__inline k_t random_spp_wavevector(double k_spp_abs, gsl_rng *r) {
k_t k;
double theta = random_double_range(r, 0.0, 2.0*M_PI);
k.kz = 0.0;
k.kx = k_spp_abs * sin(theta);
k.ky = k_spp_abs * cos(theta);
return k;
}
k_t random_spp_wavevector(double k_spp_abs, double k_light,gsl_rng *r){
k_t k;
double k_abs = 0.0;
double sigma = 0.016*k_spp_abs;
double theta = random_double_range(r, 0.0, 2.0*M_PI);
k_abs = k_spp_abs + gsl_ran_gaussian(r, sigma);
k.kz = sqrt(k_light*k_light - k_abs*k_abs);
//printf("%g %g\n",k_spp_abs,k_abs);
k.kx = k_abs * sin(theta);
k.ky = k_abs * cos(theta);
return k;
}
/*
* this is the method to create the index of the next scatter */
__inline int next_scatter_index(int current_index,int NSCAT, gsl_rng *r, index_bounds *matrix) {
int next_scatter_index,i;
double random_probability = 0.0;
random_probability = random_double_range(r, 0.0, 1.0);
for (i = 0; i < NSCAT-1; ++i) {
if (random_probability<=matrix[i].upper_bound && random_probability > matrix[i].lower_bound) {
next_scatter_index = matrix[i].index;
break;
}
}
return next_scatter_index;
}
/**
*
* This is the method to create the exponential probability function for the spp multiple scattering.
*
*/
__inline bool is_radiation_out(double pathlength, double mean_free_pathlength,gsl_rng *r) {
double random_probability = 0.0;
double out_probability = 0.0;
bool out = false;
random_probability = random_double_range(r, 0.0, 1.0);
out_probability = cexp(-(pathlength/mean_free_pathlength));
if(random_probability >= out_probability) {
out = true;
}
else {
out = false;
}
return out;
}
GAULFUNC double random_cauchy(void)
{
return tan(random_double_range(-PI/2,PI/2));
}
double random_double_range_wrapper(double *min, double *max)
{
return random_double_range(*min, *max);
}
bool
initialChromo2( population *pop, entity *adam ){
int point; /* Index of allele to seed */
/* Checks. */
if (!pop) die("Null pointer to population structure passed.");
if (!adam) die("Null pointer to entity structure passed.");
/* Seeding. */
bool success = false;
while( !success ){
// rotate angle
for (point=7; point<pop->len_chromosomes; point++)
{
((double *)adam->chromosome[0])[point]
= (double)random_double( 360 );
}
//------------------------------------------- rotate ligand ------------------------------------------------------
Molecular rotateLig = ligand ;
Molecular tempMol ;
vector<Molecular> rotateVec;
rotateVec.push_back( rotateLig );
for( int k=7; k< pop->len_chromosomes; k++ ){
double rotateAngle = ((double*)adam->chromosome[0])[k];
Molecular mole = rotateAroundBond( rotateVec.back(),
rotableBondVec[k-7].get_firstAtomIndex(),
rotableBondVec[k-7].get_secAtomIndex(), rotateAngle );
// mole.print();
rotateVec.push_back( mole );
}
Molecular finalLig = rotateVec.back();
//---------------------------------------------------------------------------------------------------------------------
size_t count = 0;
while( count < 1000 ){
count ++;
// cout<<" "<<count;
for (point=0; point<3; point++)
{
((double *)adam->chromosome[0])[point]
= ( double )random_double( 360 );
}
Molecular newLig ;
Molecular newLig2 ;
double rotateX = ((double*)adam->chromosome[0])[0];
double rotateY = ((double*)adam->chromosome[0])[1];
double rotateZ = ((double*)adam->chromosome[0])[2];
newLig = rotateAroundAtom( finalLig, rotateCenterAtomIndex, rotateX, rotateY, rotateZ );
for (point=3; point<7; point++)
{
((double *)adam->chromosome[0])[point]
= (double)random_double_range( -0.0, 0.0 );
}
double transX = ((double*)adam->chromosome[0])[3];
double transY = ((double*)adam->chromosome[0])[4];
double transZ = ((double*)adam->chromosome[0])[5];
double transDis = ((double*)adam->chromosome[0])[6];
Coord trans( transX, transY, transZ );
newLig2 = translateMol( newLig, trans, transDis );
if( ! atomsCrash( bindingAtomVec, newLig2.get_atomVec() ) ){
cout<<"-----------------------------------------------------------"<<endl;
if( 1 ){
for( int k=0; k< pop->len_chromosomes; k++ ){
cout.width(12);
cout<<left<<((double*)adam->chromosome[0])[k];
}
cout<<endl;
}
// newLig2.print();
success = true;
break;
}
}
}
return true;
}