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ray.cc
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//#include "network.h"
#include <cmath>
#include <cstdlib>
#include <cassert>
#include <voro++.hh>
#include "ray.h"
#include "zeo_consts.h"
#include "channel.h"
#include "area_and_volume.h"
#include "network.h"
#include "networkaccessibility.h"
using namespace std;
using namespace voro;
/** Using |Point_0 - center| - radius^2 = 0 and Point_0 = t(Ray_dir) + Ray_pnt. Solve
for t which is the distance. **/
void Sphere::hitSphere(ray r,hitdata& hitsphere)
{
Point newCenter = center-r.base; //map the rand_ray to the origin and move system
double temp=(r.vector*newCenter)*(r.vector*newCenter)-(newCenter*newCenter)+radius*radius;
if (temp>0) //check inside of sqrt is not negative
{
if ((r.vector * newCenter) - sqrt(temp) > 0) //If it hits the sphere twice pick the closest
{
hitsphere.hit=true;
hitsphere.dist=(r.vector*newCenter) - sqrt(temp);
hitsphere.hitpoint=r.base+r.vector.scale(hitsphere.dist);
}
else if ((r.vector * newCenter) + sqrt(temp) > 0) //Ray was inside sphere (this is possible in some cases)
{
hitsphere.hit=true;
hitsphere.dist=(r.vector*newCenter) + sqrt(temp);
hitsphere.hitpoint=r.base+r.vector.scale(hitsphere.dist);
}
}
return;
}
/** Using normal dot (Point_Plane - Point_0| = 0 and Point_Plane = t(Ray_dir) + Ray_pnt. Solve for t which is the distance to plane. **/
void Plane::hitPlane(ray r,hitdata& hitplane)
{
if (normal*r.vector >= 0){ //ray is either parallel or infront of the plane
return;
}
double dist=((normal*point)-(normal*r.base))/(normal*r.vector);
if (dist < 0){ //There is no reason that the distance should be negative
cerr << "Error: Distance = " << dist << " This means ray got outside of unitcell" << endl;
cerr << "Point: " << r.base << " Vector: " << r.vector << endl;
abort();
}
hitplane.hit=true;
hitplane.dist=dist;
hitplane.hitpoint=r.base + r.vector.scale(dist);
return;
}
/** Returns the shortest distance from point to plane **/
double Plane::distToPlane(Point pnt)
{
return fabs(normal *(pnt - point));
}
/** Returns a class hitdata which has important information of the closest object hit. Function calls hitSphere for each sphere in the list **/
hitdata findClosestSphere(vector<Sphere>& s,ray& r)
{
hitdata hitsphere;
hitdata hitobject;
assert(hitobject.object == NULL);
for (unsigned int i=0;i<s.size();i++)
{
s[i].hitSphere(r,hitsphere);
if (hitsphere.hit == true)
{
if(hitobject.hit == false || hitobject.dist > hitsphere.dist) //Conditions for this to be closest sphere found so far
{
hitobject.hit = true;
hitobject.dist = hitsphere.dist;
hitobject.hitpoint = hitsphere.hitpoint;
hitobject.id = i;
hitobject.object = &(s[i]);
}
hitsphere.hit = false;
}
}
return hitobject;
}
/** Returns a class hitdata which has important information of the closest object hit. Function calls hitPlane for each plane in the list **/
hitdata findClosestPlane(vector<Plane>& p,ray& r)
{
hitdata hitplane;
hitdata hitobject;
for (unsigned int i=0;i<p.size();i++)
{
p[i].hitPlane(r,hitplane);
if (hitplane.hit == true)
{
if(hitobject.hit == false || hitobject.dist > hitplane.dist) //Conditions for this to be closest sphere found so far
{
hitobject.hit = true;
hitobject.dist = hitplane.dist;
hitobject.hitpoint = hitplane.hitpoint;
hitobject.id = i;
hitobject.object = &(p[i]);
}
hitplane.hit = false;
}
}
return hitobject;
}
/** Calculates the normals to the faces of the unit cell order is v_a x v_b : v_b x v_c : v_a x v_c as unit vectors**/
void calcPlanesToCell(ATOM_NETWORK *cell,vector<Plane> &p)
{
XYZ norm1 = cell->v_a.cross(cell->v_b).unit();
XYZ norm2 = cell->v_c.cross(cell->v_a).unit();
XYZ norm3 = cell->v_b.cross(cell->v_c).unit();
Plane face;
//Each face with abc point 0,0,0
face.point = cell->abc_to_xyz(Point(0,0,0));
face.normal = Point(norm1.x,norm1.y,norm1.z);
p.push_back(face);
face.normal = Point(norm2.x,norm2.y,norm2.z);
p.push_back(face);
face.normal = Point(norm3.x,norm3.y,norm3.z);
p.push_back(face);
//Each face with point abc point 1,1,1 (Notice that normals are reversed this is so that a vector can easily be determined if
//it hit within the unit cell
face.point = cell->abc_to_xyz(Point(1,1,1));
face.normal = Point(-norm1.x,-norm1.y,-norm1.z);
p.push_back(face);
face.normal = Point(-norm2.x,-norm2.y,-norm2.z);
p.push_back(face);
face.normal = Point(-norm3.x,-norm3.y,-norm3.z);
p.push_back(face);
}
/** Since all the opperations in Zeo++ are done within one unit cell it is important to duplicate the atoms that would overlap with the cell walls on the other side **/
void duplicateSpheresOnFace(ATOM_NETWORK *cell,vector<Sphere>& spheres,vector<Plane>& faces)
{
Sphere temp_sphere;
bool touch_face[6];
vector<double> permutation_a;
vector<double> permutation_b;
vector<double> permutation_c;
unsigned int size = spheres.size(); //because I will be adding spheres to list (there is a smarter way to do this...)
for (unsigned int i=0; i<size; i++)
{
//Assemble touch_face[] for which faces it touches
for (unsigned int j=0; j<faces.size(); j++)
{
if (faces[j].distToPlane(spheres[i].center) < (spheres[i].radius))
{
touch_face[j] = true;
}
else
{
touch_face[j] = false;
}
}
//Add allowable permutations on the unitcell
permutation_a.clear(); permutation_a.push_back(0.0);
permutation_b.clear(); permutation_b.push_back(0.0);
permutation_c.clear(); permutation_c.push_back(0.0);
if (touch_face[0] == true)
{
permutation_c.push_back(1.0);
}
if (touch_face[1] == true)
{
permutation_b.push_back(1.0);
}
if (touch_face[2] == true)
{
permutation_a.push_back(1.0);
}
if (touch_face[3] == true)
{
permutation_c.push_back(-1.0);
}
if (touch_face[4] == true)
{
permutation_b.push_back(-1.0);
}
if (touch_face[5] == true)
{
permutation_a.push_back(-1.0);
}
//Iterate through all the permutations on the sphere
temp_sphere = spheres[i];
for (unsigned int a=0; a<permutation_a.size(); a++)
{
for (unsigned int b=0; b<permutation_b.size(); b++)
{
for (unsigned int c=0; c<permutation_c.size(); c++)
{
if (permutation_a[a] != 0 || permutation_b[b] != 0 || permutation_c[c] != 0)
{
temp_sphere.center = spheres[i].center;
temp_sphere.center = temp_sphere.center + cell->abc_to_xyz(Point(permutation_a[a],permutation_b[b],permutation_c[c]));
spheres.push_back(temp_sphere);
}
}
}
}
}
}
/** This function converts nodes to spheres it allows for a more flexible implementation of ray_tracing thus making higher abstractions easier we are only concerned with the accessible nodes thus only these will be copied **/
void convertNodeToSphere(VORONOI_NETWORK& vornet,vector<Sphere>& nodes, vector<bool>& accessInfo)
{
Sphere temp_sphere;
VOR_NODE temp_vornode;
nodes.clear();
#if DEBUG
cout << "Adding: " << vornet.nodes.size() << " nodes (if all accessible)." << endl;
#endif
// for each node check if it intersects the unitcell
for (unsigned int i=0; i<vornet.nodes.size(); i++)
{
if (accessInfo[i] ==true)
{
temp_vornode = vornet.nodes[i];
temp_sphere.center = Point(temp_vornode.x,temp_vornode.y,temp_vornode.z);
temp_sphere.radius = temp_vornode.rad_stat_sphere;
nodes.push_back(temp_sphere);
}
}
}
/** This function converts atoms to spheres it allows for a more flexible implementation of ray_tracing thus making higher abstractions easier **/
void convertAtomToSphere(ATOM_NETWORK *cell,vector<Sphere>& atoms)
{
Sphere temp_sphere;
ATOM temp_atom;
atoms.clear();
#if DEBUG
cout << "Adding: " << cell->atoms.size() << " atoms." << endl;
#endif
// for each node check if it intersects the unitcell
for (unsigned int i=0; i<cell->atoms.size(); i++)
{
temp_atom = cell->atoms[i];
temp_sphere.center = Point(temp_atom.x,temp_atom.y,temp_atom.z);
temp_sphere.radius = temp_atom.radius;
atoms.push_back(temp_sphere);
}
}
/** This function finds a nodes radius that encompasses the point raypoint. It will not count the previous node that the raypoint was in by using the reference id**/
bool findSphereOfPoint(Point p,vector<Sphere>& spheres,int& id)
{
for (unsigned int i=0; i<spheres.size(); i++){
if ((calcEuclideanDistance(p,spheres[i].center) < spheres[i].radius) && (int)i != id){
id = i;
return true;
}
}
return false;
}
/**Generates a random vector direction and unitizes it. Since we want a random ray orientation in cartesian coordinates, sphereical coordinates are used to create a point **/
Point genRandomVec()
{
// Randomly sample point on a sphere of radius 1
double theta = (rand()*1.0/RAND_MAX)*2*PI;
double cosphi = 1.0 - (rand()*1.0/RAND_MAX)*2.0;
double phi = acos(cosphi);
// Convert spherical coordinates to xyz coordinates
double x = sin(phi)*cos(theta); //Don't need abs(sin(phi)) becase phi is from 0 to PI
double y = sin(phi)*sin(theta);
double z = cosphi;
Point temp(x,y,z);
if (temp.magnitude() == 0){
temp = genRandomVec();
}
return temp.unit();
}
/** This function generates a random point within the unit cell with values 0-1 for a,b, and c **/
Point genRandomPoint()
{
// Randomly sample ray across the unit cell
double aPoint = (rand()*1.0)/RAND_MAX;
double bPoint = (rand()*1.0)/RAND_MAX;
double cPoint = (rand()*1.0)/RAND_MAX;
return Point(aPoint,bPoint,cPoint);
}
/** This function will travel within a sphere until it hits a point that is no longer within spheres. Returns hitdata on the point it hits**/
void rayTraceInsideSphere(ATOM_NETWORK *cell,vector<Sphere>& spheres,ray r, hitdata& hitobject)
{
#if DEBUG
cout << "Current Ray Length: " << hitobject.dist << endl;
#endif
if (hitobject.dist > MAXRAYDIST){
return;
}
if (findSphereOfPoint(r.base,spheres,hitobject.id) == false) //This function also updates the id of the new sphere in hitsphere
{
return; //No sphere found that included point.
}
hitobject.object = &(spheres[hitobject.id]); //set the object*
//If inside sphere this it should hit the sphere
hitdata hitsphere;
spheres[hitobject.id].hitSphere(r,hitsphere);
if (hitsphere.hit == false){
//It is possible that point is an epsilon outside lets check
if (fabs(calcEuclideanDistance(r.base,spheres[hitobject.id].center) - spheres[hitobject.id].radius) < threshold)
{
//It was round-off error so lets continue
Sphere epsilon_sphere = spheres[hitobject.id];
if (((r.base - spheres[hitobject.id].center) * r.vector) > 0)
{ //vector is headed away from sphere
epsilon_sphere.radius += threshold;
}
else
{ // vector is headed into the sphere
epsilon_sphere.radius += -threshold;
}
epsilon_sphere.hitSphere(r,hitsphere);
}
if (hitsphere.hit == false) //Epsilon Case has been covered so thid should not happen
{
cerr << "Error: Ray did not hit a sphere. findSphereOfPoint said that one was within the radius. And it failed to be within an epsilon. Output in vmd style for easy visulization" << endl;
cout << "draw sphere {" << spheres[hitobject.id].center << "} radius " << spheres[hitobject.id].radius << " resolution 10\n";
Point p = r.base+r.vector.scale(10);
cout << "draw line {" << r.base << "} {" << p << "}\n";
abort();
}
}
hitobject.hit = hitsphere.hit;
hitobject.dist += hitsphere.dist; //Updates the distance traveled in spheres
r.base = cell->shiftXYZInUC(hitsphere.hitpoint); //Move back to unit cell and set values
hitobject.hitpoint = hitsphere.hitpoint;
rayTraceInsideSphere(cell,spheres,r,hitobject);
return;
}
/** This is a recursive function that will keep on extending a ray unitl it hits an atom or exceeds the maximum distance allowed (MAXRAYDIST)**/
void rayTraceToSphere(ATOM_NETWORK *cell,vector<Sphere>& spheres,ray r, vector<Plane>& faces,hitdata& hitobject)
{
#if DEBUG
cout << "Current Ray Length: " << hitobject.dist << endl;
#endif
if (hitobject.dist > MAXRAYDIST){
return;
}
//Find the closest atom that it will hit
hitdata hitsphere = findClosestSphere(spheres,r);
//If I hit an Sphere great!
if (hitsphere.hit == true)
{
if (hitsphere.id == hitobject.id)
{
//cerr << "Just hit same atom this is not allowable" << endl;
}
hitobject.hit = true;
hitobject.hitpoint = hitsphere.hitpoint;
hitobject.dist += hitsphere.dist;
hitobject.id = hitsphere.id;
hitobject.object = hitsphere.object;
return;
}
//If I didn't hit a Sphere then I must hit a unitcell face
hitsphere = findClosestPlane(faces,r);
assert(hitsphere.hit==true); //Thus it hit a plane
hitobject.hit = true;
hitobject.hitpoint = hitsphere.hitpoint;
hitobject.dist += hitsphere.dist;
hitobject.id = -1;
hitobject.object = NULL;
//I am moving the point just slightly outside of the unit cell to be shifted back in
r.base = cell->shiftXYZInUC(hitobject.hitpoint+r.vector.scale(threshold));
//this is a recursive call to get the total length of the ray
rayTraceToSphere(cell,spheres,r,faces,hitobject);
return;
}
/** Returns data from shooting a bunch of rays from accesible regions in the network until they hit an atom. Since the cell is periodic a max ray length can be set so ray does not shoot forever*/
void calcRaysInAV(ATOM_NETWORK *hiaccatmnet, ATOM_NETWORK *orgatmnet, bool highAccuracy, double r_probe_chan,double r_probe,int numSamples, ostream &output, bool visualize,string option){
ATOM_NETWORK *cell;
if(highAccuracy) cell=orgatmnet; else cell = hiaccatmnet; // this ensures that the loops below loop over original atoms
// and not "high-acuracy" clusters, which are used only for
// voronoi decomposition
// Create an object that handles analysis of accessibility of sampled points
AccessibilityClass accessAnalysis;
if(highAccuracy) accessAnalysis.setupAndFindChannels(hiaccatmnet, orgatmnet, highAccuracy, r_probe_chan, r_probe);
else accessAnalysis.setupAndFindChannels(hiaccatmnet, hiaccatmnet, highAccuracy, r_probe_chan, r_probe);
srand(randSeed); //randSeed can be set in network.h
//Initialize Ray Trace World
vector<Sphere> atoms;
convertAtomToSphere(cell,atoms);
vector<Sphere> nodes;
convertNodeToSphere(accessAnalysis.vornet,nodes,accessAnalysis.accessInfo);
vector<Plane> faces;
calcPlanesToCell(cell,faces);
//Duplicate the nodes and atoms that intersect with the plane faces
duplicateSpheresOnFace(cell,atoms,faces);
duplicateSpheresOnFace(cell,nodes,faces);
//Lists of Accessible, Inaccessible, and Resampled Rays
vector<ray> axsray; //List of successful rays that were shot
vector<ray> inaxsray;
vector<ray> resampledray; // List of resampled rays
#if DEBUG
//List Atoms, Nodes, and Planes
cout << "List of Atoms: " << endl;
for (unsigned int i=0; i<atoms.size(); i++)
{
cout << "Center: " << atoms[i].center << " Radius: " << atoms[i].radius << endl;;
}
cout << "List of Nodes: " << endl;
for (unsigned int i=0; i<nodes.size(); i++)
{
cout << "Center: " << nodes[i].center << " Radius: " << nodes[i].radius << endl;;
}
cout << "List of Cell Wall Faces: " << endl;
for (unsigned int i=0; i<faces.size(); i++)
{
cout << "Point: " << faces[i].point << " Normal: " << faces[i].normal << endl;;
}
#endif
//Begin Implementaitons of Ray Tracing Algorithm
cout << "Begin Ray Tracing Analysis: " << endl;
if (option.compare("atom") == 0)
{
cout << "Atom Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
ray rand_ray;
ray opposite_rand_ray;
hitdata hitobject;
for (int i=0; i<numSamples; i++)
{
rand_ray.base = cell->abc_to_xyz(genRandomPoint());
rand_ray.vector = genRandomVec();
bool point_accessible = accessAnalysis.isVPointAccessible(rand_ray.base);
if (point_accessible == false)
{
rand_ray.vector = Point(0,0,0);
inaxsray.push_back(rand_ray);
}
else //point is accessible
{
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
rayTraceToSphere(cell,atoms,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
//Test negative of ray
rayTraceToSphere(cell,atoms,opposite_rand_ray,faces,hitobject);
opposite_rand_ray.vector = opposite_rand_ray.vector.scale(hitobject.dist);
rand_ray.base = rand_ray.base + opposite_rand_ray.vector;
rand_ray.vector = rand_ray.vector - opposite_rand_ray.vector;
axsray.push_back(rand_ray);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
}
}
}
if (option.compare("node") == 0)
{
cout << "Node Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
int ndx = 0;
ray rand_ray;
ray opposite_rand_ray;
hitdata hitobject;
for (int i=0; i<numSamples; i++)
{
do {
ndx++;
if (ndx >= accessAnalysis.accessInfo.size())
{
ndx = 0;
}
} while(accessAnalysis.accessInfo[ndx] != true);
rand_ray.base = nodes[ndx].center;
rand_ray.vector = genRandomVec();
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
rayTraceToSphere(cell,atoms,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
//Test negative of ray
rayTraceToSphere(cell,atoms,opposite_rand_ray,faces,hitobject);
opposite_rand_ray.vector = opposite_rand_ray.vector.scale(hitobject.dist);
rand_ray.base = rand_ray.base + opposite_rand_ray.vector;
rand_ray.vector = rand_ray.vector - opposite_rand_ray.vector;
axsray.push_back(rand_ray);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
}
}
//Does not require to be found out if point is accessible
if (option.compare("sphere") == 0)
{
cout << "Sphere Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
ray rand_ray;
ray opposite_rand_ray;
hitdata hitobject;
for (int i=0; i<numSamples; i++)
{
rand_ray.base = cell->abc_to_xyz(genRandomPoint());
rand_ray.vector = genRandomVec();
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
rayTraceInsideSphere(cell,nodes,rand_ray,hitobject);
if (hitobject.hit == false)
{
rand_ray.vector = Point(0,0,0);
inaxsray.push_back(rand_ray);
}
else
{ //It was traveling within a sphere
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.id = -1;
hitobject.object = NULL;
hitobject.hitpoint = Point(0,0,0);
rayTraceInsideSphere(cell,nodes,opposite_rand_ray,hitobject);
opposite_rand_ray.vector = opposite_rand_ray.vector.scale(hitobject.dist);
rand_ray.base = rand_ray.base + opposite_rand_ray.vector;
rand_ray.vector = rand_ray.vector - opposite_rand_ray.vector;
axsray.push_back(rand_ray);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
}
}
}
//Does not require to be found out if point is accessible
if (option.compare("andrew_sphere") == 0)
{
cout << "Andrew's Sphere Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
ray rand_ray;
ray opposite_rand_ray;
ray init_ray;
ray opposite_init_ray;
double distance = 0.0;
hitdata hitobject;
bool inside_node = true;
for (int i=0; i<numSamples; i++)
{
distance = 0.0;
rand_ray.base = cell->abc_to_xyz(genRandomPoint());
rand_ray.vector = genRandomVec();
//Ray in the opposite direction
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
//For this implementation I need a reference to the original ray
init_ray = rand_ray;
opposite_init_ray = opposite_rand_ray;
if (findSphereOfPoint(rand_ray.base,nodes,hitobject.id) == false)
{
inside_node = false; //Point is not within a node
}
while(distance < MAXRAYDIST) //Iterate Ray untill it reaches max distance
{
if (inside_node == false)
{
rayTraceToSphere(cell,nodes,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
rand_ray.base = init_ray.base + init_ray.vector.scale(distance);
inaxsray.push_back(rand_ray);
//Update Total Info
distance += hitobject.dist;
rand_ray.vector = init_ray.vector;
rand_ray.base = cell->shiftXYZInUC(hitobject.hitpoint+rand_ray.vector.scale(threshold));
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.hitpoint = Point(0,0,0);
hitobject.id = -1;
hitobject.object = NULL;
inside_node = true; //Now inside node
}
else
{ //Shoot Through Nodes
rayTraceInsideSphere(cell,nodes,rand_ray,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
rand_ray.base = init_ray.base + init_ray.vector.scale(distance);
axsray.push_back(rand_ray);
//Update Total Info
distance += hitobject.dist;
rand_ray.vector = init_ray.vector;
rand_ray.base = cell->shiftXYZInUC(hitobject.hitpoint+rand_ray.vector.scale(threshold));
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.hitpoint = Point(0,0,0);
//Notice that I am not resetting hitobject.id and setting object
hitobject.object = &(nodes[hitobject.id]);
inside_node = false; //Now outside of nodes
}
}
}
cout << "Ray Andrew Sphere Implementation Completed:" << endl;
}
//Does not require to be found out if point is accessible
if (option.compare("andrew_atom") == 0)
{
cout << "Andrew's Atom Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
ray rand_ray;
ray opposite_rand_ray;
ray init_ray;
ray opposite_init_ray;
double distance = 0.0;
hitdata hitobject;
bool inside_atom = false;
bool inside_accessible_region;
for (int i=0; i<numSamples; i++)
{
distance = 0.0;
rand_ray.base = cell->abc_to_xyz(genRandomPoint());
rand_ray.vector = genRandomVec();
//Ray in the opposite direction
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
//For this implementation I need a reference to the original ray
init_ray = rand_ray;
opposite_init_ray = opposite_rand_ray;
if ((findSphereOfPoint(rand_ray.base,atoms,hitobject.id) == true))
{
inside_atom = true; //Point is within an atom
}
else //Point is not within an atom
{
inside_atom = false;
}
inside_accessible_region = accessAnalysis.isVPointAccessible(rand_ray.base);
while(distance < MAXRAYDIST) //Iterate Ray untill it reaches max distance
{
if ((inside_atom == false) && (inside_accessible_region == true))
{
rayTraceToSphere(cell,atoms,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
//rand_ray.base = init_ray.base + init_ray.vector.scale(distance);
axsray.push_back(rand_ray);
//Update Total Info
distance += hitobject.dist;
rand_ray.vector = init_ray.vector;
rand_ray.base = cell->shiftXYZInUC(hitobject.hitpoint+rand_ray.vector.scale(threshold));
//Reset all hitobject data
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.hitpoint = Point(0,0,0);
hitobject.id = -1;
hitobject.object = NULL;
inside_atom = true; //Now inside atom
}
else if ((inside_atom == false) && (inside_accessible_region == false))
{ //not within an atom but in inaccessible region
rayTraceToSphere(cell,atoms,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
//rand_ray.base = init_ray.base + init_ray.vector.scale(distance);
inaxsray.push_back(rand_ray);
//Update Total Info
distance += hitobject.dist;
rand_ray.vector = init_ray.vector;
rand_ray.base = cell->shiftXYZInUC(hitobject.hitpoint+init_ray.vector.scale(threshold));
//Reset all hitobject data
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.hitpoint = Point(0,0,0);
hitobject.object = NULL;
hitobject.id = -1;
inside_atom = true; //Now inside atom
}
else // Ray is inside of atoms
{
rayTraceInsideSphere(cell,atoms,rand_ray,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
//rand_ray.base = init_ray.base + init_ray.vector.scale(distance);
//This is where I would push data on traveling through atoms
//but it is not here yet
//Update Total Info
distance += hitobject.dist;
rand_ray.vector = init_ray.vector;
rand_ray.base = cell->shiftXYZInUC(hitobject.hitpoint+init_ray.vector.scale(threshold));
//Reset all hitobject data besides the last object id hit
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.hitpoint = Point(0,0,0);
//Notice that I am not resetting hitobject.id and setting object
hitobject.object = &(nodes[hitobject.id]);
//So at this point I know that I am outside an atom however am
//I in an accesible region or not?
inside_atom = false; //Now outside of atoms and in accessible region
inside_accessible_region = accessAnalysis.isVPointAccessible(rand_ray.base);
}
}
}
cout << "Ray Andrew Atom Implementation Completed:" << endl;
}
//Post Process Information
if(visualize)
{
reportRays(output, axsray, inaxsray, true);
//reportAtoms(output,atoms);
//reportNodes(output,nodes);
}
else //no visulization then output a histogram
{
//This parameter can be changed in network.h
reportHistogram(output,BINSIZE,MAXBINS,axsray);
}
reportRayInfo(axsray); // A more detailed output of ray info from program
//FREE MEMORY
accessAnalysis.deconstruct();
}
/* backup of calcRayinAV
// Returns data from shooting a bunch of rays from accesible regions in the network until they hit an atom. Since the cell is periodic a max ray length can be set so ray does not shoot forever
void calcRaysInAV(ATOM_NETWORK *cell, ATOM_NETWORK *orgcell, bool highAccuracy, double r_probe_chan,double r_probe,int numSamples, ostream &output, bool visualize,string option){
// Create a temporary copy of the atomic network in which each atom's radius has been increased by the probe radius
ATOM_NETWORK newAtomNet;
cell->copy(&newAtomNet);
for(int i = 0; i < newAtomNet.numAtoms; i++){ newAtomNet.atoms[i].radius += r_probe; }
// Calculate and store the Voronoi network for this new atomic network
VORONOI_NETWORK vornet;
vector<BASIC_VCELL> vorcells;
vector<VOR_CELL> advCells;
container_periodic_poly *new_rad_con = (container_periodic_poly *)performVoronoiDecomp(true, &newAtomNet, &vornet, advCells, false, vorcells);
vector<CHANNEL> channels = vector<CHANNEL>();
vector<bool> accessInfo = vector<bool> ();
CHANNEL::findChannels(&vornet, max(0.0, r_probe_chan - r_probe), &accessInfo, &channels);
srand(randSeed); //randSeed can be set in network.h
//Initialize Ray Trace World
vector<Sphere> atoms;
convertAtomToSphere(&newAtomNet,atoms);
vector<Sphere> nodes;
convertNodeToSphere(vornet,nodes,accessInfo);
vector<Plane> faces;
calcPlanesToCell(cell,faces);
//Duplicate the nodes and atoms that intersect with the plane faces
duplicateSpheresOnFace(cell,atoms,faces);
duplicateSpheresOnFace(cell,nodes,faces);
//Lists of Accessible, Inaccessible, and Resampled Rays
vector<ray> axsray; //List of successful rays that were shot
vector<ray> inaxsray;
vector<ray> resampledray; // List of resampled rays
#if DEBUG
//List Atoms, Nodes, and Planes
cout << "List of Atoms: " << endl;
for (unsigned int i=0; i<atoms.size(); i++)
{
cout << "Center: " << atoms[i].center << " Radius: " << atoms[i].radius << endl;;
}
cout << "List of Nodes: " << endl;
for (unsigned int i=0; i<nodes.size(); i++)
{
cout << "Center: " << nodes[i].center << " Radius: " << nodes[i].radius << endl;;
}
cout << "List of Cell Wall Faces: " << endl;
for (unsigned int i=0; i<faces.size(); i++)
{
cout << "Point: " << faces[i].point << " Normal: " << faces[i].normal << endl;;
}
#endif
//Begin Implementaitons of Ray Tracing Algorithm
cout << "Begin Ray Tracing Analysis: " << endl;
if (option.compare("atom") == 0)
{
cout << "Atom Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
ray rand_ray;
ray opposite_rand_ray;
hitdata hitobject;
for (int i=0; i<numSamples; i++)
{
rand_ray.base = cell->abc_to_xyz(genRandomPoint());
rand_ray.vector = genRandomVec();
bool point_accessible = accessiblePoint(rand_ray.base,new_rad_con,r_probe,cell,vorcells,accessInfo);
if (point_accessible == false)
{
rand_ray.vector = Point(0,0,0);
inaxsray.push_back(rand_ray);
}
else //point is accessible
{
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
rayTraceToSphere(cell,atoms,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
//Test negative of ray
rayTraceToSphere(cell,atoms,opposite_rand_ray,faces,hitobject);
opposite_rand_ray.vector = opposite_rand_ray.vector.scale(hitobject.dist);
rand_ray.base = rand_ray.base + opposite_rand_ray.vector;
rand_ray.vector = rand_ray.vector - opposite_rand_ray.vector;
axsray.push_back(rand_ray);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
}
}
}
if (option.compare("node") == 0)
{
cout << "Node Implementation Chosen: " << endl;
cout << "Number of Samples: " << numSamples << endl;
int ndx = 0;
ray rand_ray;
ray opposite_rand_ray;
hitdata hitobject;
for (int i=0; i<numSamples; i++)
{
do {
ndx++;
if (ndx >= accessInfo.size())
{
ndx = 0;
}
} while(accessInfo[ndx] != true);
rand_ray.base = nodes[ndx].center;
rand_ray.vector = genRandomVec();
opposite_rand_ray.base = rand_ray.base;
opposite_rand_ray.vector = rand_ray.vector.scale(-1);
rayTraceToSphere(cell,atoms,rand_ray,faces,hitobject);
rand_ray.vector = rand_ray.vector.scale(hitobject.dist);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
//Test negative of ray
rayTraceToSphere(cell,atoms,opposite_rand_ray,faces,hitobject);
opposite_rand_ray.vector = opposite_rand_ray.vector.scale(hitobject.dist);
rand_ray.base = rand_ray.base + opposite_rand_ray.vector;
rand_ray.vector = rand_ray.vector - opposite_rand_ray.vector;
axsray.push_back(rand_ray);
hitobject.dist = 0.0;
hitobject.hit = false;
hitobject.object = NULL;
hitobject.id = -1;
hitobject.hitpoint = Point(0,0,0);
}
}