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root/group/trunk/SHAPES/GridBuilder.cpp
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Comparing trunk/SHAPES/GridBuilder.cpp (file contents):
Revision 1280 by chrisfen, Fri Jun 18 19:40:31 2004 UTC vs.
Revision 1283 by gezelter, Mon Jun 21 15:54:27 2004 UTC

# Line 9 | Line 9 | GridBuilder::GridBuilder(RigidBody* rb, int 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 –  }
12   }
13  
14   GridBuilder::~GridBuilder() {
15   }
16  
17 < void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
18 <                              vector<double> epsGrid){
17 > void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid,
18 >                              vector<double> sGrid, vector<double> epsGrid){
19 >  ofstream sigmaOut("sigma.grid");
20 >  ofstream sOut("s.grid");
21 >  ofstream epsOut("eps.grid");
22    double startDist;
23 +  double phiVal;
24 +  double thetaVal;
25    double minDist = 10.0; //minimum start distance
26          
27 +  sList = sGrid;
28 +  sigList = sigmaGrid;
29 +  epsList = epsGrid;
30    forcefield = forceField;
31      
32    //first determine the start distance - we always start at least minDist away
33    startDist = rbMol->findMaxExtent() + minDist;
34    if (startDist < minDist)
35      startDist = minDist;
36 <        
37 <  initBody();
38 <  for (i=0; i<bandwidth; i++){          
39 <    for (j=0; j<bandwidth; j++){
36 >
37 >  printf("startDist = %lf\n", startDist);
38 >
39 >  //set the initial orientation of the body and loop over theta values
40 >
41 >  for (k =0; k < bandwidth; k++) {
42 >    thetaVal = thetaMin + k*thetaStep;
43 >    for (j=0; j < bandwidth; j++) {
44 >      phiVal = j*phiStep;
45 >
46 >      printf("setting Euler, phi = %lf\ttheta = %lf\n", phiVal, thetaVal);
47 >
48 >      rbMol->setEuler(0.0, thetaVal, phiVal);
49 >
50        releaseProbe(startDist);
51  
52 <      sigmaGrid.push_back(sigDist);
53 <      sGrid.push_back(sDist);
54 <      epsGrid.push_back(epsVal);
55 <                        
56 <      stepPhi(phiStep);
52 >      printf("found sigDist = %lf\t sDist = %lf \t epsVal = %lf\n",
53 >             sigDist, sDist, epsVal);
54 >
55 >      sigList.push_back(sigDist);
56 >      sList.push_back(sDist);
57 >      epsList.push_back(epsVal);
58 >
59      }
49 –    stepTheta(thetaStep);
60    }            
61   }
62  
53 – void GridBuilder::initBody(){
54 –  //set up the rigid body in the starting configuration
55 –  stepTheta(thetaMin);
56 – }
57 –
63   void GridBuilder::releaseProbe(double farPos){
64    int tooClose;
65    double tempPotEnergy;
# Line 67 | Line 72 | void GridBuilder::releaseProbe(double farPos){
72    tooClose = 0;
73    epsVal = 0;
74    rhoStep = 0.1; //the distance the probe atom moves between steps
75 <        
71 <        
75 >                
76    while (!tooClose){
77      calcEnergy();
78      potProgress.push_back(potEnergy);
# Line 106 | Line 110 | void GridBuilder::calcEnergy(){
110   }
111  
112   void GridBuilder::calcEnergy(){
113 <        
114 < }
113 >  double rXij, rYij, rZij;
114 >  double rijSquared;
115 >  double rValSquared, rValPowerSix;
116 >  double rparHe, epsHe;
117 >  double atomRpar, atomEps;
118 >  double rbAtomPos[3];
119 >  
120 >  //first get the probe atom parameters
121 >  switch(forcefield){
122 >    case 1:{
123 >      rparHe = 1.4800;
124 >      epsHe = -0.021270;
125 >    }; break;
126 >    case 2:{
127 >      rparHe = 1.14;
128 >      epsHe = 0.0203;
129 >    }; break;
130 >    case 3:{
131 >      rparHe = 2.28;
132 >      epsHe = 0.020269601874;
133 >    }; break;
134 >    case 4:{
135 >      rparHe = 2.5560;
136 >      epsHe = 0.0200;
137 >    }; break;
138 >    case 5:{
139 >      rparHe = 1.14;
140 >      epsHe = 0.0203;
141 >    }; break;
142 >  }
143 >  
144 >  potEnergy = 0.0;
145  
146 < void GridBuilder::stepTheta(double increment){
113 <  //zero out the euler angles
114 <  for (i=0; i<3; i++)
115 <    angles[i] = 0.0;
116 <        
117 <  //the second euler angle is for rotation about the x-axis (we use the zxz convention)
118 <  angles[1] = increment;
119 <        
120 <  //obtain the rotation matrix through the rigid body class
121 <  rbMol->doEulerToRotMat(angles, rotX);
122 <        
123 <  //rotate the rigid body
124 <  rbMol->getA(rbMatrix);
125 <  matMul3(rotX, rbMatrix, rotatedMat);
126 <  rbMol->setA(rotatedMat);      
127 < }
146 >  rbMol->getAtomPos(rbAtomPos, 0);
147  
148 < void GridBuilder::stepPhi(double increment){
149 <  //zero out the euler angles
150 <  for (i=0; i<3; i++)
151 <    angles[i] = 0.0;
152 <        
153 <  //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
154 <  angles[0] = increment;
155 <        
156 <  //obtain the rotation matrix through the rigid body class
157 <  rbMol->doEulerToRotMat(angles, rotZ);
158 <        
159 <  //rotate the rigid body
160 <  rbMol->getA(rbMatrix);
161 <  matMul3(rotZ, rbMatrix, rotatedMat);
162 <  rbMol->setA(rotatedMat);      
148 >  printf("atom0 pos = %lf\t%lf\t%lf\n", rbAtomPos[0], rbAtomPos[1], rbAtomPos[2]);
149 >
150 >
151 >  
152 >  for(i=0; i<rbMol->getNumAtoms(); i++){
153 >    rbMol->getAtomPos(rbAtomPos, i);
154 >    
155 >    rXij = rbAtomPos[0];
156 >    rYij = rbAtomPos[1];
157 >    rZij = rbAtomPos[2] - probeCoor;
158 >    
159 >    rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
160 >    
161 >    //in the interest of keeping the code more compact, we are being less efficient by placing
162 >    //a switch statement in the calculation loop
163 >    switch(forcefield){
164 >      case 1:{
165 >        //we are using the CHARMm force field
166 >        atomRpar = rbMol->getAtomRpar(i);
167 >        atomEps = rbMol->getAtomEps(i);
168 >        
169 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
170 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
171 >        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
172 >      }; break;
173 >      
174 >      case 2:{
175 >        //we are using the AMBER force field
176 >        atomRpar = rbMol->getAtomRpar(i);
177 >        atomEps = rbMol->getAtomEps(i);
178 >        
179 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
180 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
181 >        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
182 >      }; break;
183 >      
184 >      case 3:{
185 >        //we are using Allen-Tildesley LJ parameters
186 >        atomRpar = rbMol->getAtomRpar(i);
187 >        atomEps = rbMol->getAtomEps(i);
188 >        
189 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (4*rijSquared);
190 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
191 >        potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
192 >        
193 >      }; break;
194 >      
195 >      case 4:{
196 >        //we are using the OPLS force field
197 >        atomRpar = rbMol->getAtomRpar(i);
198 >        atomEps = rbMol->getAtomEps(i);
199 >        
200 >        rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared);
201 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
202 >        potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
203 >      }; break;
204 >      
205 >      case 5:{
206 >        //we are using the GAFF force field
207 >        atomRpar = rbMol->getAtomRpar(i);
208 >        atomEps = rbMol->getAtomEps(i);
209 >        
210 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
211 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
212 >        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
213 >      }; break;
214 >    }    
215 >  }
216 > }
217 >
218 > void GridBuilder::printGridFiles(){
219 >  ofstream sigmaOut("sigma.grid");
220 >  ofstream sOut("s.grid");
221 >  ofstream epsOut("eps.grid");
222 >  
223 >  for (k=0; k<sigList.size(); k++){
224 >    sigmaOut << sigList[k] << "\n0\n";
225 >    sOut << sList[k] << "\n0\n";    
226 >    epsOut << epsList[k] << "\n0\n";
227 >  }
228   }

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