static void test_accuracy(){
rand_t rstat;
int seed=4;
double r0=0.2;
double dx=1./64.;
long N=1+64;
long nx=N;
long ny=N;
seed_rand(&rstat, seed);
map_t *atm=mapnew(nx, ny, dx, dx,NULL);
for(long i=0; i<nx*ny; i++){
atm->p[i]=randn(&rstat);
}
map_t *atm2=mapnew(nx, ny, dx, dx,NULL);
for(long i=0; i<nx*ny; i++){
atm2->p[i]=randn(&rstat);
}
mapwrite(atm, "atm_rand.bin");
mapwrite(atm2, "atm2_rand.bin");
fractal_do((dmat*)atm, dx, r0,L0,ninit);
mapwrite(atm, "atm_frac.bin");
fractal_inv((dmat*)atm, dx, r0,L0,ninit);
mapwrite(atm, "atm_frac_inv.bin");
fractal_trans((dmat*)atm2, dx, r0,L0,ninit);
mapwrite(atm2, "atm2_frac_trans.bin");
fractal_inv_trans((dmat*)atm2, dx, r0,L0,ninit);
mapwrite(atm2, "atm2_frac_inv_trans.bin");
/*
atm2 is u, atm is v, now comparing u'Av against v'A'u. they should be the same.
A^-1Av should be the same as v
A'^-1A'u should be the same as u.
*/
dmat *u=dread("atm2_rand.bin");
dmat *Atu=dread("atm2_frac_trans.bin");
dmat *Av=dread("atm_frac.bin");
dmat *v=dread("atm_rand.bin");
double dot1=dotdbl(u->p, Av->p, NULL, nx*ny);
double dot2=dotdbl(v->p, Atu->p, NULL, nx*ny);
info("dot1=%g, dot2=%g, diff=%g\n", dot1, dot2, dot1-dot2);
dmat *u2=dread("atm2_frac_inv_trans.bin");
dmat *v2=dread("atm_frac_inv.bin");
double d1=ddiff(u, u2);
double d2=ddiff(v, v2);
info("d1=%g, d2=%g\n", d1, d2);
}
PRIVATE void heat_capacity(char *string, float T_min, float T_max,
float h, int m)
{
int length, i;
char *structure;
float hc, kT, min_en;
length = (int) strlen(string);
do_backtrack = 0;
temperature = T_min -m*h;
/* initialize_fold(length); <- obsolete */
structure = (char *) vrna_alloc((unsigned) length+1);
min_en = fold(string, structure);
free(structure); free_arrays();
kT = (temperature+K0)*GASCONST/1000; /* in kcal */
pf_scale = exp(-(1.07*min_en)/kT/length );
/* init_pf_fold(length); <- obsolete */
vrna_exp_param_t *pf_parameters = NULL;
vrna_md_t md;
set_model_details(&md);
pf_parameters = get_boltzmann_factors(temperature, 1.0, md, pf_scale);
update_pf_params_par(length, pf_parameters);
for (i=0; i<2*m+1; i++) {
F[i] = pf_fold_par(string, NULL, pf_parameters, 0, 0, 0); /* T_min -2h */
md.temperature = temperature += h;
kT = (temperature+K0)*GASCONST/1000;
pf_scale=exp(-(F[i]/length +h*0.00727)/kT); /* try to extrapolate F */
free(pf_parameters);
pf_parameters = get_boltzmann_factors(temperature, 1.0, md, pf_scale);
update_pf_params_par(length, pf_parameters);
}
while (temperature <= (T_max+m*h+h)) {
hc = - ddiff(F,h,m)* (temperature +K0 - m*h -h);
printf("%g %g\n", (temperature-m*h-h), hc);
for (i=0; i<2*m; i++)
F[i] = F[i+1];
F[2*m] = pf_fold_par(string, NULL, pf_parameters, 0, 0, 0);
/* printf("%g\n", F[2*m]);*/
temperature += h;
kT = (temperature+K0)*GASCONST/1000;
pf_scale=exp(-(F[i]/length +h*0.00727)/kT);
free(pf_parameters);
md.temperature = temperature;
pf_parameters = get_boltzmann_factors(temperature, 1.0, md, pf_scale);
update_pf_params_par(length, pf_parameters);
}
free_pf_arrays();
}
PRIVATE void heat_capacity(char *string, float T_min, float T_max,
float h, int m)
{
int length, i;
char *structure;
float hc, kT, min_en;
length = (int) strlen(string);
do_backtrack = 0;
temperature = T_min -m*h;
initialize_fold(length);
structure = (char *) space((unsigned) length+1);
min_en = fold(string, structure);
free(structure); free_arrays();
kT = (temperature+K0)*GASCONST/1000; /* in kcal */
pf_scale = exp(-(1.07*min_en)/kT/length );
init_pf_fold(length);
for (i=0; i<2*m+1; i++) {
F[i] = pf_fold(string, NULL); /* T_min -2h */
temperature += h;
kT = (temperature+K0)*GASCONST/1000;
pf_scale=exp(-(F[i]/length +h*0.00727)/kT); /* try to extrapolate F */
update_pf_params(length);
}
while (temperature <= (T_max+m*h+h)) {
hc = - ddiff(F,h,m)* (temperature +K0 - m*h -h);
printf("%g %g\n", (temperature-m*h-h), hc);
for (i=0; i<2*m; i++)
F[i] = F[i+1];
F[2*m] = pf_fold(string, NULL);
temperature += h;
kT = (temperature+K0)*GASCONST/1000;
pf_scale=exp(-(F[i]/length +h*0.00727)/kT);
update_pf_params(length);
}
free_pf_arrays();
}
