trunk/SHAPES/GridBuilder.cpp

#include "GridBuilder.hpp"
#include "MatVec3.h"
#define PI 3.14159265359


GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) {
        rbMol = rb;
        bandwidth = bandWidth;
        thetaStep = PI / bandwidth;
        thetaMin = thetaStep / 2.0;
        phiStep = thetaStep * 2.0;
        
        //zero out the rot mats
        for (i=0; i<3; i++) {
                for (j=0; j<3; j++) {
                        rotX[i][j] = 0.0;
                        rotZ[i][j] = 0.0;
                        rbMatrix[i][j] = 0.0;
                }
        }
}

GridBuilder::~GridBuilder() {
}

void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
        vector<double> epsGrid){
        double startDist;
        double minDist = 10.0; //minimum start distance
        
        //first determine the start distance - we always start at least minDist away
        startDist = rbMol->findMaxExtent() + minDist;
        if (startDist < minDist)
                startDist = minDist;
        
        initBody();
        for (i=0; i<bandwidth; i++){            
                for (j=0; j<bandwidth; j++){
                        releaseProbe(startDist);
                        stepPhi(phiStep);
                }
                stepTheta(thetaStep);
        }
                
}

void GridBuilder::initBody(){
        //set up the rigid body in the starting configuration
        stepTheta(thetaMin);
}

void GridBuilder::releaseProbe(double farPos){
        int tooClose;
        double tempPotEnergy;
        double interpRange;
        double interpFrac;
        
        probeCoor = farPos;
        tooClose = 0;
        epsVal = 0;
        rhoStep = 0.1; //the distance the probe atom moves between steps
        
        while (!tooClose){
                calcEnergy();
                potProgress.push_back(potEnergy);
                distProgress.push_back(probeCoor);
                
                //if we've reached a new minimum, save the value and position
                if (potEnergy < epsVal){
                        epsVal = potEnergy;
                        sDist = probeCoor;
                }
                
                //test if the probe reached the origin - if so, stop stepping closer
                if (probeCoor < 0){
                        sigDist = 0.0;
                        tooClose = 1;
                }
                
                //test if the probe beyond the contact point - if not, take a step closer
                if (potEnergy < 0){
                        sigDist = probeCoor;
                        tempPotEnergy = potEnergy;
                        probeCoor -= rhoStep;
                }
                else {
                        //do a linear interpolation to obtain the sigDist 
                        interpRange = potEnergy - tempPotEnergy;
                        interpFrac = potEnergy / interpRange;
                        interpFrac = interpFrac * rhoStep;
                        sigDist = probeCoor + interpFrac;
                        
                        //end the loop
                        tooClose = 1;
                }
        }
}

void GridBuilder::calcEnergy(){
        
}

void GridBuilder::stepTheta(double increment){
        //zero out the euler angles
        for (i=0; i<3; i++)
                angles[i] = 0.0;
        
        //the second euler angle is for rotation about the x-axis (we use the zxz convention)
        angles[1] = increment;
        
        //obtain the rotation matrix through the rigid body class
        rbMol->doEulerToRotMat(angles, rotX);
        
        //rotate the rigid body
        rbMol->getA(rbMatrix);
        matMul3(rotX, rbMatrix, rotatedMat);
        rbMol->setA(rotatedMat);
        
}

void GridBuilder::stepPhi(double increment){
        //zero out the euler angles
        for (i=0; i<3; i++)
                angles[i] = 0.0;
        
        //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
        angles[0] = increment;
        
        //obtain the rotation matrix through the rigid body class
        rbMol->doEulerToRotMat(angles, rotZ);
        
        //rotate the rigid body
        rbMol->getA(rbMatrix);
        matMul3(rotZ, rbMatrix, rotatedMat);
        rbMol->setA(rotatedMat);
        
}
Revision:	1277
Committed:	Thu Jun 17 21:29:17 2004 UTC (20 years, 3 months ago) by chrisfen
File size:	3094 byte(s)
Log Message:	Added GridBuilder.cpp and .hpp. Doesn't calculate energies yet...
#	User	Rev	Content
1	chrisfen	1277	#include "GridBuilder.hpp"
2			#include "MatVec3.h"
3			#define PI 3.14159265359
4
5
6			GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) {
7			rbMol = rb;
8			bandwidth = bandWidth;
9			thetaStep = PI / bandwidth;
10			thetaMin = thetaStep / 2.0;
11			phiStep = thetaStep * 2.0;
12
13			//zero out the rot mats
14			for (i=0; i<3; i++) {
15			for (j=0; j<3; j++) {
16			rotX[i][j] = 0.0;
17			rotZ[i][j] = 0.0;
18			rbMatrix[i][j] = 0.0;
19			}
20			}
21			}
22
23			GridBuilder::~GridBuilder() {
24			}
25
26			void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
27			vector<double> epsGrid){
28			double startDist;
29			double minDist = 10.0; //minimum start distance
30
31			//first determine the start distance - we always start at least minDist away
32			startDist = rbMol->findMaxExtent() + minDist;
33			if (startDist < minDist)
34			startDist = minDist;
35
36			initBody();
37			for (i=0; i<bandwidth; i++){
38			for (j=0; j<bandwidth; j++){
39			releaseProbe(startDist);
40			stepPhi(phiStep);
41			}
42			stepTheta(thetaStep);
43			}
44
45			}
46
47			void GridBuilder::initBody(){
48			//set up the rigid body in the starting configuration
49			stepTheta(thetaMin);
50			}
51
52			void GridBuilder::releaseProbe(double farPos){
53			int tooClose;
54			double tempPotEnergy;
55			double interpRange;
56			double interpFrac;
57
58			probeCoor = farPos;
59			tooClose = 0;
60			epsVal = 0;
61			rhoStep = 0.1; //the distance the probe atom moves between steps
62
63			while (!tooClose){
64			calcEnergy();
65			potProgress.push_back(potEnergy);
66			distProgress.push_back(probeCoor);
67
68			//if we've reached a new minimum, save the value and position
69			if (potEnergy < epsVal){
70			epsVal = potEnergy;
71			sDist = probeCoor;
72			}
73
74			//test if the probe reached the origin - if so, stop stepping closer
75			if (probeCoor < 0){
76			sigDist = 0.0;
77			tooClose = 1;
78			}
79
80			//test if the probe beyond the contact point - if not, take a step closer
81			if (potEnergy < 0){
82			sigDist = probeCoor;
83			tempPotEnergy = potEnergy;
84			probeCoor -= rhoStep;
85			}
86			else {
87			//do a linear interpolation to obtain the sigDist
88			interpRange = potEnergy - tempPotEnergy;
89			interpFrac = potEnergy / interpRange;
90			interpFrac = interpFrac * rhoStep;
91			sigDist = probeCoor + interpFrac;
92
93			//end the loop
94			tooClose = 1;
95			}
96			}
97			}
98
99			void GridBuilder::calcEnergy(){
100
101			}
102
103			void GridBuilder::stepTheta(double increment){
104			//zero out the euler angles
105			for (i=0; i<3; i++)
106			angles[i] = 0.0;
107
108			//the second euler angle is for rotation about the x-axis (we use the zxz convention)
109			angles[1] = increment;
110
111			//obtain the rotation matrix through the rigid body class
112			rbMol->doEulerToRotMat(angles, rotX);
113
114			//rotate the rigid body
115			rbMol->getA(rbMatrix);
116			matMul3(rotX, rbMatrix, rotatedMat);
117			rbMol->setA(rotatedMat);
118
119			}
120
121			void GridBuilder::stepPhi(double increment){
122			//zero out the euler angles
123			for (i=0; i<3; i++)
124			angles[i] = 0.0;
125
126			//the phi euler angle is for rotation about the z-axis (we use the zxz convention)
127			angles[0] = increment;
128
129			//obtain the rotation matrix through the rigid body class
130			rbMol->doEulerToRotMat(angles, rotZ);
131
132			//rotate the rigid body
133			rbMol->getA(rbMatrix);
134			matMul3(rotZ, rbMatrix, rotatedMat);
135			rbMol->setA(rotatedMat);
136
137			}