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 */
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)
+ if(moldyn->func2b_post) {
+printf("pre(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x);
moldyn->func2b_post(moldyn,
&(itom[i]),
jtom,bc_ij);
+printf("post(%d): %.15f %.15f %.15f\n",i,itom[i].f.x,itom[i].r.x,itom[i].v.x);
+ }
}
}
exchange=&(params->exchange);
exchange->run3bp=0;
+ exchange->run2bp_post=0;
/*
* we need: f_c, df_c, f_r, df_r
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->sum1_3bp=0.0;
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;
df_a=exchange->df_a;
betan=exchange->betan;
n=*(exchange->n);
+ chi=exchange->chi;
dist_ij=&(exchange->dist_ij);
db_ij_scale1=(1+betan*exchange->sum1_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;
+printf("debug: %.20f %.20f %.20f\n",db_ij->x,exchange->sum1_3bp,exchange->sum2_3bp);
+ /* 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 */
+
+ /* add force of 3bp calculation (all three parts) */
v3_add(&(ai->f),&temp,&force);
return 0;
d2=exchange->d2;
c2d2=exchange->c2d2;
+ /* cosine of theta by scalaproduct, *
+ * derivation of theta by law of cosines! */
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);
+ cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
+printf("cos theta: %.25f\n",cos_theta);
+
+ /* hack - cos theta machine accuracy problems! */
+ if(cos_theta>1.0||cos_theta<-1.0) {
+ 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;
+ printf("THETA CORRECTION\n");
+ }
+
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_theta2=2*denom-numer*2*d_ij/d_ik;
d_theta1*=d_theta;
d_theta2*=d_theta;
+printf("FOO %.15f %.15f\n",sin_theta,cos_theta);
h_cos=(h-cos_theta);
d2_h_cos2=d2+(h_cos*h_cos);
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);
/* calc of db_ij and the 2 sums */
exchange->sum1_3bp+=bracket_n;
v3_scale(&temp,&dist_ik,d_theta2);
v3_add(&force,&force,&temp);
+printf("DA:%.20f %.20f %.20f\n",d_theta1,force.x,temp.x);
/* part 1 of db_ij */
v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
projects / physik / posic.git / blobdiff