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;
}

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;

  printf("startDist = %lf\n", startDist);

  //set the initial orientation of the body and loop over theta values

  for (k =0; k < bandwidth; k++) {
    thetaVal = thetaMin + k*thetaStep;
    for (j=0; j < bandwidth; j++) {
      phiVal = j*phiStep;

      printf("setting Euler, phi = %lf\ttheta = %lf\n", phiVal, thetaVal);

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

      releaseProbe(startDist);

      printf("found sigDist = %lf\t sDist = %lf \t epsVal = %lf\n", 
             sigDist, sDist, epsVal);

      sigList.push_back(sigDist);
      sList.push_back(sDist);
      epsList.push_back(epsVal);

    }
  }             
}

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;

  rbMol->getAtomPos(rbAtomPos, 0);

  printf("atom0 pos = %lf\t%lf\t%lf\n", rbAtomPos[0], rbAtomPos[1], rbAtomPos[2]);


  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:	1283
Committed:	Mon Jun 21 15:54:27 2004 UTC (20 years ago) by gezelter
File size:	6226 byte(s)
Log Message:	a few bug fixes
#	Content
1	#include "GridBuilder.hpp"
2	#include "MatVec3.h"
3	#define PI 3.14159265359
4
5
6	GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) {
7	rbMol = rb;
8	bandwidth = bandWidth;
9	thetaStep = PI / bandwidth;
10	thetaMin = thetaStep / 2.0;
11	phiStep = thetaStep * 2.0;
12	}
13
14	GridBuilder::~GridBuilder() {
15	}
16
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	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	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	}
60	}
61	}
62
63	void GridBuilder::releaseProbe(double farPos){
64	int tooClose;
65	double tempPotEnergy;
66	double interpRange;
67	double interpFrac;
68
69	probeCoor = farPos;
70	potProgress.clear();
71	distProgress.clear();
72	tooClose = 0;
73	epsVal = 0;
74	rhoStep = 0.1; //the distance the probe atom moves between steps
75
76	while (!tooClose){
77	calcEnergy();
78	potProgress.push_back(potEnergy);
79	distProgress.push_back(probeCoor);
80
81	//if we've reached a new minimum, save the value and position
82	if (potEnergy < epsVal){
83	epsVal = potEnergy;
84	sDist = probeCoor;
85	}
86
87	//test if the probe reached the origin - if so, stop stepping closer
88	if (probeCoor < 0){
89	sigDist = 0.0;
90	tooClose = 1;
91	}
92
93	//test if the probe beyond the contact point - if not, take a step closer
94	if (potEnergy < 0){
95	sigDist = probeCoor;
96	tempPotEnergy = potEnergy;
97	probeCoor -= rhoStep;
98	}
99	else {
100	//do a linear interpolation to obtain the sigDist
101	interpRange = potEnergy - tempPotEnergy;
102	interpFrac = potEnergy / interpRange;
103	interpFrac = interpFrac * rhoStep;
104	sigDist = probeCoor + interpFrac;
105
106	//end the loop
107	tooClose = 1;
108	}
109	}
110	}
111
112	void GridBuilder::calcEnergy(){
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	rbMol->getAtomPos(rbAtomPos, 0);
147
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(epsHeatomEps)(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(epsHeatomEps)(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)) / (4rijSquared);
190	rValPowerSix = rValSquared * rValSquared * rValSquared;
191	potEnergy += 4sqrt(epsHeatomEps)(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 += 4sqrt(epsHeatomEps)(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(epsHeatomEps)(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	}