return 0;
}
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+ moldyn->func2b_post=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
moldyn->func3b=func;
}
lc->dnlc=count1;
- lc->countn=27;
- return count2;
+ return count1;
}
int link_cell_shutdown(t_moldyn *moldyn) {
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+
/* calculate initial forces */
potential_force_calc(moldyn);
- /* do some checks before we actually start calculating bullshit */
+ /* some stupid checks before we actually start calculating bullshit */
if(moldyn->cutoff>0.5*moldyn->dim.x)
printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
if(moldyn->cutoff>0.5*moldyn->dim.y)
/* zero absolute time */
moldyn->time=0.0;
+
+ /* debugging, ignre */
+ moldyn->debug=0;
+
+ /* executing the schedule */
for(sched=0;sched<moldyn->schedule.content_count;sched++) {
/* setting amount of runs and finite time step size */
for(i=0;i<moldyn->time_steps;i++) {
/* integration step */
+printf("MOVE\n");
moldyn->integrate(moldyn);
/* p/t scaling */
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d",sched,i);
+ printf("\rsched: %d, steps: %d, theta: %d",
+ sched,i,moldyn->debug);
fflush(stdout);
}
}
if(schedule->hook)
schedule->hook(moldyn,schedule->hook_params);
+ /* get a new info line */
+ printf("\n");
+
}
return 0;
/* forces depending on chosen potential */
potential_force_calc(moldyn);
- //moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
/* again velocities */
t_list neighbour_i2[27];
//t_list neighbour_j[27];
t_list *this,*that;
- u8 bc_ij,bc_ijk;
- int countn,dnlc;
+ u8 bc_ij,bc_ik;
+ int dnlc;
count=moldyn->count;
itom=moldyn->atom;
/* reset energy */
moldyn->energy=0.0;
+ /* get energy and force of every atom */
for(i=0;i<count;i++) {
/* reset force */
(itom[i].r.z+moldyn->dim.z/2)/lc->z,
neighbour_i);
- countn=lc->countn;
dnlc=lc->dnlc;
- for(j=0;j<countn;j++) {
+ for(j=0;j<27;j++) {
this=&(neighbour_i[j]);
list_reset(this);
!(jtom->attr&ATOM_ATTR_3BP))
continue;
- /*
- * according to mr. nordlund, we dont need to take the
- * sum over all atoms now, as 'this is centered' around
- * atom i ...
- * i am not quite sure though! there is a not vanishing
- * part even if f_c_ik is zero ...
- * this analytical potentials suck!
- * switching from mc to md to dft soon!
- */
-
- // link_cell_neighbour_index(moldyn,
- // (jtom->r.x+moldyn->dim.x/2)/lc->x,
- // (jtom->r.y+moldyn->dim.y/2)/lc->y,
- // (jtom->r.z+moldyn->dim.z/2)/lc->z,
- // neighbour_j);
-
-// /* neighbours of j */
-// for(k=0;k<lc->countn;k++) {
-//
-// that=&(neighbour_j[k]);
-// list_reset(that);
-//
-// if(that->start==NULL)
-// continue;
-//
-// bc_ijk=(k<lc->dnlc)?0:1;
-//
-// do {
-//
-// ktom=that->current->data;
-//
-// if(!(ktom->attr&ATOM_ATTR_3BP))
-// continue;
-//
-// if(ktom==jtom)
-// continue;
-//
-// if(ktom==&(itom[i]))
-// continue;
-//
-// moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-//
-/* } while(list_next(that)!=\ */
-// L_NO_NEXT_ELEMENT);
-//
-// }
-
/* copy the neighbour lists */
memcpy(neighbour_i2,neighbour_i,
27*sizeof(t_list));
/* get neighbours of i */
- for(k=0;k<countn;k++) {
+ for(k=0;k<27;k++) {
that=&(neighbour_i2[k]);
list_reset(that);
if(that->start==NULL)
continue;
- bc_ijk=(k<dnlc)?0:1;
+ bc_ik=(k<dnlc)?0:1;
do {
if(ktom==&(itom[i]))
continue;
-printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
- moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+ moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij);
} while(list_next(that)!=\
L_NO_NEXT_ELEMENT);
}
} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /* 2bp post function */
+ if(moldyn->func2b_post) {
+ moldyn->func2b_post(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+ }
+
}
}
+printf("debug atom %d: %.15f %.15f %.15f\n",i,itom[i].r.x,itom[i].v.x,itom[i].f.x);
}
return 0;
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");
+ printf(" S (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (m) | %.12f | %.12f | %.12f\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);
+ printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
+ 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(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+ printf(" n | %f | %f\n",p->n[0],p->n[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(" chi | %f \n",p->chi);
+
return 0;
}
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=&(params->exchange);
exchange->run3bp=0;
+ exchange->run2bp_post=0;
/*
* we need: f_c, df_c, f_r, df_r
d_ij=v3_norm(&dist_ij);
/* save for use in 3bp */
- exchange->dist_ij=dist_ij; /* <- needed ? */
exchange->d_ij=d_ij;
+ exchange->dist_ij=dist_ij;
/* constants */
if(num==aj->bnum) {
S=params->S[num];
R=params->R[num];
A=params->A[num];
+ B=params->B[num];
lambda=params->lambda[num];
- /* more constants depending of atoms i and j, needed in 3bp */
- params->exchange.B=&(params->B[num]);
- params->exchange.mu=&(params->mu[num]);
mu=params->mu[num];
params->exchange.chi=1.0;
}
S=params->Smixed;
R=params->Rmixed;
A=params->Amixed;
+ B=params->Bmixed;
lambda=params->lambda_m;
- /* more constants depending of atoms i and j, needed in 3bp */
- params->exchange.B=&(params->Bmixed);
- params->exchange.mu=&(params->mu_m);
mu=params->mu_m;
params->exchange.chi=params->chi;
}
-
if(d_ij>S)
return 0;
f_r=A*exp(-lambda*d_ij);
df_r=-lambda*f_r/d_ij;
- /* f_a, df_a calc + save for 3bp use */
+ /* f_a, df_a calc + save for later use */
exchange->f_a=-B*exp(-mu*d_ij);
exchange->df_a=-mu*exchange->f_a/d_ij;
exchange->f_c=f_c;
exchange->df_c=df_c;
- /* enable the run of 3bp function */
+ /* enable the run of 3bp function and 2bp post processing */
exchange->run3bp=1;
+ exchange->run2bp_post=1;
+
+ /* reset 3bp sums */
+ exchange->zeta=0.0;
+ v3_zero(&(exchange->db_ij));
+
+ return 0;
+}
+
+/* tersoff 2 body post part */
+
+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 */
+
+ 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;
+ double f_c,df_c,f_a,df_a;
+ double chi,n,n_betan;
+ double zeta;
+
+ params=moldyn->pot2b_params;
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was detected to be 0! */
+ 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);
+ 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);
+ v3_scale(&force,&force,f_c);
+
+ /* df_c part */
+ v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
+
+ /* add energy of 3bp sum */
+ moldyn->energy+=(0.5*f_c*b_ij*f_a);
+
+ /* add force of 3bp calculation (all three parts) */
+ v3_add(&(ai->f),&temp,&force);
return 0;
}
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
- t_3dvec dist_ij,dist_ik,dist_jk;
+ t_3dvec dist_ij,dist_ik;
t_3dvec temp,force;
double R,S,s_r;
- double d_ij,d_ij2,d_ik,d_jk;
- double f_c,df_c,b_ij,f_a,df_a;
+ double d_ij,d_ik;
+ double rijrik,dijdik;
+ double f_c,df_c,f_a,df_a;
double f_c_ik,df_c_ik,arg;
- double scale;
- double chi;
- double n,c,d,h,beta,betan;
+ double n,c,d,h;
double c2,d2,c2d2;
- double numer,denom;
- double theta,cos_theta,sin_theta;
- double d_theta,d_theta1,d_theta2;
- double h_cos,h_cos2,d2_h_cos2;
- double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
- double bracket3,bracket3_pow_1,bracket3_pow;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac;
+ double g;
int num;
params=moldyn->pot3b_params;
*/
d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
+ dist_ij=exchange->dist_ij;
f_a=params->exchange.f_a;
df_a=params->exchange.df_a;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
/* d_ij is <= S, as we didn't return so far! */
*
* - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
*
- * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
- * w_ik,
+ * - for db_ij: d_costheta, cos_theta, f_c_ik, df_c_ik, w_ik
*
*/
-
v3_sub(&dist_ik,&(ai->r),&(ak->r));
if(bc) check_per_bound(moldyn,&dist_ik);
d_ik=v3_norm(&dist_ik);
- /* constants for f_c_ik calc */
+ /* constants */
if(num==ak->bnum) {
R=params->R[num];
S=params->S[num];
S=params->Smixed;
}
- /* calc of f_c_ik */
+ /* there is no contribution if f_c_ik = 0 */
if(d_ik>S)
return 0;
- if(d_ik<R) {
- /* f_c_ik = 1, df_c_ik = 0 */
- 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));
- }
-
- v3_sub(&dist_jk,&(aj->r),&(ak->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk=v3_norm(&dist_jk);
-
- beta=*(exchange->beta);
- betan=exchange->betan;
+ /* get exchange data */
n=*(exchange->n);
c=*(exchange->c);
d=*(exchange->d);
d2=exchange->d2;
c2d2=exchange->c2d2;
- numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
- denom=2*d_ij*d_ik;
- cos_theta=numer/denom;
- sin_theta=sqrt(1.0-(cos_theta*cos_theta));
- theta=acos(cos_theta);
- d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
- d_theta1=2*denom-numer*2*d_ik/d_ij;
- d_theta2=2*denom-numer*2*d_ij/d_ik;
- d_theta1*=d_theta;
- d_theta2*=d_theta;
+ /* 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;
+ }
+ else {
+ cos_theta=1.0;
+ }
+ }
+
+ d_costheta1=dijdik-rijrik*d_ik/d_ij;
+ d_costheta2=dijdik-rijrik*d_ij/d_ik;
h_cos=(h-cos_theta);
- h_cos2=h_cos*h_cos;
- d2_h_cos2=d2-h_cos2;
-
- /* some usefull expressions */
- frac1=c2/(d2-h_cos2);
- bracket1=1+c2d2-frac1;
- bracket2=f_c_ik*bracket1;
- bracket2_n_1=pow(bracket2,n-1.0);
- bracket2_n=bracket2_n_1*bracket2;
- bracket3=1+betan*bracket2_n;
- bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
- bracket3_pow=bracket3_pow_1*bracket3;
-
- /* now go on with calc of b_ij and derivation of b_ij */
- b_ij=chi*bracket3_pow;
-
- /* derivation of theta */
- v3_scale(&force,&dist_ij,d_theta1);
- v3_scale(&temp,&dist_ik,d_theta2);
+ d2_h_cos2=d2+(h_cos*h_cos);
+
+ frac=c2/(d2_h_cos2);
+ g=1.0+c2d2-frac;
+
+ /* 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 */
- /* part 1 of derivation of b_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
+ if(d_ik<R) {
+ /* f_c_ik = 1, df_c_ik = 0 */
+ /* => only d_costheta contrib to db_ij */
+ // => do nothing ...
- /* part 2 of derivation of b_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
+ /* 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));
- /* sum up and scale ... */
- v3_add(&temp,&temp,&force);
- scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
- v3_scale(&temp,&temp,scale);
+ /* scale d_costheta contrib with f_c_ik */
+ v3_scale(&force,&force,f_c_ik);
- /* now construct an energy and a force out of that */
- v3_scale(&temp,&temp,f_a);
- v3_scale(&force,&dist_ij,df_a*b_ij);
- v3_add(&temp,&temp,&force);
- v3_scale(&temp,&temp,f_c);
- v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
- v3_add(&force,&force,&temp);
+ /* df_c_ik contrib to db_ij */
+ v3_scale(&temp,&dist_ik,df_c_ik*g);
- /* add forces */
- v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
- moldyn->energy+=(0.25*f_a*b_ij*f_c);
+ /* sum up both parts */
+ v3_add(&force,&force,&temp);
+
+ /* zeta */
+ exchange->zeta+=f_c_ik*g;
+ }
+printf("%.30f\n",exchange->zeta);
+
+ /* add to db_ij */
+ v3_add(&(exchange->db_ij),&(exchange->db_ij),&force);
return 0;
}
projects / physik / posic.git / blobdiff