
+	double d;
+	u8 brand;
+
+	v3_sub(&dist,&(aj->r),&(ai->r));
+	if(bc) check_per_bound(moldyn,&dist);
+	d=v3_absolute_square(&dist);
+
+	params=moldyn->pot_params;
+	brand=ai->brand;
+
+	if(brand==aj->brand) {
+		if(d<=params->S2[brand])
+			return TRUE;
+	}
+	else {
+		if(d<=params->S2mixed)
+			return TRUE;
+	}
+
+	return FALSE;
+}
+