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){
  ofstream sigmaOut("sigma.grid");
  ofstream sOut("s.grid");
  ofstream epsOut("eps.grid");
  double startDist;
  double phiVal;
  double thetaVal;
  double minDist = 10.0; //minimum start distance
        
  sList = sGrid;
  sigList = sigmaGrid;
  epsList = epsGrid;
  forcefield = forceField;
    
  //first determine the start distance - we always start at least minDist away
  startDist = rbMol->findMaxExtent() + minDist;
  if (startDist < minDist)
    startDist = minDist;

  //set the initial orientation of the body and loop over theta values
  phiVal = 0.0;
  thetaVal = thetaMin;
  rotBody(phiVal, thetaVal);
  for (k=0; k<bandwidth; k++){  
        //loop over phi values starting with phi = 0.0
    for (j=0; j<bandwidth; j++){
      releaseProbe(startDist);

      sigList.push_back(sigDist);
      sList.push_back(sDist);
      epsList.push_back(epsVal);
      
      phiVal += phiStep;
      rotBody(phiVal, thetaVal);
    }
    phiVal = 0.0;
    thetaVal += thetaStep;
    rotBody(phiVal, thetaVal);
    printf("step theta %i\n",k);
  }             
}

void GridBuilder::releaseProbe(double farPos){
  int tooClose;
  double tempPotEnergy;
  double interpRange;
  double interpFrac;
        
  probeCoor = farPos;
  potProgress.clear();
  distProgress.clear();
  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(){
  double rXij, rYij, rZij;
  double rijSquared;
  double rValSquared, rValPowerSix;
  double rparHe, epsHe;
  double atomRpar, atomEps;
  double rbAtomPos[3];
  
  //first get the probe atom parameters
  switch(forcefield){
    case 1:{
      rparHe = 1.4800;
      epsHe = -0.021270;
    }; break;
    case 2:{
      rparHe = 1.14;
      epsHe = 0.0203;
    }; break;
    case 3:{
      rparHe = 2.28;
      epsHe = 0.020269601874;
    }; break;
    case 4:{
      rparHe = 2.5560;
      epsHe = 0.0200;
    }; break;
    case 5:{
      rparHe = 1.14;
      epsHe = 0.0203;
    }; break;
  }
  
  potEnergy = 0.0;
  
  for(i=0; i<rbMol->getNumAtoms(); i++){
    rbMol->getAtomPos(rbAtomPos, i);
    
    rXij = rbAtomPos[0];
    rYij = rbAtomPos[1];
    rZij = rbAtomPos[2] - probeCoor;
    
    rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
    
    //in the interest of keeping the code more compact, we are being less efficient by placing 
    //a switch statement in the calculation loop
    switch(forcefield){
      case 1:{
        //we are using the CHARMm force field
        atomRpar = rbMol->getAtomRpar(i);
        atomEps = rbMol->getAtomEps(i);
        
        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
        rValPowerSix = rValSquared * rValSquared * rValSquared;
        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
      }; break;
      
      case 2:{
        //we are using the AMBER force field
        atomRpar = rbMol->getAtomRpar(i);
        atomEps = rbMol->getAtomEps(i);
        
        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
        rValPowerSix = rValSquared * rValSquared * rValSquared;
        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
      }; break;
      
      case 3:{
        //we are using Allen-Tildesley LJ parameters
        atomRpar = rbMol->getAtomRpar(i);
        atomEps = rbMol->getAtomEps(i);
        
        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (4*rijSquared);
        rValPowerSix = rValSquared * rValSquared * rValSquared;
        potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
        
      }; break;
      
      case 4:{
        //we are using the OPLS force field
        atomRpar = rbMol->getAtomRpar(i);
        atomEps = rbMol->getAtomEps(i);
        
        rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared);
        rValPowerSix = rValSquared * rValSquared * rValSquared;
        potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
      }; break;
      
      case 5:{
        //we are using the GAFF force field
        atomRpar = rbMol->getAtomRpar(i);
        atomEps = rbMol->getAtomEps(i);
        
        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
        rValPowerSix = rValSquared * rValSquared * rValSquared;
        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
      }; break;
    }    
  }
} 

void GridBuilder::rotBody(double pValue, double tValue){
  //zero out the euler angles
  for (l=0; l<3; l++)
    angles[i] = 0.0;
        
  //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
  angles[0] = pValue;
  //the second euler angle is for rotation about the x-axis (we use the zxz convention)
  angles[1] = tValue;
        
  //obtain the rotation matrix through the rigid body class
  rbMol->doEulerToRotMat(angles, rotX);
  
  //start from the reference position
  identityMat3(rbMatrix);
  rbMol->setA(rbMatrix);
  
  //rotate the rigid body
  matMul3(rotX, rbMatrix, rotatedMat);
  rbMol->setA(rotatedMat);      
}

void GridBuilder::printGridFiles(){
  ofstream sigmaOut("sigma.grid");
  ofstream sOut("s.grid");
  ofstream epsOut("eps.grid");
  
  for (k=0; k<sigList.size(); k++){
    sigmaOut << sigList[k] << "\n0\n";
    sOut << sList[k] << "\n0\n";    
    epsOut << epsList[k] << "\n0\n";
  }
}
Revision:	1282
Committed:	Mon Jun 21 15:10:29 2004 UTC (21 years, 4 months ago) by chrisfen
File size:	6851 byte(s)
Log Message:	Fixed the grid builder rotation problems
#	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	chrisfen	1280	rbMol = rb;
8			bandwidth = bandWidth;
9			thetaStep = PI / bandwidth;
10			thetaMin = thetaStep / 2.0;
11			phiStep = thetaStep * 2.0;
12	chrisfen	1277
13	chrisfen	1280	//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	chrisfen	1277	}
22
23			GridBuilder::~GridBuilder() {
24			}
25
26			void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
27	chrisfen	1280	vector<double> epsGrid){
28	chrisfen	1281	ofstream sigmaOut("sigma.grid");
29			ofstream sOut("s.grid");
30			ofstream epsOut("eps.grid");
31	chrisfen	1280	double startDist;
32	chrisfen	1282	double phiVal;
33			double thetaVal;
34	chrisfen	1280	double minDist = 10.0; //minimum start distance
35	chrisfen	1277
36	chrisfen	1281	sList = sGrid;
37			sigList = sigmaGrid;
38			epsList = epsGrid;
39	chrisfen	1280	forcefield = forceField;
40
41			//first determine the start distance - we always start at least minDist away
42			startDist = rbMol->findMaxExtent() + minDist;
43			if (startDist < minDist)
44			startDist = minDist;
45	chrisfen	1281
46	chrisfen	1282	//set the initial orientation of the body and loop over theta values
47			phiVal = 0.0;
48			thetaVal = thetaMin;
49			rotBody(phiVal, thetaVal);
50			for (k=0; k<bandwidth; k++){
51			//loop over phi values starting with phi = 0.0
52	chrisfen	1280	for (j=0; j<bandwidth; j++){
53			releaseProbe(startDist);
54	chrisfen	1279
55	chrisfen	1281	sigList.push_back(sigDist);
56			sList.push_back(sDist);
57			epsList.push_back(epsVal);
58	chrisfen	1282
59			phiVal += phiStep;
60			rotBody(phiVal, thetaVal);
61	chrisfen	1280	}
62	chrisfen	1282	phiVal = 0.0;
63			thetaVal += thetaStep;
64			rotBody(phiVal, thetaVal);
65			printf("step theta %i\n",k);
66	chrisfen	1280	}
67	chrisfen	1277	}
68
69			void GridBuilder::releaseProbe(double farPos){
70	chrisfen	1280	int tooClose;
71			double tempPotEnergy;
72			double interpRange;
73			double interpFrac;
74	chrisfen	1277
75	chrisfen	1280	probeCoor = farPos;
76			potProgress.clear();
77			distProgress.clear();
78			tooClose = 0;
79			epsVal = 0;
80			rhoStep = 0.1; //the distance the probe atom moves between steps
81	chrisfen	1277
82	chrisfen	1279
83	chrisfen	1280	while (!tooClose){
84			calcEnergy();
85			potProgress.push_back(potEnergy);
86			distProgress.push_back(probeCoor);
87	chrisfen	1277
88	chrisfen	1280	//if we've reached a new minimum, save the value and position
89			if (potEnergy < epsVal){
90			epsVal = potEnergy;
91			sDist = probeCoor;
92			}
93	chrisfen	1277
94	chrisfen	1280	//test if the probe reached the origin - if so, stop stepping closer
95			if (probeCoor < 0){
96			sigDist = 0.0;
97			tooClose = 1;
98			}
99	chrisfen	1277
100	chrisfen	1280	//test if the probe beyond the contact point - if not, take a step closer
101			if (potEnergy < 0){
102			sigDist = probeCoor;
103			tempPotEnergy = potEnergy;
104			probeCoor -= rhoStep;
105			}
106			else {
107			//do a linear interpolation to obtain the sigDist
108			interpRange = potEnergy - tempPotEnergy;
109			interpFrac = potEnergy / interpRange;
110			interpFrac = interpFrac * rhoStep;
111			sigDist = probeCoor + interpFrac;
112	chrisfen	1277
113	chrisfen	1280	//end the loop
114			tooClose = 1;
115			}
116			}
117	chrisfen	1277	}
118
119			void GridBuilder::calcEnergy(){
120	chrisfen	1281	double rXij, rYij, rZij;
121			double rijSquared;
122			double rValSquared, rValPowerSix;
123			double rparHe, epsHe;
124			double atomRpar, atomEps;
125			double rbAtomPos[3];
126
127			//first get the probe atom parameters
128			switch(forcefield){
129			case 1:{
130			rparHe = 1.4800;
131			epsHe = -0.021270;
132			}; break;
133			case 2:{
134			rparHe = 1.14;
135			epsHe = 0.0203;
136			}; break;
137			case 3:{
138			rparHe = 2.28;
139			epsHe = 0.020269601874;
140			}; break;
141			case 4:{
142			rparHe = 2.5560;
143			epsHe = 0.0200;
144			}; break;
145			case 5:{
146			rparHe = 1.14;
147			epsHe = 0.0203;
148			}; break;
149			}
150
151			potEnergy = 0.0;
152
153			for(i=0; i<rbMol->getNumAtoms(); i++){
154			rbMol->getAtomPos(rbAtomPos, i);
155
156			rXij = rbAtomPos[0];
157			rYij = rbAtomPos[1];
158			rZij = rbAtomPos[2] - probeCoor;
159
160			rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
161
162			//in the interest of keeping the code more compact, we are being less efficient by placing
163			//a switch statement in the calculation loop
164			switch(forcefield){
165			case 1:{
166			//we are using the CHARMm force field
167			atomRpar = rbMol->getAtomRpar(i);
168			atomEps = rbMol->getAtomEps(i);
169
170			rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
171			rValPowerSix = rValSquared * rValSquared * rValSquared;
172			potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
173			}; break;
174
175			case 2:{
176			//we are using the AMBER force field
177			atomRpar = rbMol->getAtomRpar(i);
178			atomEps = rbMol->getAtomEps(i);
179
180			rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
181			rValPowerSix = rValSquared * rValSquared * rValSquared;
182			potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
183			}; break;
184
185			case 3:{
186			//we are using Allen-Tildesley LJ parameters
187			atomRpar = rbMol->getAtomRpar(i);
188			atomEps = rbMol->getAtomEps(i);
189
190			rValSquared = ((rparHe+atomRpar)(rparHe+atomRpar)) / (4rijSquared);
191			rValPowerSix = rValSquared * rValSquared * rValSquared;
192			potEnergy += 4sqrt(epsHeatomEps)(rValPowerSix (rValPowerSix - 1.0));
193
194			}; break;
195
196			case 4:{
197			//we are using the OPLS force field
198			atomRpar = rbMol->getAtomRpar(i);
199			atomEps = rbMol->getAtomEps(i);
200
201			rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared);
202			rValPowerSix = rValSquared * rValSquared * rValSquared;
203			potEnergy += 4sqrt(epsHeatomEps)(rValPowerSix (rValPowerSix - 1.0));
204			}; break;
205
206			case 5:{
207			//we are using the GAFF force field
208			atomRpar = rbMol->getAtomRpar(i);
209			atomEps = rbMol->getAtomEps(i);
210
211			rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
212			rValPowerSix = rValSquared * rValSquared * rValSquared;
213			potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
214			}; break;
215			}
216			}
217			}
218	chrisfen	1277
219	chrisfen	1282	void GridBuilder::rotBody(double pValue, double tValue){
220	chrisfen	1280	//zero out the euler angles
221	chrisfen	1281	for (l=0; l<3; l++)
222	chrisfen	1280	angles[i] = 0.0;
223	chrisfen	1277
224	chrisfen	1282	//the phi euler angle is for rotation about the z-axis (we use the zxz convention)
225			angles[0] = pValue;
226	chrisfen	1280	//the second euler angle is for rotation about the x-axis (we use the zxz convention)
227	chrisfen	1282	angles[1] = tValue;
228	chrisfen	1277
229	chrisfen	1280	//obtain the rotation matrix through the rigid body class
230			rbMol->doEulerToRotMat(angles, rotX);
231	chrisfen	1282
232			//start from the reference position
233			identityMat3(rbMatrix);
234			rbMol->setA(rbMatrix);
235
236	chrisfen	1280	//rotate the rigid body
237			matMul3(rotX, rbMatrix, rotatedMat);
238			rbMol->setA(rotatedMat);
239	chrisfen	1277	}
240
241	chrisfen	1281	void GridBuilder::printGridFiles(){
242			ofstream sigmaOut("sigma.grid");
243			ofstream sOut("s.grid");
244			ofstream epsOut("eps.grid");
245
246			for (k=0; k<sigList.size(); k++){
247			sigmaOut << sigList[k] << "\n0\n";
248			sOut << sList[k] << "\n0\n";
249			epsOut << epsList[k] << "\n0\n";
250			}
251			}