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voronoicell.cc
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//#include "network.h"
#include <cstdlib>
#include "voronoicell.h"
#include "graphstorage.h"
using namespace std;
/* This file contains two definitions of Voronoi cells: one that stores
* information about the faces, edges and nodes in each cell and one that only
* stores information about the node coordinates. The first definition, VOR_CELL, is used
* when visualization is important. The other, BASIC_VCELL, is used in surface area/volume
* calculations to decrease overhead time.
*
* The file also contains all of the functions required to visualize an ATOM_NETWORK
* and VORONOI_NETWORK using the ZeoVis tool.
*/
/* Store the provided vertices and their ids. */
VOR_FACE::VOR_FACE(vector<Point> vertices, ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet){
orderedVertices = vertices;
for(unsigned int i = 0; i < orderedVertices.size(); i++){
nodeIDs.push_back(getNodeID(orderedVertices.at(i), atmnet, vornet));
}
}
/* Store the provided vertices and their ids. */
VOR_FACE::VOR_FACE(vector<Point> vertices, vector<int> vertexIDs) {
orderedVertices = vertices;
nodeIDs = vertexIDs;
}
/* Returns a vector of pairs of integers and Points, where each entry represents
* the pair (node id, node coordinates).*/
vector< pair<int,Point> > VOR_FACE::getNodes(){
vector< pair<int,Point> > results = vector< pair<int,Point> > ();
for(unsigned int i = 0; i < orderedVertices.size(); i++){
results.push_back(pair<int,Point> (nodeIDs[i], orderedVertices[i]));
}
return results;
}
/* Returns a vector of pairs of Points representing the start and end coordinates
* of each edge that outlines the face. */
vector< pair<Point, Point> > VOR_FACE::getEdgeCoords() {
vector< pair<Point, Point> > results = vector< pair<Point,Point> > ();
for(unsigned int i = 0; i < orderedVertices.size() - 1; i++){
Point curPt = orderedVertices[i];
Point nextPt = orderedVertices[i+1];
results.push_back(pair<Point,Point> (curPt,nextPt));
}
results.push_back(pair<Point,Point> (orderedVertices[orderedVertices.size() - 1],orderedVertices[0]));
return results;
}
/* Using the provided ouput stream, write the geometric objects that would fill the Voronoi
* face when drawn. */
void VOR_FACE::writeVMDFilled(fstream &output){
Point p1 = orderedVertices[0];
unsigned int n2 = 1;
unsigned int n3 = 2;
while(n3 < orderedVertices.size()){
Point p2 = orderedVertices.at(n2);
Point p3 = orderedVertices.at(n3);
output << "{triangle {"
<< p1[0] << " " << p1[1] << " " << p1[2] << "} {"
<< p2[0] << " " << p2[1] << " " << p2[2] << "} {"
<< p3[0] << " " << p3[1] << " " << p3[2] << "} }" << "\n";
n2++;
n3++;
}
}
/*Constructs a VOR_CELL that does not initially have any faces or vertices.*/
VOR_CELL::VOR_CELL(){
faces = vector<VOR_FACE> ();
numVertices = 0;
vertexIDs = map<Point, int, bool(*)(Point,Point)> (pointIsLess);
idMappings = map<int,int> ();
reverseIDMappings = map<int, vector<int> > ();
vertexCoords = map<int,Point> ();
edgeConnections = vector< set<int> > ();
}
/* Add the provided coordinate and its corresponding node id if
* no such vertex has been previously added.*/
void VOR_CELL::addNode(int nodeID, Point coord){
if(vertexIDs.find(coord) == vertexIDs.end()){
idMappings.insert(pair<int,int> (numVertices, nodeID));
map<int, vector<int> >::iterator revMap = reverseIDMappings.find(nodeID);
if(revMap == reverseIDMappings.end()){
vector<int> newList = vector<int> ();
newList.push_back(numVertices);
reverseIDMappings.insert(pair<int, vector<int> > (nodeID, newList));
}
else {
revMap->second.push_back(numVertices);
}
vertexIDs.insert(pair<Point,int> (coord, numVertices));
vertexCoords.insert(pair<int,Point> (numVertices, coord));
edgeConnections.push_back(set<int>());
numVertices++;
}
}
/* Add the edge that spans the two points if it has not yet been added.*/
void VOR_CELL::addEdge(Point from, Point to){
map<Point,int>::iterator iter1 = vertexIDs.find(from);
map<Point,int>::iterator iter2 = vertexIDs.find(to);
if((iter1 == vertexIDs.end()) || (iter2 == vertexIDs.end())){
cerr << "Unable to add edge because nodes have not been added." << "\n"
<< "Point 1: (" << from[0] << ", " << from[1] << ", " << from[2] << ")" << "\n"
<< "Point 2: (" << to[0] << ", " << to[1] << ", " << to[2] << ")" << "\n"
<< "Exiting..." << "\n";
exit(1);
}
if(edgeConnections[iter2->second].find(iter1->second) == edgeConnections[iter2->second].end())
edgeConnections[iter1->second].insert(iter2->second);
}
/* Add the face to the VOR_CELL. Adds all edges and vertices that have not yet been added
* to the cell.*/
void VOR_CELL::addFace(VOR_FACE face) {
faces.push_back(face);
vector< pair<int,Point> > nodes = face.getNodes();
for(unsigned int i = 0; i < nodes.size(); i++){
pair<int, Point> node = nodes[i];
addNode(node.first, node.second);
}
vector< pair<Point, Point> > edges= face.getEdgeCoords();
for(unsigned int i = 0; i < edges.size(); i++){
pair<Point,Point> coord = edges[i];
addEdge(coord.first, coord.second);
}
}
/* Returns a vector containing all of the coordinates in the VOR_CELL that
* whose node id is as provided.*/
vector<Point> VOR_CELL::getNodeCoords(int nodeID){
map<int, vector<int> >::iterator iter = reverseIDMappings.find(nodeID);
if(iter == reverseIDMappings.end()){
cerr << "Error: Node #" << nodeID << " isn't in this Voronoi cell." << "\n";
cerr << "Cell contains these nodes: ";
map<int, vector<int> >::iterator nIter = reverseIDMappings.begin();
while(nIter != reverseIDMappings.end()){
cerr << nIter->first << " ";
nIter++;
}
cerr << "\n";
cerr << "Exiting..." << "\n";
exit(1);
}
vector<int> vertexIDs = iter->second;
vector<Point> coords = vector<Point> ();
for(unsigned int i = 0; i < vertexIDs.size(); i++){
coords.push_back(vertexCoords.find(vertexIDs[i])->second);
}
return coords;
}
/* Using the underlying list of faces, write the set of commands necessary
* to fill the VOR_CELL's exterior to the provided output stream. Labels
* the corresponding commands as faces(n).*/
void VOR_CELL::writeVMDFilled(fstream &output, int n){
output << "set faces(" << n << ") {" << "\n"
<< "{color $faceColors(" << n << ") }" << "\n";
for(unsigned int i = 0; i < faces.size(); i++){
faces[i].writeVMDFilled(output);
}
output << "}" << "\n";
}
/* Using the set of nodes and edges, write the set of commands necessary to
* draw the outline of the VOR_CELL to the provided output stream. Labels
* the corresponding commands as vorcells(n)*/
void VOR_CELL::writeVMDOutlined(fstream &output, int n){
output << "set vorcells(" << n <<") {" << "\n";
// Iterate over all nodes in VOR_CELL
for(int i = 0; i < numVertices; i++){
Point curPoint = vertexCoords.find(i)->second;
int nodeID = idMappings.find(i)->second;
output << "{color $nodeColors(" << nodeID << ") }" << "\n";
output << "{sphere {" << curPoint[0] << " " << curPoint[1] << " " << curPoint[2] << "} radius $nodeRadii(" << nodeID << ") resolution $sphere_resolution}" << "\n";
}
// Iterate over all edges in VOR_CELL
output << "{color $vorcellColors(" << n << ") }" << "\n";
for(int i = 0; i < numVertices; i++){
Point p1 = vertexCoords[i];
set<int>::iterator vertexIter = edgeConnections[i].begin();
while(vertexIter != edgeConnections[i].end()){
Point p2 = vertexCoords[*vertexIter];
output << "{line {"
<< p1[0] << " " << p1[1] << " " << p1[2] << "} {"
<< p2[0] << " " << p2[1] << " " << p2[2] << "} width 1}" << "\n";
vertexIter++;
}
}
output << "}" << "\n";
}
/* Using the provided list of VOR_FACEs, reconstruct each VOR_CELL
* and store it using the provided vector pointer. */
void VOR_CELL::getVoronoiCells(vector<VOR_CELL> *cells, vector< vector<VOR_FACE> > faceInfo,
ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet){
cells->clear();
for(unsigned int i = 0; i < faceInfo.size(); i++){
VOR_CELL newCell;
for(unsigned int j = 0; j < faceInfo[i].size(); j++)
newCell.addFace(faceInfo[i][j]);
cells->push_back(newCell);
}
}
BASIC_VCELL::BASIC_VCELL(){
nodeCoords = vector<Point> ();
nodeIDs = vector<int> ();
}
BASIC_VCELL::BASIC_VCELL (vector<Point> myNodeCoords, vector<int> myNodeIDs){
nodeCoords = myNodeCoords;
nodeIDs = myNodeIDs;
}
int BASIC_VCELL::getNumNodes(){
return nodeCoords.size();
}
Point BASIC_VCELL::getNodeCoord(int index){
return nodeCoords[index];
}
int BASIC_VCELL::getNodeID(int index){
return nodeIDs[index];
}
/* Removes the nodes from the cell which would overlap with a sphere center around
the provided atom with a radius of r_probe + r_atom*/
void BASIC_VCELL::removeOverlappedNodes(int atomID, ATOM_NETWORK *atmnet, double r_probe){
vector<int> newIDs;
vector<Point> newCoords;
ATOM center = atmnet->atoms[atomID];
for(unsigned int i = 0; i < nodeCoords.size(); i++){
Point node = nodeCoords[i];
if(calcEuclideanDistance(node[0], node[1], node[2], center.x, center.y, center.z) >=
(center.radius + r_probe)){
newIDs.push_back(nodeIDs[i]);
newCoords.push_back(nodeCoords[i]);
}
}
nodeIDs = newIDs;
nodeCoords = newCoords;
}
void BASIC_VCELL::writeToVMD(fstream &output, int n){
output << "set nodecells(" << n <<") {" << "\n";
// Iterate over all nodes in the cell
for(unsigned int i = 0; i < nodeCoords.size(); i++){
Point curPoint = nodeCoords[i];
int nodeID = nodeIDs[i];
output << "{color $nodeColors(" << nodeID << ") }" << "\n";
output << "{sphere {" << curPoint[0] << " " << curPoint[1] << " " << curPoint[2]
<< "} radius $nodeRadii(" << nodeID << ") resolution $sphere_resolution}" << "\n";
}
output << "}" << "\n";
}
/* Writes the commands to the provided output stream necessary to approriately
* display the unit cell in the ZeoVis visualization tool. Labels the unitcell
* as unitcells(0).
*/
void writeVMDUC(fstream &output, ATOM_NETWORK *atmnet){
XYZ v_a = atmnet->v_a;
XYZ v_b = atmnet->v_b;
XYZ v_c = atmnet->v_c;
output << "set unitcells(0) {" << "\n"
<< "{color $unitcellColors(0)}" << "\n";
DELTA_POS directions [3] = {DELTA_POS(1,0,0), DELTA_POS(0,1,0), DELTA_POS(0,0,1)};
DELTA_POS limits [3] = {DELTA_POS(0,1,1), DELTA_POS(1,0,1), DELTA_POS(1,1,0)};
for(unsigned int i = 0; i < 3; i++){
DELTA_POS direction = directions[i];
DELTA_POS limit = limits[i];
for(int a = 0; a < 2; a++){
for(int b = 0; b < 2; b++){
for(int c = 0; c < 2; c++){
if((limit.x < a) || (limit.y < b) || (limit.z < c))
continue;
// Calculate starting coordinate
double x1 = v_a.x *a + v_b.x*b + v_c.x*c;
double y1 = v_a.y *a + v_b.y*b + v_c.y*c;
double z1 = v_a.z *a + v_b.z*b + v_c.z*c;
// Calculate ending coordinate
double x2 = x1 + v_a.x*direction.x + v_b.x*direction.y + v_c.x*direction.z;
double y2 = y1 + v_a.y*direction.x + v_b.y*direction.y + v_c.y*direction.z;
double z2 = z1 + v_a.z*direction.x + v_b.z*direction.y + v_c.z*direction.z;
output << "{line "
<< "{" << x1 << " " << y1 << " " << z1 << "} "
<< "{" << x2 << " " << y2 << " " << z2 << "} }" << "\n";
}
}
}
}
output << "}" << "\n";
}
/* Writes the commands to the provided output stream necessary to display
* the entire Voronoi network. Labels the Voronoi network as vornets(0).
*/
void writeVornet(fstream &output, ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet){
output << "set vornets(0) {" << "\n";
// Iterate over all Voronoi nodes
for(unsigned int i = 0; i < vornet->nodes.size(); i++){
VOR_NODE curNode = vornet->nodes.at(i);
output << "{color $nodeColors("<< i << ") }" << "\n"
<< "{sphere {" << curNode.x << " " << curNode.y << " " << curNode.z
<< "} radius $nodeRadii(" << i << ") resolution $sphere_resolution}" << "\n";
}
// Iterate over all Voronoi edges
output << "{color $vornetColors(0)}" << "\n";
for(unsigned int i = 0; i < vornet->edges.size(); i++){
VOR_EDGE curEdge = vornet->edges.at(i);
VOR_NODE startNode = vornet->nodes.at(curEdge.from);
Point start = Point(startNode.x, startNode.y, startNode.z);
VOR_NODE endNode = vornet->nodes.at(curEdge.to);
Point end = Point(endNode.x, endNode.y, endNode.z);
atmnet->translatePoint(&end, curEdge.delta_uc_x, curEdge.delta_uc_y, curEdge.delta_uc_z);
output << "{line {"
<< start[0] << " " << start[1] << " " << start[2] << "} "
<< "{" << end[0] << " " << end[1] << " " << end[2] << "}"
<< "}" << "\n";
}
output << "}" << "\n";
}
/* Writes the commands to the provided output stream necessary to display all atoms and
* Voronoi nodes in ZeoVis. Labels each atom as atoms(i) and each node as nodes(j).
*/
void writeVMDAtomsAndNodes(fstream &output, ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet){
// Iterate over all atoms. Set the radius of the atom to its actual value
for(unsigned int i = 0; i < atmnet->atoms.size(); i++){
ATOM curAtom = atmnet->atoms.at(i);
output << "set atoms(" << i << ") {" << "\n"
<< "{color $atomColors(" << i << ") }" << "\n"
<< "{sphere {" << curAtom.x << " " << curAtom.y << " " << curAtom.z
<< "} radius $atomRadii(" << i << ") resolution $sphere_resolution}"
<< "\n" << "}" << "\n";
output << "set atomRadii(" << i << ") " << curAtom.radius << "\n";
}
// Iterate over all nodes. Set the radius of the node to that of the maximum static sphere
for(unsigned int i = 0; i < vornet->nodes.size(); i++){
VOR_NODE curNode = vornet->nodes.at(i);
output << "set nodes(" << i << ") {" << "\n"
<< "{color $nodeColors("<< i << ") }" << "\n"
<< "{sphere {" << curNode.x << " " << curNode.y << " " << curNode.z
<< "} radius $nodeRadii(" << i << ") resolution $sphere_resolution}" << "\n"
<< "}" << "\n";
output << "set nodeRadii(" << i << ") " << curNode.rad_stat_sphere << "\n";
}
}
/* Writes the commands to the provided output stream for ZeoVis
* that establishes the number of each component as well as
* unitcell vector information.
*/
void writeVMDEnvVars(fstream &output, ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet){
// Write information about the number of each component
output << "set num_vorcells " << atmnet->numAtoms << "\n";
output << "set num_faces " << atmnet->numAtoms << "\n";
output << "set num_vornets 1" << "\n";
output << "set num_nodes " << vornet->nodes.size() << "\n";
output << "set num_atoms " << atmnet->numAtoms << "\n";
output << "set num_unitcells 1" << "\n";
output << "set num_channels 0" << "\n";
// Write unitcell vector information
output << "set uc_a_vector {" << atmnet->v_a.x << " " << atmnet->v_a.y
<< " " << atmnet->v_a.z << "}" << "\n";
output << "set uc_b_vector {" << atmnet->v_b.x << " " << atmnet->v_b.y
<< " " << atmnet->v_b.z << "}" << "\n";
output << "set uc_c_vector {" << atmnet->v_c.x << " " << atmnet->v_c.y
<< " " << atmnet->v_c.z << "}" << "\n";
output << "set sphere_resolution 100" << "\n";
}
/* Writes all of the information necessary to properly visualize the Voronoi
* and atom network in ZeoVis to the file referred to by filename. Information
* includes atoms, nodes, the unitcell, the voronoi network,
* voronoi cells (outlined and filled) and environment variables.
*/
void writeZeoVisFile(char *filename, vector<VOR_CELL> *cells,
ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet)
{
fstream output;
output.open(filename, fstream::out);
if(!output.is_open()){
cout << "Error: Failed to open output file for ZeoVis settings" << filename;
cout << "Exiting ..." << "\n";
exit(1);
}
else{
cout << "Writing ZeoVis information to " << filename << "\n";
writeVMDEnvVars(output, atmnet, vornet);
writeVMDAtomsAndNodes(output, atmnet, vornet);
writeVornet(output, atmnet, vornet);
writeVMDUC(output, atmnet);
for(unsigned int i = 0; i < cells->size(); i++){
cells->at(i).writeVMDOutlined(output, i);
cells->at(i).writeVMDFilled(output, i);
}
output << "set num_faces " << cells->size() << "\n"
<< "set num_channels " << 0 << "\n"
<< "set num_features " << 0 << "\n"
<< "set num_segments " << 0 << "\n"
<< "set num_cages " << 0 << "\n";
}
output.close();
}
/* Identical to writeZeoVisFile except that information about the basic voronoi
* cells is also outputted. */
void writeSpecialZeoVisFile(char *filename, vector<VOR_CELL> *cells,
ATOM_NETWORK *atmnet, VORONOI_NETWORK *vornet, vector<BASIC_VCELL> &vcells)
{
fstream output;
output.open(filename, fstream::out);
if(!output.is_open()){
cout << "Error: Failed to open output file for ZeoVis settings" << filename;
cout << "Exiting ..." << "\n";
exit(1);
}
else{
cout << "Writing ZeoVis information to " << filename << "\n";
writeVMDEnvVars(output, atmnet, vornet);
writeVMDAtomsAndNodes(output, atmnet, vornet);
writeVornet(output, atmnet, vornet);
writeVMDUC(output, atmnet);
for(unsigned int i = 0; i < cells->size(); i++){
cells->at(i).writeVMDOutlined(output, i);
cells->at(i).writeVMDFilled(output, i);
}
output << "set num_faces " << cells->size() << "\n";
output << "set num_channels " << 0 << "\n";
for(unsigned int i = 0; i < vcells.size(); i++){
vcells[i].writeToVMD(output, i);
}
}
output.close();
}