| 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; |
| 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 |
< |
} |
| 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 |
< |
double startDist; |
| 29 |
< |
double minDist = 10.0; //minimum start distance |
| 27 |
> |
vector<double> epsGrid){ |
| 28 |
> |
ofstream sigmaOut("sigma.grid"); |
| 29 |
> |
ofstream sOut("s.grid"); |
| 30 |
> |
ofstream epsOut("eps.grid"); |
| 31 |
> |
double startDist; |
| 32 |
> |
double phiVal; |
| 33 |
> |
double thetaVal; |
| 34 |
> |
double minDist = 10.0; //minimum start distance |
| 35 |
|
|
| 36 |
< |
//first determine the start distance - we always start at least minDist away |
| 37 |
< |
startDist = rbMol->findMaxExtent() + minDist; |
| 38 |
< |
if (startDist < minDist) |
| 39 |
< |
startDist = minDist; |
| 40 |
< |
|
| 41 |
< |
initBody(); |
| 42 |
< |
for (i=0; i<bandwidth; i++){ |
| 43 |
< |
for (j=0; j<bandwidth; j++){ |
| 44 |
< |
releaseProbe(startDist); |
| 36 |
> |
sList = sGrid; |
| 37 |
> |
sigList = sigmaGrid; |
| 38 |
> |
epsList = epsGrid; |
| 39 |
> |
forcefield = forceField; |
| 40 |
> |
|
| 41 |
> |
//first determine the start distance - we always start at least minDist away |
| 42 |
> |
startDist = rbMol->findMaxExtent() + minDist; |
| 43 |
> |
if (startDist < minDist) |
| 44 |
> |
startDist = minDist; |
| 45 |
|
|
| 46 |
< |
sigmaGrid.push_back(sigDist); |
| 47 |
< |
sGrid.push_back(sDist); |
| 48 |
< |
epsGrid.push_back(epsVal); |
| 49 |
< |
|
| 50 |
< |
stepPhi(phiStep); |
| 51 |
< |
} |
| 52 |
< |
stepTheta(thetaStep); |
| 53 |
< |
} |
| 49 |
< |
|
| 50 |
< |
} |
| 46 |
> |
//set the initial orientation of the body and loop over theta values |
| 47 |
> |
phiVal = 0.0; |
| 48 |
> |
thetaVal = thetaMin; |
| 49 |
> |
rotBody(phiVal, thetaVal); |
| 50 |
> |
for (k=0; k<bandwidth; k++){ |
| 51 |
> |
//loop over phi values starting with phi = 0.0 |
| 52 |
> |
for (j=0; j<bandwidth; j++){ |
| 53 |
> |
releaseProbe(startDist); |
| 54 |
|
|
| 55 |
< |
void GridBuilder::initBody(){ |
| 56 |
< |
//set up the rigid body in the starting configuration |
| 57 |
< |
stepTheta(thetaMin); |
| 55 |
> |
sigList.push_back(sigDist); |
| 56 |
> |
sList.push_back(sDist); |
| 57 |
> |
epsList.push_back(epsVal); |
| 58 |
> |
|
| 59 |
> |
phiVal += phiStep; |
| 60 |
> |
rotBody(phiVal, thetaVal); |
| 61 |
> |
} |
| 62 |
> |
phiVal = 0.0; |
| 63 |
> |
thetaVal += thetaStep; |
| 64 |
> |
rotBody(phiVal, thetaVal); |
| 65 |
> |
printf("step theta %i\n",k); |
| 66 |
> |
} |
| 67 |
|
} |
| 68 |
|
|
| 69 |
|
void GridBuilder::releaseProbe(double farPos){ |
| 70 |
< |
int tooClose; |
| 71 |
< |
double tempPotEnergy; |
| 72 |
< |
double interpRange; |
| 73 |
< |
double interpFrac; |
| 70 |
> |
int tooClose; |
| 71 |
> |
double tempPotEnergy; |
| 72 |
> |
double interpRange; |
| 73 |
> |
double interpFrac; |
| 74 |
|
|
| 75 |
< |
probeCoor = farPos; |
| 76 |
< |
potProgress.clear(); |
| 77 |
< |
distProgress.clear(); |
| 78 |
< |
tooClose = 0; |
| 79 |
< |
epsVal = 0; |
| 80 |
< |
rhoStep = 0.1; //the distance the probe atom moves between steps |
| 75 |
> |
probeCoor = farPos; |
| 76 |
> |
potProgress.clear(); |
| 77 |
> |
distProgress.clear(); |
| 78 |
> |
tooClose = 0; |
| 79 |
> |
epsVal = 0; |
| 80 |
> |
rhoStep = 0.1; //the distance the probe atom moves between steps |
| 81 |
|
|
| 82 |
|
|
| 83 |
< |
while (!tooClose){ |
| 84 |
< |
calcEnergy(); |
| 85 |
< |
potProgress.push_back(potEnergy); |
| 86 |
< |
distProgress.push_back(probeCoor); |
| 83 |
> |
while (!tooClose){ |
| 84 |
> |
calcEnergy(); |
| 85 |
> |
potProgress.push_back(potEnergy); |
| 86 |
> |
distProgress.push_back(probeCoor); |
| 87 |
|
|
| 88 |
< |
//if we've reached a new minimum, save the value and position |
| 89 |
< |
if (potEnergy < epsVal){ |
| 90 |
< |
epsVal = potEnergy; |
| 91 |
< |
sDist = probeCoor; |
| 92 |
< |
} |
| 88 |
> |
//if we've reached a new minimum, save the value and position |
| 89 |
> |
if (potEnergy < epsVal){ |
| 90 |
> |
epsVal = potEnergy; |
| 91 |
> |
sDist = probeCoor; |
| 92 |
> |
} |
| 93 |
|
|
| 94 |
< |
//test if the probe reached the origin - if so, stop stepping closer |
| 95 |
< |
if (probeCoor < 0){ |
| 96 |
< |
sigDist = 0.0; |
| 97 |
< |
tooClose = 1; |
| 98 |
< |
} |
| 94 |
> |
//test if the probe reached the origin - if so, stop stepping closer |
| 95 |
> |
if (probeCoor < 0){ |
| 96 |
> |
sigDist = 0.0; |
| 97 |
> |
tooClose = 1; |
| 98 |
> |
} |
| 99 |
|
|
| 100 |
< |
//test if the probe beyond the contact point - if not, take a step closer |
| 101 |
< |
if (potEnergy < 0){ |
| 102 |
< |
sigDist = probeCoor; |
| 103 |
< |
tempPotEnergy = potEnergy; |
| 104 |
< |
probeCoor -= rhoStep; |
| 105 |
< |
} |
| 106 |
< |
else { |
| 107 |
< |
//do a linear interpolation to obtain the sigDist |
| 108 |
< |
interpRange = potEnergy - tempPotEnergy; |
| 109 |
< |
interpFrac = potEnergy / interpRange; |
| 110 |
< |
interpFrac = interpFrac * rhoStep; |
| 111 |
< |
sigDist = probeCoor + interpFrac; |
| 100 |
> |
//test if the probe beyond the contact point - if not, take a step closer |
| 101 |
> |
if (potEnergy < 0){ |
| 102 |
> |
sigDist = probeCoor; |
| 103 |
> |
tempPotEnergy = potEnergy; |
| 104 |
> |
probeCoor -= rhoStep; |
| 105 |
> |
} |
| 106 |
> |
else { |
| 107 |
> |
//do a linear interpolation to obtain the sigDist |
| 108 |
> |
interpRange = potEnergy - tempPotEnergy; |
| 109 |
> |
interpFrac = potEnergy / interpRange; |
| 110 |
> |
interpFrac = interpFrac * rhoStep; |
| 111 |
> |
sigDist = probeCoor + interpFrac; |
| 112 |
|
|
| 113 |
< |
//end the loop |
| 114 |
< |
tooClose = 1; |
| 115 |
< |
} |
| 116 |
< |
} |
| 113 |
> |
//end the loop |
| 114 |
> |
tooClose = 1; |
| 115 |
> |
} |
| 116 |
> |
} |
| 117 |
|
} |
| 118 |
|
|
| 119 |
|
void GridBuilder::calcEnergy(){ |
| 120 |
< |
|
| 121 |
< |
} |
| 120 |
> |
double rXij, rYij, rZij; |
| 121 |
> |
double rijSquared; |
| 122 |
> |
double rValSquared, rValPowerSix; |
| 123 |
> |
double rparHe, epsHe; |
| 124 |
> |
double atomRpar, atomEps; |
| 125 |
> |
double rbAtomPos[3]; |
| 126 |
> |
|
| 127 |
> |
//first get the probe atom parameters |
| 128 |
> |
switch(forcefield){ |
| 129 |
> |
case 1:{ |
| 130 |
> |
rparHe = 1.4800; |
| 131 |
> |
epsHe = -0.021270; |
| 132 |
> |
}; break; |
| 133 |
> |
case 2:{ |
| 134 |
> |
rparHe = 1.14; |
| 135 |
> |
epsHe = 0.0203; |
| 136 |
> |
}; break; |
| 137 |
> |
case 3:{ |
| 138 |
> |
rparHe = 2.28; |
| 139 |
> |
epsHe = 0.020269601874; |
| 140 |
> |
}; break; |
| 141 |
> |
case 4:{ |
| 142 |
> |
rparHe = 2.5560; |
| 143 |
> |
epsHe = 0.0200; |
| 144 |
> |
}; break; |
| 145 |
> |
case 5:{ |
| 146 |
> |
rparHe = 1.14; |
| 147 |
> |
epsHe = 0.0203; |
| 148 |
> |
}; break; |
| 149 |
> |
} |
| 150 |
> |
|
| 151 |
> |
potEnergy = 0.0; |
| 152 |
> |
|
| 153 |
> |
for(i=0; i<rbMol->getNumAtoms(); i++){ |
| 154 |
> |
rbMol->getAtomPos(rbAtomPos, i); |
| 155 |
> |
|
| 156 |
> |
rXij = rbAtomPos[0]; |
| 157 |
> |
rYij = rbAtomPos[1]; |
| 158 |
> |
rZij = rbAtomPos[2] - probeCoor; |
| 159 |
> |
|
| 160 |
> |
rijSquared = rXij * rXij + rYij * rYij + rZij * rZij; |
| 161 |
> |
|
| 162 |
> |
//in the interest of keeping the code more compact, we are being less efficient by placing |
| 163 |
> |
//a switch statement in the calculation loop |
| 164 |
> |
switch(forcefield){ |
| 165 |
> |
case 1:{ |
| 166 |
> |
//we are using the CHARMm force field |
| 167 |
> |
atomRpar = rbMol->getAtomRpar(i); |
| 168 |
> |
atomEps = rbMol->getAtomEps(i); |
| 169 |
> |
|
| 170 |
> |
rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared); |
| 171 |
> |
rValPowerSix = rValSquared * rValSquared * rValSquared; |
| 172 |
> |
potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0)); |
| 173 |
> |
}; break; |
| 174 |
> |
|
| 175 |
> |
case 2:{ |
| 176 |
> |
//we are using the AMBER force field |
| 177 |
> |
atomRpar = rbMol->getAtomRpar(i); |
| 178 |
> |
atomEps = rbMol->getAtomEps(i); |
| 179 |
> |
|
| 180 |
> |
rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared); |
| 181 |
> |
rValPowerSix = rValSquared * rValSquared * rValSquared; |
| 182 |
> |
potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0)); |
| 183 |
> |
}; break; |
| 184 |
> |
|
| 185 |
> |
case 3:{ |
| 186 |
> |
//we are using Allen-Tildesley LJ parameters |
| 187 |
> |
atomRpar = rbMol->getAtomRpar(i); |
| 188 |
> |
atomEps = rbMol->getAtomEps(i); |
| 189 |
> |
|
| 190 |
> |
rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (4*rijSquared); |
| 191 |
> |
rValPowerSix = rValSquared * rValSquared * rValSquared; |
| 192 |
> |
potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0)); |
| 193 |
> |
|
| 194 |
> |
}; break; |
| 195 |
> |
|
| 196 |
> |
case 4:{ |
| 197 |
> |
//we are using the OPLS force field |
| 198 |
> |
atomRpar = rbMol->getAtomRpar(i); |
| 199 |
> |
atomEps = rbMol->getAtomEps(i); |
| 200 |
> |
|
| 201 |
> |
rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared); |
| 202 |
> |
rValPowerSix = rValSquared * rValSquared * rValSquared; |
| 203 |
> |
potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0)); |
| 204 |
> |
}; break; |
| 205 |
> |
|
| 206 |
> |
case 5:{ |
| 207 |
> |
//we are using the GAFF force field |
| 208 |
> |
atomRpar = rbMol->getAtomRpar(i); |
| 209 |
> |
atomEps = rbMol->getAtomEps(i); |
| 210 |
> |
|
| 211 |
> |
rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared); |
| 212 |
> |
rValPowerSix = rValSquared * rValSquared * rValSquared; |
| 213 |
> |
potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0)); |
| 214 |
> |
}; break; |
| 215 |
> |
} |
| 216 |
> |
} |
| 217 |
> |
} |
| 218 |
|
|
| 219 |
< |
void GridBuilder::stepTheta(double increment){ |
| 220 |
< |
//zero out the euler angles |
| 221 |
< |
for (i=0; i<3; i++) |
| 222 |
< |
angles[i] = 0.0; |
| 219 |
> |
void GridBuilder::rotBody(double pValue, double tValue){ |
| 220 |
> |
//zero out the euler angles |
| 221 |
> |
for (l=0; l<3; l++) |
| 222 |
> |
angles[i] = 0.0; |
| 223 |
|
|
| 224 |
< |
//the second euler angle is for rotation about the x-axis (we use the zxz convention) |
| 225 |
< |
angles[1] = increment; |
| 224 |
> |
//the phi euler angle is for rotation about the z-axis (we use the zxz convention) |
| 225 |
> |
angles[0] = pValue; |
| 226 |
> |
//the second euler angle is for rotation about the x-axis (we use the zxz convention) |
| 227 |
> |
angles[1] = tValue; |
| 228 |
|
|
| 229 |
< |
//obtain the rotation matrix through the rigid body class |
| 230 |
< |
rbMol->doEulerToRotMat(angles, rotX); |
| 231 |
< |
|
| 232 |
< |
//rotate the rigid body |
| 233 |
< |
rbMol->getA(rbMatrix); |
| 234 |
< |
matMul3(rotX, rbMatrix, rotatedMat); |
| 235 |
< |
rbMol->setA(rotatedMat); |
| 236 |
< |
|
| 229 |
> |
//obtain the rotation matrix through the rigid body class |
| 230 |
> |
rbMol->doEulerToRotMat(angles, rotX); |
| 231 |
> |
|
| 232 |
> |
//start from the reference position |
| 233 |
> |
identityMat3(rbMatrix); |
| 234 |
> |
rbMol->setA(rbMatrix); |
| 235 |
> |
|
| 236 |
> |
//rotate the rigid body |
| 237 |
> |
matMul3(rotX, rbMatrix, rotatedMat); |
| 238 |
> |
rbMol->setA(rotatedMat); |
| 239 |
|
} |
| 240 |
|
|
| 241 |
< |
void GridBuilder::stepPhi(double increment){ |
| 242 |
< |
//zero out the euler angles |
| 243 |
< |
for (i=0; i<3; i++) |
| 244 |
< |
angles[i] = 0.0; |
| 245 |
< |
|
| 246 |
< |
//the phi euler angle is for rotation about the z-axis (we use the zxz convention) |
| 247 |
< |
angles[0] = increment; |
| 248 |
< |
|
| 249 |
< |
//obtain the rotation matrix through the rigid body class |
| 250 |
< |
rbMol->doEulerToRotMat(angles, rotZ); |
| 251 |
< |
|
| 140 |
< |
//rotate the rigid body |
| 141 |
< |
rbMol->getA(rbMatrix); |
| 142 |
< |
matMul3(rotZ, rbMatrix, rotatedMat); |
| 143 |
< |
rbMol->setA(rotatedMat); |
| 144 |
< |
|
| 145 |
< |
} |
| 241 |
> |
void GridBuilder::printGridFiles(){ |
| 242 |
> |
ofstream sigmaOut("sigma.grid"); |
| 243 |
> |
ofstream sOut("s.grid"); |
| 244 |
> |
ofstream epsOut("eps.grid"); |
| 245 |
> |
|
| 246 |
> |
for (k=0; k<sigList.size(); k++){ |
| 247 |
> |
sigmaOut << sigList[k] << "\n0\n"; |
| 248 |
> |
sOut << sList[k] << "\n0\n"; |
| 249 |
> |
epsOut << epsList[k] << "\n0\n"; |
| 250 |
> |
} |
| 251 |
> |
} |
