p->mu[0]=ALBE_MU_SI;
p->gamma[0]=ALBE_GAMMA_SI;
p->c[0]=ALBE_C_SI;
+ p->c2[0]=p->c[0]*p->c[0];
p->d[0]=ALBE_D_SI;
+ p->d2[0]=p->d[0]*p->d[0];
+ p->c2d2[0]=p->c2[0]/p->d2[0];
p->h[0]=ALBE_H_SI;
switch(element2) {
case C:
p->mu[1]=ALBE_MU_C;
p->gamma[1]=ALBE_GAMMA_C;
p->c[1]=ALBE_C_C;
+ p->c2[1]=p->c[1]*p->c[1];
p->d[1]=ALBE_D_C;
+ p->d2[1]=p->d[1]*p->d[1];
+ p->c2d2[1]=p->c2[1]/p->d2[1];
p->h[1]=ALBE_H_C;
/* mixed type: silicon carbide */
p->Smixed=ALBE_S_SIC;
p->mu_m=ALBE_MU_SIC;
p->gamma_m=ALBE_GAMMA_SIC;
p->c_mixed=ALBE_C_SIC;
+ p->c2_mixed=p->c_mixed*p->c_mixed;
p->d_mixed=ALBE_D_SIC;
+ p->d2_mixed=p->d_mixed*p->d_mixed;
+ p->c2d2_m=p->c2_mixed/p->d2_mixed;
p->h_mixed=ALBE_H_SIC;
break;
default:
printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
p->lambda_m);
printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
- printf(" gamma | %f | %f\n",p->gamma[0],p->gamma[1]);
- printf(" c | %f | %f\n",p->c[0],p->c[1]);
- printf(" d | %f | %f\n",p->d[0],p->d[1]);
- printf(" h | %f | %f\n",p->h[0],p->h[1]);
+ printf(" gamma | %f | %f | %f\n",p->gamma[0],p->gamma[1],p->gamma_m);
+ printf(" c | %f | %f | %f\n",p->c[0],p->c[1],p->c_mixed);
+ printf(" d | %f | %f | %f\n",p->d[0],p->d[1],p->d_mixed);
+ printf(" c2 | %f | %f | %f\n",p->c2[0],p->c2[1],p->c2_mixed);
+ printf(" d2 | %f | %f | %f\n",p->d2[0],p->d2[1],p->d2_mixed);
+ printf(" c2d2 | %f | %f | %f\n",p->c2d2[0],p->c2d2[1],p->c2d2_m);
+ printf(" h | %f | %f | %f\n",p->h[0],p->h[1],p->h_mixed);
return 0;
}
-/* albe 3 body potential function (first ij loop) */
-int albe_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+/* first i loop */
+int albe_mult_i0(t_moldyn *moldyn,t_atom *ai) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- unsigned char brand;
- double S2;
- t_3dvec dist_ij;
- double d_ij2,d_ij;
+
+ int i;
params=moldyn->pot_params;
exchange=&(params->exchange);
- /* reset zeta sum */
- exchange->zeta_ij=0.0;
+ /* zero exchange values */
+ memset(exchange->zeta,0,ALBE_MAXN*sizeof(double));
+ for(i=0;i<ALBE_MAXN;i++)
+ memset(exchange->dzeta[i],0,ALBE_MAXN*sizeof(t_3dvec));
+ exchange->jcnt=0;
+ exchange->j2cnt=0;
- /*
- * set ij depending values
- */
+ return 0;
+}
+/* first j loop within first i loop */
+int albe_mult_i0_j0(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_albe_mult_params *params;
+ t_albe_exchange *exchange;
+
+ double S2,S,R,d2,d,s_r,arg;
+ t_3dvec dist;
+ int j;
+ u8 brand;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* get j counter */
+ j=exchange->jcnt;
+
+ /* set ij depending values */
brand=ai->brand;
if(brand==aj->brand) {
S2=params->S2[brand];
}
/* dist_ij, d_ij2 */
- v3_sub(&dist_ij,&(aj->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ij);
- d_ij2=v3_absolute_square(&dist_ij);
+ v3_sub(&dist,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist);
+ exchange->dist[j]=dist;
+ d2=v3_absolute_square(&dist);
+ exchange->d2[j]=d2;
/* if d_ij2 > S2 => no force & potential energy contribution */
- if(d_ij2>S2) {
+ if(d2>S2) {
moldyn->run3bp=0;
+ exchange->skip[j]=1;
+ exchange->jcnt+=1;
return 0;
}
+ exchange->skip[j]=0;
+
+ /* more ij depending values */
+ if(brand==aj->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ /* albe needs i,(j/k) depending c,d,h and gamma values */
+ exchange->gamma_[j]=&(params->gamma[brand]);
+ exchange->c_[j]=&(params->c[brand]);
+ exchange->d_[j]=&(params->d[brand]);
+ exchange->h_[j]=&(params->h[brand]);
+ exchange->c2_[j]=&(params->c2[brand]);
+ exchange->d2_[j]=&(params->d2[brand]);
+ exchange->c2d2_[j]=&(params->c2d2[brand]);
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ /* albe needs i,(j/k) depending c,d,h and gamma values */
+ exchange->gamma_[j]=&(params->gamma_m);
+ exchange->c_[j]=&(params->c_mixed);
+ exchange->d_[j]=&(params->d_mixed);
+ exchange->h_[j]=&(params->h_mixed);
+ exchange->c2_[j]=&(params->c2_mixed);
+ exchange->d2_[j]=&(params->d2_mixed);
+ exchange->c2d2_[j]=&(params->c2d2_m);
+ }
/* d_ij */
- d_ij=sqrt(d_ij2);
+ d=sqrt(d2);
+ exchange->d[j]=d;
+
+ /* f_c, df_c */
+ if(d<R) {
+ exchange->f_c[j]=1.0;
+ exchange->df_c[j]=0.0;
+ }
+ else {
+ s_r=S-R;
+ arg=M_PI*(d-R)/s_r;
+ exchange->f_c[j]=0.5+0.5*cos(arg);
+ exchange->df_c[j]=0.5*sin(arg)*(M_PI/(s_r*d));
+ }
- /* store values */
- exchange->dist_ij=dist_ij;
- exchange->d_ij2=d_ij2;
- exchange->d_ij=d_ij;
+ /* reset k counter */
+ exchange->kcnt=0;
- /* reset k counter for first k loop */
- exchange->kcount=0;
-
return 0;
}
-/* albe 3 body potential function (first k loop) */
-int albe_mult_3bp_k1(t_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+/* first k loop within first j loop within first i loop */
+int albe_mult_i0_j0_k0(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- unsigned char brand;
- double R,S,S2;
- t_3dvec dist_ij,dist_ik;
- double d_ik2,d_ik,d_ij;
- double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg;
- double f_c_ik,df_c_ik;
- int kcount;
+
+ int j,k;
+ t_3dvec distj,distk;
+ double dj,dk,djdk_inv,cos_theta;
+ double gj,dgj,h_cos_j,d2_h_cos2_j,frac_j;
+ double gk,dgk,h_cos_k,d2_h_cos2_k,frac_k;
+ t_3dvec dcosdrj,dcosdrk,tmp;
+ t_3dvec *dzjj,*dzkk,*dzjk,*dzkj;
params=moldyn->pot_params;
exchange=&(params->exchange);
- kcount=exchange->kcount;
- if(kcount>ALBE_MAXN) {
- printf("FATAL: neighbours = %d\n",kcount);
- printf(" -> %d %d %d\n",ai->tag,aj->tag,ak->tag);
+ if(aj==ak) {
+ exchange->kcnt+=1;
+ return 0;
}
- /* ik constants */
- brand=ai->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- /* albe needs i,k depending c,d,h and gamma values */
- exchange->gamma_i=&(params->gamma[brand]);
- exchange->c_i=&(params->c[brand]);
- exchange->d_i=&(params->d[brand]);
- exchange->h_i=&(params->h[brand]);
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- /* albe needs i,k depending c,d,h and gamma values */
- exchange->gamma_i=&(params->gamma_m);
- exchange->c_i=&(params->c_mixed);
- exchange->d_i=&(params->d_mixed);
- exchange->h_i=&(params->h_mixed);
+ /* k<j & check whether to run k */
+ j=exchange->jcnt;
+ k=exchange->kcnt;
+ if(k>=ALBE_MAXN) {
+ printf("FATAL: too many neighbours! (%d)\n",k);
+ printf(" atom i:%d | j:%d | k:%d\n",ai->tag,aj->tag,ak->tag);
}
- exchange->ci2=*(exchange->c_i)**(exchange->c_i);
- exchange->di2=*(exchange->d_i)**(exchange->d_i);
- exchange->ci2di2=exchange->ci2/exchange->di2;
-
- /* dist_ik, d_ik2 */
- v3_sub(&dist_ik,&(ak->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik2=v3_absolute_square(&dist_ik);
-
- /* store data for second k loop */
- exchange->dist_ik[kcount]=dist_ik;
- exchange->d_ik2[kcount]=d_ik2;
-
- /* return if not within cutoff */
- if(d_ik2>S2) {
- exchange->kcount++;
+ if((k>=j)|(exchange->skip[k])) {
+ exchange->kcnt+=1;
return 0;
}
- /* d_ik */
- d_ik=sqrt(d_ik2);
-
- /* dist_ij, d_ij */
- dist_ij=exchange->dist_ij;
- d_ij=exchange->d_ij;
+ /* distances */
+ distj=exchange->dist[j];
+ distk=exchange->dist[k];
+ dj=exchange->d[j];
+ dk=exchange->d[k];
+ djdk_inv=1.0/(dj*dk);
/* cos theta */
- cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
-
- /* g_ijk */
- h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism
- d2_h_cos2=exchange->di2+(h_cos*h_cos);
- frac=exchange->ci2/d2_h_cos2;
- g=*(exchange->gamma_i)*(1.0+exchange->ci2di2-frac);
- dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f..
-
- /* zeta sum += f_c_ik * g_ijk */
- if(d_ik<=R) {
- exchange->zeta_ij+=g;
- f_c_ik=1.0;
- df_c_ik=0.0;
+ cos_theta=v3_scalar_product(&distj,&distk)*djdk_inv;
+
+ /* g(cos(theta)) ij and ik values */
+ h_cos_j=*(exchange->h_[j])+cos_theta; // + in albe formalism
+ d2_h_cos2_j=*exchange->d2_[j]+(h_cos_j*h_cos_j);
+ frac_j=*exchange->c2_[j]/d2_h_cos2_j;
+ gj=1.0+*exchange->c2d2_[j]-frac_j;
+ gj*=*(exchange->gamma_[j]);
+ dgj=*(exchange->gamma_[j])*2.0*frac_j*h_cos_j/d2_h_cos2_j; // + in albe
+ if(ak->brand==aj->brand) {
+ gk=gj;
+ dgk=dgj;
}
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));
- exchange->zeta_ij+=f_c_ik*g;
+ h_cos_k=*(exchange->h_[k])+cos_theta;
+ d2_h_cos2_k=*exchange->d2_[k]+(h_cos_k*h_cos_k);
+ frac_k=*exchange->c2_[k]/d2_h_cos2_k;
+ gk=1.0+*exchange->c2d2_[k]-frac_k;
+ gk*=*(exchange->gamma_[k]);
+ dgk=*(exchange->gamma_[k])*2.0*frac_k*h_cos_k/d2_h_cos2_k;
}
#ifdef DEBUG
exchange->df_c_ik[kcount]=df_c_ik;
/* increase k counter */
- exchange->kcount++;
+ exchange->kcnt+=1;
+
+ return 0;
+}
+
+/* first j loop within first i loop */
+int albe_mult_i0_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_albe_mult_params *params;
+ t_albe_exchange *exchange;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* increase j counter */
+ exchange->jcnt+=1;
return 0;
}
-int albe_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+/* second j loop within first i loop */
+int albe_mult_i0_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_albe_mult_params *params;
t_albe_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;
- double lambda,A;
- double d_ij,r0;
- unsigned char brand;
- double S,R,s_r,arg;
+
+ int j;
+ double d,f_a,df_a,f_r,df_r,f_c,df_c,b,db;
+ double A,B,mu,lambda,r0;
double energy;
+ t_3dvec *dist,force;
+ double scale;
+ u8 brand;
params=moldyn->pot_params;
exchange=&(params->exchange);
+ /* get j counter */
+ j=exchange->j2cnt;
+
+ /* skip if j not within cutoff */
+ if(exchange->skip[j]) {
+ moldyn->run3bp=0;
+ exchange->j2cnt+=1;
+ return 0;
+ }
+
+ /* distance */
+ d=exchange->d[j];
+ dist=&(exchange->dist[j]);
+ f_c=exchange->f_c[j];
+ df_c=exchange->df_c[j];
+
+ /* determine parameters to calculate fa, dfa, fr, dfr */
brand=aj->brand;
if(brand==ai->brand) {
- S=params->S[brand];
- R=params->R[brand];
B=params->B[brand];
A=params->A[brand];
r0=params->r0[brand];
lambda=params->lambda[brand];
}
else {
- S=params->Smixed;
- R=params->Rmixed;
B=params->Bmixed;
A=params->Amixed;
r0=params->r0_mixed;
lambda=params->lambda_m;
}
- d_ij=exchange->d_ij;
-
- /* f_c, df_c */
- if(d_ij<R) {
- f_c=1.0;
- df_c=0.0;
- }
- 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));
- }
-
/* f_a, df_a */
- f_a=-B*exp(-mu*(d_ij-r0));
- df_a=mu*f_a/d_ij;
+ f_a=-B*exp(-mu*(d-r0));
+ df_a=mu*f_a/d;
/* f_r, df_r */
- f_r=A*exp(-lambda*(d_ij-r0));
- df_r=lambda*f_r/d_ij;
+ f_r=A*exp(-lambda*(d-r0));
+ df_r=lambda*f_r/d;
/* b, db */
- if(exchange->zeta_ij==0.0) {
- b=1.0;
- db=0.0;
- }
- else {
- b=1.0/sqrt(1.0+exchange->zeta_ij);
- db=-0.5*b/(1.0+exchange->zeta_ij);
- }
+ b=1.0/sqrt(1.0+exchange->zeta[j]);
+ db=-0.5*b/(1.0+exchange->zeta[j]);
+
+ /* energy contribution */
+ energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
+ moldyn->energy+=energy;
+ ai->e+=energy;
- /* force contribution for atom i */
+ /* force contribution for atom i due to ij bond */
scale=-0.5*(f_c*(df_r-b*df_a)+df_c*(f_r-b*f_a)); // - in albe formalism
- v3_scale(&force,&(exchange->dist_ij),scale);
+ v3_scale(&force,dist,scale);
v3_add(&(ai->f),&(ai->f),&force);
- /* force contribution for atom j */
+#ifdef NDEBUG
+if(ai->tag==0) {
+printf("force: %.15f %.15f %.15f | %d %d (ij) %.15f\n",force.x,force.y,force.z,ai->tag,aj->tag,exchange->zeta[j]);
+printf(" t: %.15f %.15f %.15f\n",ai->f.x,ai->f.y,ai->f.z);
+}
+#endif
+
+ /* force contribution for atom j due to ij bond */
v3_scale(&force,&force,-1.0); // dri rij = - drj rij
v3_add(&(aj->f),&(aj->f),&force);
}
#endif
+ /* virial */
+ virial_calc(ai,&force,dist);
+
/* dzeta prefactor = - f_c f_a db, (* -0.5 due to force calc) */
exchange->pre_dzeta=0.5*f_a*f_c*db;
- /* energy contribution */
- energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
- moldyn->energy+=energy;
- ai->e+=energy;
+ /* force contribution (drj derivative) */
+ v3_scale(&force,&(exchange->dzeta[j][j]),exchange->pre_dzeta);
+ v3_add(&(aj->f),&(aj->f),&force);
+
+#ifdef NDEBUG
+if(aj->tag==0) {
+printf("force: %.15f %.15f %.15f | %d %d (j der)\n",force.x,force.y,force.z,aj->tag,ai->tag);
+printf(" t: %.15f %.15f %.15f\n",aj->f.x,aj->f.y,aj->f.z);
+}
+#endif
+
+ /* virial */
+ virial_calc(ai,&force,dist);
+
+ v3_scale(&force,&force,-1.0);
+ v3_add(&(ai->f),&(ai->f),&force);
+
+#ifdef NDEBUG
+if(ai->tag==0) {
+printf("force: %.15f %.15f %.15f | %d %d (i contr j der)\n",force.x,force.y,force.z,ai->tag,aj->tag);
+printf(" t: %.15f %.15f %.15f\n",ai->f.x,ai->f.y,ai->f.z);
+}
+#endif
/* reset k counter for second k loop */
- exchange->kcount=0;
+ exchange->kcnt=0;
return 0;
}
-/* albe 3 body potential function (second k loop) */
-int albe_mult_3bp_k2(t_moldyn *moldyn,
- t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+/* second k loop within second j loop within first i loop */
+int albe_mult_i0_j2_k0(t_moldyn *moldyn,
+ t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
t_albe_mult_params *params;
t_albe_exchange *exchange;
- int kcount;
- t_3dvec dist_ik,dist_ij;
- double d_ik2,d_ik,d_ij2,d_ij;
- unsigned char brand;
- double S2;
- double g,dg,cos_theta;
- double pre_dzeta;
- double f_c_ik,df_c_ik;
- double dijdik_inv,fcdg,dfcg;
- t_3dvec dcosdrj,dcosdrk;
- t_3dvec force,tmp;
+
+ int j,k;
+ t_3dvec force;
params=moldyn->pot_params;
exchange=&(params->exchange);
- kcount=exchange->kcount;
-
- if(kcount>ALBE_MAXN)
- printf("FATAL: neighbours!\n");
-
- /* d_ik2 */
- d_ik2=exchange->d_ik2[kcount];
- brand=ak->brand;
- if(brand==ai->brand)
- S2=params->S2[brand];
- else
- S2=params->S2mixed;
-
- /* return if d_ik > S */
- if(d_ik2>S2) {
- exchange->kcount++;
+ if(aj==ak) {
+ exchange->kcnt+=1;
return 0;
}
v3_add(&force,&force,&tmp);
v3_scale(&force,&force,pre_dzeta);
- /* force contribution */
- v3_add(&(ak->f),&(ak->f),&force);
+ v3_scale(&force,&force,-1.0);
+ v3_add(&(ai->f),&(ai->f),&force);
#ifdef DEBUG
if(ak==&(moldyn->atom[DATOM])) {
v3_add(&(ai->f),&(ai->f),&force);
/* increase k counter */
- exchange->kcount++;
+ exchange->kcnt+=1;
return 0;
+}
+
+int albe_mult_i0_j3(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ t_albe_mult_params *params;
+ t_albe_exchange *exchange;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* increase j counter */
+ exchange->j2cnt+=1;
+
+ return 0;
}
int albe_mult_check_2b_bond(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,u8 bc) {
projects / physik / posic.git / blobdiff