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;
        
  //zero out the rot mats
  for (i=0; i<3; i++) {
    for (j=0; j<3; j++) {
      rotX[i][j] = 0.0;
      rotZ[i][j] = 0.0;
      rbMatrix[i][j] = 0.0;
    }
  }
}

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 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;

  initBody();
  for (k=0; k<bandwidth; k++){          
    printf("step theta...\n");
    for (j=0; j<bandwidth; j++){
      releaseProbe(startDist);

      sigList.push_back(sigDist);
      sList.push_back(sDist);
      epsList.push_back(epsVal);
                        
      stepPhi(phiStep);
    }
    stepTheta(thetaStep);
  }             
  /*
  //write out the grid files
  printf("the grid size is %d\n",sigmaGrid.size());
  for (k=0; k<sigmaGrid.size(); k++){
    sigmaOut << sigmaGrid[k] << "\n0\n";
    sOut << sGrid[k] << "\n0\n";
    epsOut << epsGrid[k] << "\n0\n";
  }
   */
}

void GridBuilder::initBody(){
  //set up the rigid body in the starting configuration
  stepTheta(thetaMin);
}

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;
  
  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::stepTheta(double increment){
  //zero out the euler angles
  for (l=0; l<3; l++)
    angles[i] = 0.0;
        
  //the second euler angle is for rotation about the x-axis (we use the zxz convention)
  angles[1] = increment;
        
  //obtain the rotation matrix through the rigid body class
  rbMol->doEulerToRotMat(angles, rotX);
        
  //rotate the rigid body
  rbMol->getA(rbMatrix);
  matMul3(rotX, rbMatrix, rotatedMat);
  rbMol->setA(rotatedMat);      
}

void GridBuilder::stepPhi(double increment){
  //zero out the euler angles
  for (l=0; l<3; l++)
    angles[i] = 0.0;
        
  //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
  angles[0] = increment;
        
  //obtain the rotation matrix through the rigid body class
  rbMol->doEulerToRotMat(angles, rotZ);
        
  //rotate the rigid body
  rbMol->getA(rbMatrix);
  matMul3(rotZ, rbMatrix, rotatedMat);
  rbMol->setA(rotatedMat);      
}

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:	1281
Committed:	Mon Jun 21 13:38:55 2004 UTC (20 years ago) by chrisfen
File size:	7193 byte(s)
Log Message:	Now calculates energies and builds the grid files. There are still bugs, but it compiles and runs...
#	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	//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	}
21	}
22
23	GridBuilder::~GridBuilder() {
24	}
25
26	void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
27	vector<double> epsGrid){
28	ofstream sigmaOut("sigma.grid");
29	ofstream sOut("s.grid");
30	ofstream epsOut("eps.grid");
31	double startDist;
32	double minDist = 10.0; //minimum start distance
33
34	sList = sGrid;
35	sigList = sigmaGrid;
36	epsList = epsGrid;
37	forcefield = forceField;
38
39	//first determine the start distance - we always start at least minDist away
40	startDist = rbMol->findMaxExtent() + minDist;
41	if (startDist < minDist)
42	startDist = minDist;
43
44	initBody();
45	for (k=0; k<bandwidth; k++){
46	printf("step theta...\n");
47	for (j=0; j<bandwidth; j++){
48	releaseProbe(startDist);
49
50	sigList.push_back(sigDist);
51	sList.push_back(sDist);
52	epsList.push_back(epsVal);
53
54	stepPhi(phiStep);
55	}
56	stepTheta(thetaStep);
57	}
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	*/
67	}
68
69	void GridBuilder::initBody(){
70	//set up the rigid body in the starting configuration
71	stepTheta(thetaMin);
72	}
73
74	void GridBuilder::releaseProbe(double farPos){
75	int tooClose;
76	double tempPotEnergy;
77	double interpRange;
78	double interpFrac;
79
80	probeCoor = farPos;
81	potProgress.clear();
82	distProgress.clear();
83	tooClose = 0;
84	epsVal = 0;
85	rhoStep = 0.1; //the distance the probe atom moves between steps
86
87
88	while (!tooClose){
89	calcEnergy();
90	potProgress.push_back(potEnergy);
91	distProgress.push_back(probeCoor);
92
93	//if we've reached a new minimum, save the value and position
94	if (potEnergy < epsVal){
95	epsVal = potEnergy;
96	sDist = probeCoor;
97	}
98
99	//test if the probe reached the origin - if so, stop stepping closer
100	if (probeCoor < 0){
101	sigDist = 0.0;
102	tooClose = 1;
103	}
104
105	//test if the probe beyond the contact point - if not, take a step closer
106	if (potEnergy < 0){
107	sigDist = probeCoor;
108	tempPotEnergy = potEnergy;
109	probeCoor -= rhoStep;
110	}
111	else {
112	//do a linear interpolation to obtain the sigDist
113	interpRange = potEnergy - tempPotEnergy;
114	interpFrac = potEnergy / interpRange;
115	interpFrac = interpFrac * rhoStep;
116	sigDist = probeCoor + interpFrac;
117
118	//end the loop
119	tooClose = 1;
120	}
121	}
122	}
123
124	void GridBuilder::calcEnergy(){
125	double rXij, rYij, rZij;
126	double rijSquared;
127	double rValSquared, rValPowerSix;
128	double rparHe, epsHe;
129	double atomRpar, atomEps;
130	double rbAtomPos[3];
131
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
156	potEnergy = 0.0;
157
158	for(i=0; i<rbMol->getNumAtoms(); i++){
159	rbMol->getAtomPos(rbAtomPos, i);
160
161	rXij = rbAtomPos[0];
162	rYij = rbAtomPos[1];
163	rZij = rbAtomPos[2] - probeCoor;
164
165	rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
166
167	//in the interest of keeping the code more compact, we are being less efficient by placing
168	//a switch statement in the calculation loop
169	switch(forcefield){
170	case 1:{
171	//we are using the CHARMm force field
172	atomRpar = rbMol->getAtomRpar(i);
173	atomEps = rbMol->getAtomEps(i);
174
175	rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
176	rValPowerSix = rValSquared * rValSquared * rValSquared;
177	potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
178	}; break;
179
180	case 2:{
181	//we are using the AMBER force field
182	atomRpar = rbMol->getAtomRpar(i);
183	atomEps = rbMol->getAtomEps(i);
184
185	rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
186	rValPowerSix = rValSquared * rValSquared * rValSquared;
187	potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
188	}; break;
189
190	case 3:{
191	//we are using Allen-Tildesley LJ parameters
192	atomRpar = rbMol->getAtomRpar(i);
193	atomEps = rbMol->getAtomEps(i);
194
195	rValSquared = ((rparHe+atomRpar)(rparHe+atomRpar)) / (4rijSquared);
196	rValPowerSix = rValSquared * rValSquared * rValSquared;
197	potEnergy += 4sqrt(epsHeatomEps)(rValPowerSix (rValPowerSix - 1.0));
198
199	}; break;
200
201
202	case 4:{
203	//we are using the OPLS force field
204	atomRpar = rbMol->getAtomRpar(i);
205	atomEps = rbMol->getAtomEps(i);
206
207	rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared);
208	rValPowerSix = rValSquared * rValSquared * rValSquared;
209	potEnergy += 4sqrt(epsHeatomEps)(rValPowerSix (rValPowerSix - 1.0));
210	}; break;
211
212	case 5:{
213	//we are using the GAFF force field
214	atomRpar = rbMol->getAtomRpar(i);
215	atomEps = rbMol->getAtomEps(i);
216
217	rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared);
218	rValPowerSix = rValSquared * rValSquared * rValSquared;
219	potEnergy += sqrt(epsHeatomEps)(rValPowerSix * (rValPowerSix - 2.0));
220	}; break;
221	}
222	}
223	}
224
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
259	void GridBuilder::printGridFiles(){
260	ofstream sigmaOut("sigma.grid");
261	ofstream sOut("s.grid");
262	ofstream epsOut("eps.grid");
263
264	for (k=0; k<sigList.size(); k++){
265	sigmaOut << sigList[k] << "\n0\n";
266	sOut << sList[k] << "\n0\n";
267	epsOut << epsList[k] << "\n0\n";
268	}
269	}