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root/group/trunk/SHAPES/GridBuilder.cpp
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Comparing trunk/SHAPES/GridBuilder.cpp (file contents):
Revision 1281 by chrisfen, Mon Jun 21 13:38:55 2004 UTC vs.
Revision 1285 by chrisfen, Tue Jun 22 18:04:58 2004 UTC

# Line 3 | Line 3
3   #define PI 3.14159265359
4  
5  
6 < GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) {
6 > GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) {
7    rbMol = rb;
8 <  bandwidth = bandWidth;
9 <  thetaStep = PI / bandwidth;
8 >  gridwidth = gridWidth;
9 >  thetaStep = PI / gridwidth;
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 sigTemp, sTemp, epsTemp, sigProbe;
26    double minDist = 10.0; //minimum start distance
27          
28    sList = sGrid;
29    sigList = sigmaGrid;
30    epsList = epsGrid;
31    forcefield = forceField;
32 +  
33 +  //load the probe atom parameters
34 +  switch(forcefield){
35 +    case 1:{
36 +      rparHe = 1.4800;
37 +      epsHe = -0.021270;
38 +    }; break;
39 +    case 2:{
40 +      rparHe = 1.14;
41 +      epsHe = 0.0203;
42 +    }; break;
43 +    case 3:{
44 +      rparHe = 2.28;
45 +      epsHe = 0.020269601874;
46 +    }; break;
47 +    case 4:{
48 +      rparHe = 2.5560;
49 +      epsHe = 0.0200;
50 +    }; break;
51 +    case 5:{
52 +      rparHe = 1.14;
53 +      epsHe = 0.0203;
54 +    }; break;
55 +  }
56      
57 <  //first determine the start distance - we always start at least minDist away
57 >  if (rparHe < 2.2)
58 >    sigProbe = 2*rparHe/1.12246204831;
59 >  else
60 >    sigProbe = rparHe;
61 >  
62 >  //determine the start distance - we always start at least minDist away
63    startDist = rbMol->findMaxExtent() + minDist;
64    if (startDist < minDist)
65      startDist = minDist;
66  
67 <  initBody();
68 <  for (k=0; k<bandwidth; k++){          
69 <    printf("step theta...\n");
70 <    for (j=0; j<bandwidth; j++){
67 >  //set the initial orientation of the body and loop over theta values
68 >
69 >  for (k =0; k < gridwidth; k++) {
70 >    thetaVal = thetaMin + k*thetaStep;
71 >    printf("Theta step %i\n", k);
72 >    for (j=0; j < gridwidth; j++) {
73 >      phiVal = j*phiStep;
74 >
75 >      rbMol->setEuler(0.0, thetaVal, phiVal);
76 >
77        releaseProbe(startDist);
78  
79 <      sigList.push_back(sigDist);
80 <      sList.push_back(sDist);
81 <      epsList.push_back(epsVal);
82 <                        
83 <      stepPhi(phiStep);
79 >      //translate the values to sigma, s, and epsilon of the rigid body
80 >      sigTemp = 2*sigDist - sigProbe;
81 >      sTemp = (2*(sDist - sigDist))/(0.122462048309) - sigProbe;
82 >      epsTemp = pow(epsVal, 2)/fabs(epsHe);
83 >      
84 >      sigList.push_back(sigTemp);
85 >      sList.push_back(sTemp);
86 >      epsList.push_back(epsTemp);
87      }
56 –    stepTheta(thetaStep);
88    }            
58 –  /*
59 –  //write out the grid files
60 –  printf("the grid size is %d\n",sigmaGrid.size());
61 –  for (k=0; k<sigmaGrid.size(); k++){
62 –    sigmaOut << sigmaGrid[k] << "\n0\n";
63 –    sOut << sGrid[k] << "\n0\n";
64 –    epsOut << epsGrid[k] << "\n0\n";
65 –  }
66 –   */
89   }
90  
69 – void GridBuilder::initBody(){
70 –  //set up the rigid body in the starting configuration
71 –  stepTheta(thetaMin);
72 – }
73 –
91   void GridBuilder::releaseProbe(double farPos){
92    int tooClose;
93    double tempPotEnergy;
# Line 83 | Line 100 | void GridBuilder::releaseProbe(double farPos){
100    tooClose = 0;
101    epsVal = 0;
102    rhoStep = 0.1; //the distance the probe atom moves between steps
103 <        
87 <        
103 >                
104    while (!tooClose){
105      calcEnergy();
106      potProgress.push_back(potEnergy);
# Line 125 | Line 141 | void GridBuilder::calcEnergy(){
141    double rXij, rYij, rZij;
142    double rijSquared;
143    double rValSquared, rValPowerSix;
128 –  double rparHe, epsHe;
144    double atomRpar, atomEps;
145    double rbAtomPos[3];
146 <  
132 <  //first get the probe atom parameters
133 <  switch(forcefield){
134 <    case 1:{
135 <      rparHe = 1.4800;
136 <      epsHe = -0.021270;
137 <    }; break;
138 <    case 2:{
139 <      rparHe = 1.14;
140 <      epsHe = 0.0203;
141 <    }; break;
142 <    case 3:{
143 <      rparHe = 2.28;
144 <      epsHe = 0.020269601874;
145 <    }; break;
146 <    case 4:{
147 <      rparHe = 2.5560;
148 <      epsHe = 0.0200;
149 <    }; break;
150 <    case 5:{
151 <      rparHe = 1.14;
152 <      epsHe = 0.0203;
153 <    }; break;
154 <  }
155 <  
146 >    
147    potEnergy = 0.0;
148 <  
148 >
149    for(i=0; i<rbMol->getNumAtoms(); i++){
150      rbMol->getAtomPos(rbAtomPos, i);
151      
# Line 164 | Line 155 | void GridBuilder::calcEnergy(){
155      
156      rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
157      
158 <    //in the interest of keeping the code more compact, we are being less efficient by placing
159 <    //a switch statement in the calculation loop
158 >    //in the interest of keeping the code more compact, we are being less
159 >    //efficient by placing a switch statement in the calculation loop
160      switch(forcefield){
161        case 1:{
162          //we are using the CHARMm force field
# Line 197 | Line 188 | void GridBuilder::calcEnergy(){
188          potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
189          
190        }; break;
200 –        
191        
192        case 4:{
193          //we are using the OPLS force field
# Line 222 | Line 212 | void GridBuilder::calcEnergy(){
212    }
213   }
214  
225 – void GridBuilder::stepTheta(double increment){
226 –  //zero out the euler angles
227 –  for (l=0; l<3; l++)
228 –    angles[i] = 0.0;
229 –        
230 –  //the second euler angle is for rotation about the x-axis (we use the zxz convention)
231 –  angles[1] = increment;
232 –        
233 –  //obtain the rotation matrix through the rigid body class
234 –  rbMol->doEulerToRotMat(angles, rotX);
235 –        
236 –  //rotate the rigid body
237 –  rbMol->getA(rbMatrix);
238 –  matMul3(rotX, rbMatrix, rotatedMat);
239 –  rbMol->setA(rotatedMat);      
240 – }
241 –
242 – void GridBuilder::stepPhi(double increment){
243 –  //zero out the euler angles
244 –  for (l=0; l<3; l++)
245 –    angles[i] = 0.0;
246 –        
247 –  //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
248 –  angles[0] = increment;
249 –        
250 –  //obtain the rotation matrix through the rigid body class
251 –  rbMol->doEulerToRotMat(angles, rotZ);
252 –        
253 –  //rotate the rigid body
254 –  rbMol->getA(rbMatrix);
255 –  matMul3(rotZ, rbMatrix, rotatedMat);
256 –  rbMol->setA(rotatedMat);      
257 – }
258 –
215   void GridBuilder::printGridFiles(){
216    ofstream sigmaOut("sigma.grid");
217    ofstream sOut("s.grid");
# Line 266 | Line 222 | void GridBuilder::printGridFiles(){
222      sOut << sList[k] << "\n0\n";    
223      epsOut << epsList[k] << "\n0\n";
224    }
225 < }
225 > }

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