trunk/SHAPES/GridBuilder.cpp

#include "GridBuilder.hpp"
#define PI 3.14159265359


GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) {
  rbMol = rb;
  gridwidth = gridWidth;
  thetaStep = PI / gridwidth;
  thetaMin = thetaStep / 2.0;
  phiStep = thetaStep * 2.0;
}

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 sigTemp, sTemp, epsTemp, sigProbe;
  double minDist = 10.0; //minimum start distance
        
  sigList = sigmaGrid;
  sList = sGrid;
  epsList = epsGrid;
  forcefield = forceField;
  
  //load 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;
  }
    
  if (rparHe < 2.2)
    sigProbe = 2*rparHe/1.12246204831;
  else
    sigProbe = rparHe;
  
  //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

  for (k =0; k < gridwidth; k++) {
    thetaVal = thetaMin + k*thetaStep;
    for (j=0; j < gridwidth; j++) {
      phiVal = j*phiStep + 0.5*PI;
      if (phiVal>=2*PI)
        phiVal -= 2*PI;

      rbMol->setEuler(0.0, thetaVal, phiVal);

      releaseProbe(startDist);

      //translate the values to sigma, s, and epsilon of the rigid body
      sigTemp = 2*sigDist - sigProbe;
      sTemp = (2*(sDist - sigDist))/(0.122462048309) - sigProbe;
      epsTemp = pow(epsVal, 2)/fabs(epsHe);
      
      sigList.push_back(sigTemp);
      sList.push_back(sTemp);
      epsList.push_back(epsTemp);
    }
  }             
}

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 atomRpar, atomEps;
  double rbAtomPos[3];
    
  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::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:	1306
Committed:	Fri Jun 25 17:54:51 2004 UTC (20 years, 2 months ago) by chrisfen
File size:	6241 byte(s)
Log Message:	Really fixed the phi range problem. Apparently s2Kit10 has a data in ordering problem
#	User	Rev	Content
1	chrisfen	1277	#include "GridBuilder.hpp"
2			#define PI 3.14159265359
3
4
5	chrisfen	1285	GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) {
6	chrisfen	1280	rbMol = rb;
7	chrisfen	1285	gridwidth = gridWidth;
8			thetaStep = PI / gridwidth;
9	chrisfen	1280	thetaMin = thetaStep / 2.0;
10			phiStep = thetaStep * 2.0;
11	chrisfen	1277	}
12
13			GridBuilder::~GridBuilder() {
14			}
15
16	gezelter	1283	void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid,
17			vector<double> sGrid, vector<double> epsGrid){
18	chrisfen	1281	ofstream sigmaOut("sigma.grid");
19			ofstream sOut("s.grid");
20			ofstream epsOut("eps.grid");
21	chrisfen	1280	double startDist;
22	chrisfen	1282	double phiVal;
23			double thetaVal;
24	chrisfen	1285	double sigTemp, sTemp, epsTemp, sigProbe;
25	chrisfen	1280	double minDist = 10.0; //minimum start distance
26	chrisfen	1277
27	chrisfen	1287	sigList = sigmaGrid;
28	chrisfen	1281	sList = sGrid;
29			epsList = epsGrid;
30	chrisfen	1280	forcefield = forceField;
31	chrisfen	1285
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	chrisfen	1280
56	chrisfen	1285	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	chrisfen	1280	startDist = rbMol->findMaxExtent() + minDist;
63			if (startDist < minDist)
64			startDist = minDist;
65	chrisfen	1281
66	chrisfen	1282	//set the initial orientation of the body and loop over theta values
67	gezelter	1283
68	chrisfen	1285	for (k =0; k < gridwidth; k++) {
69	gezelter	1283	thetaVal = thetaMin + k*thetaStep;
70	chrisfen	1285	for (j=0; j < gridwidth; j++) {
71	chrisfen	1305	phiVal = jphiStep + 0.5PI;
72	chrisfen	1306	if (phiVal>=2*PI)
73			phiVal -= 2*PI;
74	gezelter	1283
75			rbMol->setEuler(0.0, thetaVal, phiVal);
76
77	chrisfen	1280	releaseProbe(startDist);
78	chrisfen	1279
79	chrisfen	1285	//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	chrisfen	1280	}
88			}
89	chrisfen	1277	}
90
91			void GridBuilder::releaseProbe(double farPos){
92	chrisfen	1280	int tooClose;
93			double tempPotEnergy;
94			double interpRange;
95			double interpFrac;
96	chrisfen	1277
97	chrisfen	1280	probeCoor = farPos;
98			potProgress.clear();
99			distProgress.clear();
100			tooClose = 0;
101			epsVal = 0;
102			rhoStep = 0.1; //the distance the probe atom moves between steps
103	gezelter	1283
104	chrisfen	1280	while (!tooClose){
105			calcEnergy();
106			potProgress.push_back(potEnergy);
107			distProgress.push_back(probeCoor);
108	chrisfen	1277
109	chrisfen	1280	//if we've reached a new minimum, save the value and position
110			if (potEnergy < epsVal){
111			epsVal = potEnergy;
112			sDist = probeCoor;
113			}
114	chrisfen	1277
115	chrisfen	1280	//test if the probe reached the origin - if so, stop stepping closer
116			if (probeCoor < 0){
117			sigDist = 0.0;
118			tooClose = 1;
119			}
120	chrisfen	1277
121	chrisfen	1280	//test if the probe beyond the contact point - if not, take a step closer
122			if (potEnergy < 0){
123			sigDist = probeCoor;
124			tempPotEnergy = potEnergy;
125			probeCoor -= rhoStep;
126			}
127			else {
128			//do a linear interpolation to obtain the sigDist
129			interpRange = potEnergy - tempPotEnergy;
130			interpFrac = potEnergy / interpRange;
131			interpFrac = interpFrac * rhoStep;
132			sigDist = probeCoor + interpFrac;
133	chrisfen	1277
134	chrisfen	1280	//end the loop
135			tooClose = 1;
136			}
137			}
138	chrisfen	1277	}
139
140			void GridBuilder::calcEnergy(){
141	chrisfen	1281	double rXij, rYij, rZij;
142			double rijSquared;
143			double rValSquared, rValPowerSix;
144			double atomRpar, atomEps;
145			double rbAtomPos[3];
146	chrisfen	1285
147	chrisfen	1281	potEnergy = 0.0;
148	gezelter	1283
149	chrisfen	1281	for(i=0; i<rbMol->getNumAtoms(); i++){
150			rbMol->getAtomPos(rbAtomPos, i);
151
152			rXij = rbAtomPos[0];
153			rYij = rbAtomPos[1];
154			rZij = rbAtomPos[2] - probeCoor;
155
156			rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
157
158	chrisfen	1285	//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	chrisfen	1281	switch(forcefield){
161			case 1:{
162			//we are using the CHARMm force field
163			atomRpar = rbMol->getAtomRpar(i);
164			atomEps = rbMol->getAtomEps(i);
165
166			rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
167			rValPowerSix = rValSquared * rValSquared * rValSquared;
168			potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
169			}; break;
170
171			case 2:{
172			//we are using the AMBER force field
173			atomRpar = rbMol->getAtomRpar(i);
174			atomEps = rbMol->getAtomEps(i);
175
176			rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
177			rValPowerSix = rValSquared * rValSquared * rValSquared;
178			potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
179			}; break;
180
181			case 3:{
182			//we are using Allen-Tildesley LJ parameters
183			atomRpar = rbMol->getAtomRpar(i);
184			atomEps = rbMol->getAtomEps(i);
185
186			rValSquared = ((rparHe+atomRpar)(rparHe+atomRpar)) / (4rijSquared);
187			rValPowerSix = rValSquared * rValSquared * rValSquared;
188			potEnergy += 4sqrt(epsHeatomEps)(rValPowerSix (rValPowerSix - 1.0));
189
190			}; break;
191
192			case 4:{
193			//we are using the OPLS force field
194			atomRpar = rbMol->getAtomRpar(i);
195			atomEps = rbMol->getAtomEps(i);
196
197			rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared);
198			rValPowerSix = rValSquared * rValSquared * rValSquared;
199			potEnergy += 4sqrt(epsHeatomEps)(rValPowerSix (rValPowerSix - 1.0));
200			}; break;
201
202			case 5:{
203			//we are using the GAFF force field
204			atomRpar = rbMol->getAtomRpar(i);
205			atomEps = rbMol->getAtomEps(i);
206
207			rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
208			rValPowerSix = rValSquared * rValSquared * rValSquared;
209			potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
210			}; break;
211			}
212			}
213			}
214	chrisfen	1277
215	chrisfen	1281	void GridBuilder::printGridFiles(){
216			ofstream sigmaOut("sigma.grid");
217			ofstream sOut("s.grid");
218			ofstream epsOut("eps.grid");
219
220			for (k=0; k<sigList.size(); k++){
221			sigmaOut << sigList[k] << "\n0\n";
222			sOut << sList[k] << "\n0\n";
223			epsOut << epsList[k] << "\n0\n";
224			}
225	gezelter	1283	}
226	chrisfen	1287