int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
- moldyn->func2b=func;
+ moldyn->func2b_post=func;
moldyn->pot2b_params=params;
return 0;
}
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;
- /* neighbourhood of atom j is not needed! */
-
- // 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)
+ 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;
/* save for use in 3bp */
exchange->d_ij=d_ij;
exchange->dist_ij=dist_ij;
- exchange->d_ij2=d_ij*d_ij;
/* constants */
if(num==aj->bnum) {
mu=params->mu_m;
params->exchange.chi=params->chi;
}
-
if(d_ij>S)
return 0;
exchange->run2bp_post=1;
/* reset 3bp sums */
- exchange->sum1_3bp=0.0;
- exchange->sum2_3bp=0.0;
+ exchange->zeta=0.0;
v3_zero(&(exchange->db_ij));
return 0;
double db_ij_scale1,db_ij_scale2;
double b_ij;
double f_c,df_c,f_a,df_a;
- double chi,betan;
- double help;
- double n;
+ double chi,n,n_betan;
+ double zeta;
params=moldyn->pot2b_params;
exchange=&(params->exchange);
- /* we do not run if f_c_ij was dtected to be 0! */
+ /* we do not run if f_c_ij was detected to be 0! */
if(!(exchange->run2bp_post))
return 0;
df_c=exchange->df_c;
f_a=exchange->f_a;
df_a=exchange->df_a;
- betan=exchange->betan;
+ n_betan=exchange->n_betan;
n=*(exchange->n);
chi=exchange->chi;
dist_ij=&(exchange->dist_ij);
+ zeta=exchange->zeta;
- db_ij_scale1=(1+betan*exchange->sum1_3bp);
- db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp);
- help=pow(db_ij_scale1,-1.0/(2*n)-1);
- b_ij=chi*db_ij_scale1*help;
- db_ij_scale1=-chi/(2*n)*help;
+ 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));
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 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 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 cos_theta,d_costheta1,d_costheta2;
double h_cos,d2_h_cos2;
- double frac,bracket,bracket_n_1,bracket_n;
+ double frac;
double g;
int num;
*/
d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
dist_ij=exchange->dist_ij;
f_a=params->exchange.f_a;
*
* - 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
*
*/
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 */
- if(d_ik>S) {
- f_c_ik=0.0;
- df_c_ik=0.0;
- }
- else if(d_ik<R) {
- 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);
+ /* there is no contribution if f_c_ik = 0 */
+ if(d_ik>S)
+ return 0;
/* get exchange data */
n=*(exchange->n);
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;
- /* prefere law of cosines, dot product -> nan (often) */
- //cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
- 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);
d2_h_cos2=d2+(h_cos*h_cos);
frac=c2/(d2_h_cos2);
g=1.0+c2d2-frac;
- if(f_c_ik==0.0) {
- bracket=0.0;
- bracket_n_1=0.0;
- bracket_n=0.0;
- //printf("Foo -> 0: ");
- }
- else {
- bracket=f_c_ik*g;
- bracket_n_1=pow(bracket,n-1.0);
- bracket_n=bracket_n_1*bracket;
- //printf("Foo -> 1: ");
- }
-//printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket);
+ /* 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 */
- /* calc of db_ij and the 2 sums */
- exchange->sum1_3bp+=bracket_n;
- exchange->sum2_3bp+=bracket_n_1;
+ if(d_ik<R) {
+ /* f_c_ik = 1, df_c_ik = 0 */
+ /* => only d_costheta contrib to db_ij */
+ // => do nothing ...
- /* derivation of theta */
- v3_scale(&force,&dist_ij,d_theta1);
- v3_scale(&temp,&dist_ik,d_theta2);
- v3_add(&force,&force,&temp);
+ /* 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));
- /* part 1 of db_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
+ /* scale d_costheta contrib with f_c_ik */
+ v3_scale(&force,&force,f_c_ik);
- /* part 2 of db_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*g);
+ /* df_c_ik contrib to db_ij */
+ v3_scale(&temp,&dist_ik,df_c_ik*g);
- /* sum up and add to db_ij */
- v3_add(&temp,&temp,&force);
- v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp);
+ /* 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