#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);
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) {
t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
t_3dvec dist_ij,force;
double d_ij,d_ij2;
- double A,B,R,S,S2,lambda,mu;
+ double A,R,S,S2,lambda;
double f_r,df_r;
double f_c,df_c;
int brand;
double s_r;
double arg;
+ double energy;
- params=moldyn->pot_params;
- brand=aj->brand;
- exchange=&(params->exchange);
+ printf("WARNING! - tersoff_mult_2bp is obsolete.\n");
+ printf("WARNING! - repulsive part handled in 3bp/j2 routine.\n");
- /* clear 3bp and 2bp post run */
- exchange->run3bp=0;
- exchange->run2bp_post=0;
+ /* use newtons third law */
+ if(ai<aj) return 0;
- /* reset S > r > R mark */
- exchange->d_ij_between_rs=0;
-
- /*
- * 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
- *
- */
+ params=moldyn->pot_params;
+ brand=aj->brand;
- /* constants */
- if(brand==ai->brand) {
- S=params->S[brand];
+ /* determine cutoff square */
+ if(brand==ai->brand)
S2=params->S2[brand];
- R=params->R[brand];
- A=params->A[brand];
- B=params->B[brand];
- lambda=params->lambda[brand];
- mu=params->mu[brand];
- exchange->chi=1.0;
- }
- else {
- S=params->Smixed;
+ else
S2=params->S2mixed;
- R=params->Rmixed;
- A=params->Amixed;
- B=params->Bmixed;
- lambda=params->lambda_m;
- mu=params->mu_m;
- params->exchange.chi=params->chi;
- }
- /* dist_ij, d_ij */
+ /* 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);
/* if d_ij2 > S2 => no force & potential energy contribution */
- if(d_ij2>S2)
+ if(d_ij2>S2) {
return 0;
+ }
/* now we will need the distance */
- //d_ij=v3_norm(&dist_ij);
d_ij=sqrt(d_ij2);
- /* save for use in 3bp */
- exchange->d_ij=d_ij;
- exchange->d_ij2=d_ij2;
- exchange->dist_ij=dist_ij;
-
/* more constants */
- exchange->beta_j=&(params->beta[brand]);
- exchange->n_j=&(params->n[brand]);
- exchange->c_j=&(params->c[brand]);
- exchange->d_j=&(params->d[brand]);
- exchange->h_j=&(params->h[brand]);
if(brand==ai->brand) {
- exchange->betajnj=exchange->betaini;
- exchange->cj2=exchange->ci2;
- exchange->dj2=exchange->di2;
- exchange->cj2dj2=exchange->ci2di2;
+ S=params->S[brand];
+ R=params->R[brand];
+ A=params->A[brand];
+ lambda=params->lambda[brand];
}
else {
- exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
- exchange->cj2=params->c[brand]*params->c[brand];
- exchange->dj2=params->d[brand]*params->d[brand];
- exchange->cj2dj2=exchange->cj2/exchange->dj2;
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ lambda=params->lambda_m;
}
- /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
+ /* f_r_ij, df_r_ij */
f_r=A*exp(-lambda*d_ij);
df_r=lambda*f_r/d_ij;
- /* 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) */
+ /* f_c, df_c */
if(d_ij<R) {
- /* f_c = 1, df_c = 0 */
f_c=1.0;
df_c=0.0;
- /* two body contribution (ij, ji) */
v3_scale(&force,&dist_ij,-df_r);
}
else {
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));
- /* two body contribution (ij, ji) */
v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
- /* tell 3bp that S > r > R */
- exchange->d_ij_between_rs=1;
}
- /* add forces of 2bp (ij, ji) contribution
- * dVij = dVji and we sum up both: no 1/2) */
+ /* add forces */
v3_add(&(ai->f),&(ai->f),&force);
-
- /* virial */
- 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;
+ 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])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
-}
+ if((ai==&(moldyn->atom[0]))|(aj==&(moldyn->atom[0]))) {
+ printf("force 2bp: [%d %d]\n",ai->tag,aj->tag);
+ printf("adding %f %f %f\n",force.x,force.y,force.z);
+ if(ai==&(moldyn->atom[0]))
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+ if(aj==&(moldyn->atom[0]))
+ printf("total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
+ }
#endif
- /* 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 */
- exchange->f_c=f_c;
- exchange->df_c=df_c;
-
- /* enable the run of 3bp function and 2bp post processing */
- exchange->run3bp=1;
- exchange->run2bp_post=1;
+ /* virial */
+ virial_calc(ai,&force,&dist_ij);
- /* reset 3bp sums */
- exchange->zeta_ij=0.0;
- exchange->zeta_ji=0.0;
- v3_zero(&(exchange->dzeta_ij));
- v3_zero(&(exchange->dzeta_ji));
+ /* energy 2bp contribution */
+ energy=f_r*f_c;
+ moldyn->energy+=energy;
+ ai->e+=0.5*energy;
+ aj->e+=0.5*energy;
return 0;
}
-/* tersoff 2 body post part */
+/* tersoff 3 body potential function (first ij loop) */
+int tersoff_mult_3bp_j1(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) {
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ unsigned char brand;
+ double S2;
+ t_3dvec dist_ij;
+ double d_ij2,d_ij;
+
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ /* reset zeta sum */
+ exchange->zeta_ij=0.0;
/*
- * 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
- *
+ * set ij depending values
*/
+ brand=ai->brand;
+
+ if(brand==aj->brand)
+ S2=params->S2[brand];
+ else
+ S2=params->S2mixed;
+
+ /* 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);
+
+ /* if d_ij2 > S2 => no force & potential energy contribution */
+ if(d_ij2>S2) {
+ moldyn->run3bp=0;
+ return 0;
+ }
+
+ /* d_ij */
+ d_ij=sqrt(d_ij2);
+
+ /* store values */
+ exchange->dist_ij=dist_ij;
+ exchange->d_ij2=d_ij2;
+ exchange->d_ij=d_ij;
+
+ /* reset k counter for first k loop */
+ exchange->kcount=0;
+
+ return 0;
+}
+
+/* tersoff 3 body potential function (first k loop) */
+int tersoff_mult_3bp_k1(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 force,temp;
- t_3dvec *dist_ij;
- double b,db,tmp;
- double f_c,df_c,f_a,df_a;
- double chi,ni,betaini,nj,betajnj;
- double zeta;
+ 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;
params=moldyn->pot_params;
exchange=&(params->exchange);
+ kcount=exchange->kcount;
- /* we do not run if f_c_ij was detected to be 0! */
- if(!(exchange->run2bp_post))
- return 0;
+ if(kcount>TERSOFF_MAXN) {
+ printf("FATAL: neighbours = %d\n",kcount);
+ printf(" -> %d %d %d\n",ai->tag,aj->tag,ak->tag);
+ }
- f_c=exchange->f_c;
- df_c=exchange->df_c;
- f_a=exchange->f_a;
- df_a=exchange->df_a;
- betaini=exchange->betaini;
- betajnj=exchange->betajnj;
- ni=*(exchange->n_i);
- nj=*(exchange->n_j);
- chi=exchange->chi;
- dist_ij=&(exchange->dist_ij);
-
- /* Vij and dVij */
- zeta=exchange->zeta_ij;
- if(zeta==0.0) {
- moldyn->debug++; /* just for debugging ... */
- b=chi;
- v3_scale(&force,dist_ij,df_a*b*f_c);
+ /* ik constants */
+ brand=ai->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ S2=params->S2[brand];
}
else {
- 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); /* x(...)^(-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);
+ R=params->Rmixed;
+ S=params->Smixed;
+ S2=params->S2mixed;
}
- v3_scale(&temp,dist_ij,df_c*b*f_a);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,-0.5);
- /* add force */
- v3_add(&(ai->f),&(ai->f),&force);
+ /* 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);
- /* virial */
- 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;
+ /* 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++;
+ return 0;
+ }
+
+ /* d_ik */
+ d_ik=sqrt(d_ik2);
+
+ /* dist_ij, d_ij */
+ dist_ij=exchange->dist_ij;
+ d_ij=exchange->d_ij;
+
+ /* cos theta */
+ cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
+
+ /* g_ijk */
+ 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 */
+ if(d_ik<=R) {
+ exchange->zeta_ij+=g;
+ f_c_ik=1.0;
+ df_c_ik=0.0;
+ }
+ 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;
+ }
#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
+ if(ai==&(moldyn->atom[DATOM]))
+ printf("zeta_ij: %f %f %f %f\n",f_c_ik*g,f_c_ik,g,d_ik);
#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+
+ /* store even more data for second k loop */
+ exchange->g[kcount]=g;
+ exchange->dg[kcount]=dg;
+ exchange->d_ik[kcount]=d_ik;
+ exchange->cos_theta[kcount]=cos_theta;
+ exchange->f_c_ik[kcount]=f_c_ik;
+ exchange->df_c_ik[kcount]=df_c_ik;
+
+ /* increase k counter */
+ exchange->kcount++;
+
+ return 0;
}
-#endif
- /* add energy of 3bp sum */
- moldyn->energy+=(0.5*f_c*b*f_a);
+int tersoff_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ 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;
- /* dVji */
- zeta=exchange->zeta_ji;
- if(zeta==0.0) {
- moldyn->debug++;
+ params=moldyn->pot_params;
+ exchange=&(params->exchange);
+
+ 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;
+ }
+
+ 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);
+ 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;
- v3_scale(&force,dist_ij,df_a*b*f_c);
+ db=0.0;
}
else {
- 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); /* x(...)^(-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);
+ 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/(2.0*ni)-1.0);
+ b=db*b;
+ db*=-0.5*tmp;
}
- v3_scale(&temp,dist_ij,df_c*b*f_a);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,-0.5);
- /* add force */
+ /* force contribution */
+ 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);
-
- /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-// TEST ... with a minus instead
- 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;
+ v3_scale(&force,&force,-1.0); // dri rij = - drj rij
+ v3_add(&(aj->f),&(aj->f),&force);
#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
-}
+ 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[DATOM]))
+ printf("total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
+ 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));
+
+ /* dzeta prefactor = - 0.5 f_c f_a db */
+ exchange->pre_dzeta=-0.5*f_a*f_c*db;
+
+ /* energy contribution */
+ 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;
+
return 0;
}
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+/* tersoff 3 body potential function (second k loop) */
+int tersoff_mult_3bp_k2(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,dist_jk;
- t_3dvec temp1,temp2;
- t_3dvec *dzeta;
- double R,S,S2,s_r;
- double B,mu;
- double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
- 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,g,zeta,chi;
- double tmp;
- int brand;
+ 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;
params=moldyn->pot_params;
exchange=&(params->exchange);
+ kcount=exchange->kcount;
+
+ if(kcount>TERSOFF_MAXN)
+ printf("FATAL: neighbours!\n");
+
+ /* d_ik2 */
+ d_ik2=exchange->d_ik2[kcount];
- if(!(exchange->run3bp))
+ 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++;
return 0;
+ }
- /*
- * 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
- *
- */
+ /* prefactor dzeta */
+ pre_dzeta=exchange->pre_dzeta;
- /*
- * get exchange data
- */
+ /* dist_ik, d_ik */
+ dist_ik=exchange->dist_ik[kcount];
+ d_ik=exchange->d_ik[kcount];
- /* dist_ij, d_ij - this is < S_ij ! */
+ /* f_c_ik, df_c_ik */
+ f_c_ik=exchange->f_c_ik[kcount];
+ df_c_ik=exchange->df_c_ik[kcount];
+
+ /* dist_ij, d_ij2, d_ij */
dist_ij=exchange->dist_ij;
- d_ij=exchange->d_ij;
d_ij2=exchange->d_ij2;
+ d_ij=exchange->d_ij;
- /* f_c_ij, df_c_ij (same for ji) */
- f_c=exchange->f_c;
- df_c=exchange->df_c;
+ /* g, dg, cos_theta */
+ g=exchange->g[kcount];
+ dg=exchange->dg[kcount];
+ cos_theta=exchange->cos_theta[kcount];
- /*
- * calculate unknown values now ...
- */
+ /* cos_theta derivatives wrt i,j,k */
+ dijdik_inv=1.0/(d_ij*d_ik);
+ v3_scale(&dcosdrj,&dist_ik,dijdik_inv);
+ v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
+ v3_add(&dcosdrj,&dcosdrj,&tmp);
+ v3_scale(&dcosdrk,&dist_ij,dijdik_inv);
+ v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
+ v3_add(&dcosdrk,&dcosdrk,&tmp);
- /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+ /* f_c_ik * dg, df_c_ik * g */
+ fcdg=f_c_ik*dg;
+ dfcg=df_c_ik*g;
- /* dist_ik, d_ik */
- v3_sub(&dist_ik,&(ak->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik2=v3_absolute_square(&dist_ik);
+ /* derivative wrt j */
+ v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
- /* ik constants */
- brand=ai->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- }
+ /* force contribution */
+ v3_add(&(aj->f),&(aj->f),&force);
- /* zeta_ij/dzeta_ij contribution only for d_ik < S */
- if(d_ik2<S2) {
-
- /* now we need d_ik */
- d_ik=sqrt(d_ik2);
-
- /* 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 */
- rr=v3_scalar_product(&dist_ij,&dist_ik);
- dd=d_ij*d_ik;
- cos_theta=rr/dd;
-
- /* d_costheta */
- tmp=1.0/dd;
- d_costheta1=cos_theta/d_ij2-tmp;
- d_costheta2=cos_theta/d_ik2-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 */
- dzeta=&(exchange->dzeta_ij);
- 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,dzeta,&temp1);
- }
- else {
- /* {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(&temp1,&temp1,&temp2);
- v3_add(dzeta,dzeta,&temp1);
- }
+#ifdef DEBUG
+ 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(" angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+ printf(" d ij ik = %f %f\n",d_ij,d_ik);
}
+#endif
- /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+ /* virial */
+ virial_calc(ai,&force,&dist_ij);
- /* dist_jk, d_jk */
- v3_sub(&dist_jk,&(ak->r),&(aj->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk2=v3_absolute_square(&dist_jk);
+ /* force contribution to atom i */
+ v3_scale(&force,&force,-1.0);
+ v3_add(&(ai->f),&(ai->f),&force);
- /* jk constants */
- brand=aj->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- B=params->B[brand];
- mu=params->mu[brand];
- chi=1.0;
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- B=params->Bmixed;
- mu=params->mu_m;
- chi=params->chi;
- }
+ /* derivative wrt k */
+ 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);
- /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
- if(d_jk2<S2) {
-
- /* now we need d_ik */
- d_jk=sqrt(d_jk2);
-
- /* 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 */
- rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
- dd=d_ij*d_jk;
- cos_theta=rr/dd;
-
- /* d_costheta */
- d_costheta1=1.0/dd;
- d_costheta2=cos_theta/d_ij2;
-
- /* 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_jik 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_sub(&temp1,&temp1,&temp2); /* there is a minus! */
- v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
-
- /* store dg in temp2 and use it for dVjk later */
- v3_copy(&temp2,&temp1);
-
- /* 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;
-
- /* zeta_ji */
- exchange->zeta_ji+=g;
-
- /* dzeta_ji */
- v3_add(dzeta,dzeta,&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);
-
- /* zeta_ji */
- exchange->zeta_ji+=f_c_jk*g;
-
- /* dzeta_ji */
- v3_scale(&temp1,&temp1,f_c_jk);
- 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,&temp2,f_c);
- v3_scale(&temp2,&dist_ij,df_c*g);
- v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
- }
- else {
- zeta=g;
- // dzeta_jk is simply dg, which is stored in temp2
- }
- /* 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(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
- v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
- /* scaled with 0.5 ^ */
-
- /* virial */
- ai->virial.xx-=temp2.x*dist_jk.x;
- ai->virial.yy-=temp2.y*dist_jk.y;
- ai->virial.zz-=temp2.z*dist_jk.z;
- ai->virial.xy-=temp2.x*dist_jk.y;
- ai->virial.xz-=temp2.x*dist_jk.z;
- ai->virial.yz-=temp2.y*dist_jk.z;
+ /* force contribution */
+ v3_add(&(ak->f),&(ak->f),&force);
#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x,ai->f.x);
- printf("%f | %f\n",temp2.y,ai->f.y);
- printf("%f | %f\n",temp2.z,ai->f.z);
-}
+ 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(" angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
+ printf(" d ij ik = %f %f\n",d_ij,d_ik);
+ }
#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
- printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
- printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
+
+ /* virial */
+ 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++;
+
+ return 0;
+
}
-#endif
+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 0;
+ return FALSE;
}
projects / physik / posic.git / blobdiff