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root/group/trunk/SHAPES/GridBuilder.cpp
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Comparing trunk/SHAPES/GridBuilder.cpp (file contents):
Revision 1279 by chrisfen, Fri Jun 18 19:01:40 2004 UTC vs.
Revision 1305 by chrisfen, Fri Jun 25 17:51:51 2004 UTC

# Line 1 | Line 1
1   #include "GridBuilder.hpp"
2 – #include "MatVec3.h"
2   #define PI 3.14159265359
3  
4  
5 < GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) {
6 <        rbMol = rb;
7 <        bandwidth = bandWidth;
8 <        thetaStep = PI / bandwidth;
9 <        thetaMin = thetaStep / 2.0;
10 <        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 <        }
5 > GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) {
6 >  rbMol = rb;
7 >  gridwidth = gridWidth;
8 >  thetaStep = PI / gridwidth;
9 >  thetaMin = thetaStep / 2.0;
10 >  phiStep = thetaStep * 2.0;
11   }
12  
13   GridBuilder::~GridBuilder() {
14   }
15  
16 < void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
17 <        vector<double> epsGrid){
18 <        double startDist;
19 <        double minDist = 10.0; //minimum start distance
16 > void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid,
17 >                              vector<double> sGrid, vector<double> epsGrid){
18 >  ofstream sigmaOut("sigma.grid");
19 >  ofstream sOut("s.grid");
20 >  ofstream epsOut("eps.grid");
21 >  double startDist;
22 >  double phiVal;
23 >  double thetaVal;
24 >  double sigTemp, sTemp, epsTemp, sigProbe;
25 >  double minDist = 10.0; //minimum start distance
26          
27 <        //first determine the start distance - we always start at least minDist away
28 <        startDist = rbMol->findMaxExtent() + minDist;
29 <        if (startDist < minDist)
30 <                startDist = minDist;
31 <        
32 <        initBody();
33 <        for (i=0; i<bandwidth; i++){            
34 <                for (j=0; j<bandwidth; j++){
35 <                        releaseProbe(startDist);
27 >  sigList = sigmaGrid;
28 >  sList = sGrid;
29 >  epsList = epsGrid;
30 >  forcefield = forceField;
31 >  
32 >  //load the probe atom parameters
33 >  switch(forcefield){
34 >    case 1:{
35 >      rparHe = 1.4800;
36 >      epsHe = -0.021270;
37 >    }; break;
38 >    case 2:{
39 >      rparHe = 1.14;
40 >      epsHe = 0.0203;
41 >    }; break;
42 >    case 3:{
43 >      rparHe = 2.28;
44 >      epsHe = 0.020269601874;
45 >    }; break;
46 >    case 4:{
47 >      rparHe = 2.5560;
48 >      epsHe = 0.0200;
49 >    }; break;
50 >    case 5:{
51 >      rparHe = 1.14;
52 >      epsHe = 0.0203;
53 >    }; break;
54 >  }
55 >    
56 >  if (rparHe < 2.2)
57 >    sigProbe = 2*rparHe/1.12246204831;
58 >  else
59 >    sigProbe = rparHe;
60 >  
61 >  //determine the start distance - we always start at least minDist away
62 >  startDist = rbMol->findMaxExtent() + minDist;
63 >  if (startDist < minDist)
64 >    startDist = minDist;
65  
66 <                        sigmaGrid.push_back(sigDist);
42 <                        sGrid.push_back(sDist);
43 <                        epsGrid.push_back(epsVal);
44 <                        
45 <                        stepPhi(phiStep);
46 <                }
47 <                stepTheta(thetaStep);
48 <        }
49 <                
50 < }
66 >  //set the initial orientation of the body and loop over theta values
67  
68 < void GridBuilder::initBody(){
69 <        //set up the rigid body in the starting configuration
70 <        stepTheta(thetaMin);
68 >  for (k =0; k < gridwidth; k++) {
69 >    thetaVal = thetaMin + k*thetaStep;
70 >    for (j=0; j < gridwidth; j++) {
71 >      phiVal = j*phiStep + 0.5*PI;
72 >
73 >      rbMol->setEuler(0.0, thetaVal, phiVal);
74 >
75 >      releaseProbe(startDist);
76 >
77 >      //translate the values to sigma, s, and epsilon of the rigid body
78 >      sigTemp = 2*sigDist - sigProbe;
79 >      sTemp = (2*(sDist - sigDist))/(0.122462048309) - sigProbe;
80 >      epsTemp = pow(epsVal, 2)/fabs(epsHe);
81 >      
82 >      sigList.push_back(sigTemp);
83 >      sList.push_back(sTemp);
84 >      epsList.push_back(epsTemp);
85 >    }
86 >  }            
87   }
88  
89   void GridBuilder::releaseProbe(double farPos){
90 <        int tooClose;
91 <        double tempPotEnergy;
92 <        double interpRange;
93 <        double interpFrac;
90 >  int tooClose;
91 >  double tempPotEnergy;
92 >  double interpRange;
93 >  double interpFrac;
94          
95 <        probeCoor = farPos;
96 <        potProgress.clear();
97 <        distProgress.clear();
98 <        tooClose = 0;
99 <        epsVal = 0;
100 <        rhoStep = 0.1; //the distance the probe atom moves between steps
69 <        
70 <        
71 <        while (!tooClose){
72 <                calcEnergy();
73 <                potProgress.push_back(potEnergy);
74 <                distProgress.push_back(probeCoor);
95 >  probeCoor = farPos;
96 >  potProgress.clear();
97 >  distProgress.clear();
98 >  tooClose = 0;
99 >  epsVal = 0;
100 >  rhoStep = 0.1; //the distance the probe atom moves between steps
101                  
102 <                //if we've reached a new minimum, save the value and position
103 <                if (potEnergy < epsVal){
104 <                        epsVal = potEnergy;
105 <                        sDist = probeCoor;
80 <                }
102 >  while (!tooClose){
103 >    calcEnergy();
104 >    potProgress.push_back(potEnergy);
105 >    distProgress.push_back(probeCoor);
106                  
107 <                //test if the probe reached the origin - if so, stop stepping closer
108 <                if (probeCoor < 0){
109 <                        sigDist = 0.0;
110 <                        tooClose = 1;
111 <                }
107 >    //if we've reached a new minimum, save the value and position
108 >    if (potEnergy < epsVal){
109 >      epsVal = potEnergy;
110 >      sDist = probeCoor;
111 >    }
112                  
113 <                //test if the probe beyond the contact point - if not, take a step closer
114 <                if (potEnergy < 0){
115 <                        sigDist = probeCoor;
116 <                        tempPotEnergy = potEnergy;
117 <                        probeCoor -= rhoStep;
118 <                }
119 <                else {
120 <                        //do a linear interpolation to obtain the sigDist
121 <                        interpRange = potEnergy - tempPotEnergy;
122 <                        interpFrac = potEnergy / interpRange;
123 <                        interpFrac = interpFrac * rhoStep;
124 <                        sigDist = probeCoor + interpFrac;
113 >    //test if the probe reached the origin - if so, stop stepping closer
114 >    if (probeCoor < 0){
115 >      sigDist = 0.0;
116 >      tooClose = 1;
117 >    }
118 >                
119 >    //test if the probe beyond the contact point - if not, take a step closer
120 >    if (potEnergy < 0){
121 >      sigDist = probeCoor;
122 >      tempPotEnergy = potEnergy;
123 >      probeCoor -= rhoStep;
124 >    }
125 >    else {
126 >      //do a linear interpolation to obtain the sigDist
127 >      interpRange = potEnergy - tempPotEnergy;
128 >      interpFrac = potEnergy / interpRange;
129 >      interpFrac = interpFrac * rhoStep;
130 >      sigDist = probeCoor + interpFrac;
131                          
132 <                        //end the loop
133 <                        tooClose = 1;
134 <                }
135 <        }
132 >      //end the loop
133 >      tooClose = 1;
134 >    }
135 >  }
136   }
137  
138   void GridBuilder::calcEnergy(){
139 <        
140 < }
139 >  double rXij, rYij, rZij;
140 >  double rijSquared;
141 >  double rValSquared, rValPowerSix;
142 >  double atomRpar, atomEps;
143 >  double rbAtomPos[3];
144 >    
145 >  potEnergy = 0.0;
146  
147 < void GridBuilder::stepTheta(double increment){
148 <        //zero out the euler angles
149 <        for (i=0; i<3; i++)
150 <                angles[i] = 0.0;
151 <        
152 <        //the second euler angle is for rotation about the x-axis (we use the zxz convention)
153 <        angles[1] = increment;
154 <        
155 <        //obtain the rotation matrix through the rigid body class
156 <        rbMol->doEulerToRotMat(angles, rotX);
157 <        
158 <        //rotate the rigid body
159 <        rbMol->getA(rbMatrix);
160 <        matMul3(rotX, rbMatrix, rotatedMat);
161 <        rbMol->setA(rotatedMat);
162 <        
163 < }
147 >  for(i=0; i<rbMol->getNumAtoms(); i++){
148 >    rbMol->getAtomPos(rbAtomPos, i);
149 >    
150 >    rXij = rbAtomPos[0];
151 >    rYij = rbAtomPos[1];
152 >    rZij = rbAtomPos[2] - probeCoor;
153 >    
154 >    rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
155 >    
156 >    //in the interest of keeping the code more compact, we are being less
157 >    //efficient by placing a switch statement in the calculation loop
158 >    switch(forcefield){
159 >      case 1:{
160 >        //we are using the CHARMm force field
161 >        atomRpar = rbMol->getAtomRpar(i);
162 >        atomEps = rbMol->getAtomEps(i);
163 >        
164 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
165 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
166 >        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
167 >      }; break;
168 >      
169 >      case 2:{
170 >        //we are using the AMBER force field
171 >        atomRpar = rbMol->getAtomRpar(i);
172 >        atomEps = rbMol->getAtomEps(i);
173 >        
174 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
175 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
176 >        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
177 >      }; break;
178 >      
179 >      case 3:{
180 >        //we are using Allen-Tildesley LJ parameters
181 >        atomRpar = rbMol->getAtomRpar(i);
182 >        atomEps = rbMol->getAtomEps(i);
183 >        
184 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (4*rijSquared);
185 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
186 >        potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
187 >        
188 >      }; break;
189 >      
190 >      case 4:{
191 >        //we are using the OPLS force field
192 >        atomRpar = rbMol->getAtomRpar(i);
193 >        atomEps = rbMol->getAtomEps(i);
194 >        
195 >        rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared);
196 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
197 >        potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
198 >      }; break;
199 >      
200 >      case 5:{
201 >        //we are using the GAFF force field
202 >        atomRpar = rbMol->getAtomRpar(i);
203 >        atomEps = rbMol->getAtomEps(i);
204 >        
205 >        rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
206 >        rValPowerSix = rValSquared * rValSquared * rValSquared;
207 >        potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0));
208 >      }; break;
209 >    }    
210 >  }
211 > }
212  
213 < void GridBuilder::stepPhi(double increment){
214 <        //zero out the euler angles
215 <        for (i=0; i<3; i++)
216 <                angles[i] = 0.0;
217 <        
218 <        //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
219 <        angles[0] = increment;
220 <        
221 <        //obtain the rotation matrix through the rigid body class
222 <        rbMol->doEulerToRotMat(angles, rotZ);
139 <        
140 <        //rotate the rigid body
141 <        rbMol->getA(rbMatrix);
142 <        matMul3(rotZ, rbMatrix, rotatedMat);
143 <        rbMol->setA(rotatedMat);
144 <        
213 > void GridBuilder::printGridFiles(){
214 >  ofstream sigmaOut("sigma.grid");
215 >  ofstream sOut("s.grid");
216 >  ofstream epsOut("eps.grid");
217 >  
218 >  for (k=0; k<sigList.size(); k++){
219 >    sigmaOut << sigList[k] << "\n0\n";
220 >    sOut << sList[k] << "\n0\n";    
221 >    epsOut << epsList[k] << "\n0\n";
222 >  }
223   }
224 +

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