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#include "GridBuilder.hpp" |
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#define PI 3.14159265359 |
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|
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|
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GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) { |
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rbMol = rb; |
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gridwidth = gridWidth; |
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thetaStep = PI / gridwidth; |
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thetaMin = thetaStep / 2.0; |
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phiStep = thetaStep * 2.0; |
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} |
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|
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GridBuilder::~GridBuilder() { |
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} |
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|
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void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, |
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vector<double> sGrid, vector<double> epsGrid){ |
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ofstream sigmaOut("sigma.grid"); |
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ofstream sOut("s.grid"); |
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ofstream epsOut("eps.grid"); |
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double startDist; |
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double phiVal; |
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double thetaVal; |
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double sigTemp, sTemp, epsTemp, sigProbe; |
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double minDist = 10.0; //minimum start distance |
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|
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sigList = sigmaGrid; |
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sList = sGrid; |
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epsList = epsGrid; |
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forcefield = forceField; |
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|
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//load the probe atom parameters |
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switch(forcefield){ |
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case 1:{ |
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rparHe = 1.4800; |
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epsHe = -0.021270; |
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}; break; |
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case 2:{ |
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rparHe = 1.14; |
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epsHe = 0.0203; |
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}; break; |
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case 3:{ |
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rparHe = 2.28; |
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epsHe = 0.020269601874; |
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}; break; |
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case 4:{ |
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rparHe = 2.5560; |
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epsHe = 0.0200; |
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}; break; |
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case 5:{ |
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rparHe = 1.14; |
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epsHe = 0.0203; |
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}; break; |
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} |
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|
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if (rparHe < 2.2) |
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sigProbe = 2*rparHe/1.12246204831; |
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else |
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sigProbe = rparHe; |
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|
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//determine the start distance - we always start at least minDist away |
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startDist = rbMol->findMaxExtent() + minDist; |
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if (startDist < minDist) |
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startDist = minDist; |
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|
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//set the initial orientation of the body and loop over theta values |
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|
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for (k =0; k < gridwidth; k++) { |
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thetaVal = thetaMin + k*thetaStep; |
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for (j=0; j < gridwidth; j++) { |
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phiVal = j*phiStep + 0.5*PI; |
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if (phiVal>=2*PI) |
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phiVal -= 2*PI; |
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|
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rbMol->setEuler(0.0, thetaVal, phiVal); |
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|
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releaseProbe(startDist); |
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|
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//translate the values to sigma, s, and epsilon of the rigid body |
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sigTemp = 2*sigDist - sigProbe; |
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sTemp = (2*(sDist - sigDist))/(0.122462048309) - sigProbe; |
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epsTemp = pow(epsVal, 2)/fabs(epsHe); |
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|
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sigList.push_back(sigTemp); |
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sList.push_back(sTemp); |
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epsList.push_back(epsTemp); |
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} |
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} |
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} |
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|
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void GridBuilder::releaseProbe(double farPos){ |
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int tooClose; |
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double tempPotEnergy; |
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double interpRange; |
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double interpFrac; |
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|
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probeCoor = farPos; |
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potProgress.clear(); |
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distProgress.clear(); |
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tooClose = 0; |
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epsVal = 0; |
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rhoStep = 0.1; //the distance the probe atom moves between steps |
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|
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while (!tooClose){ |
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calcEnergy(); |
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potProgress.push_back(potEnergy); |
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distProgress.push_back(probeCoor); |
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|
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//if we've reached a new minimum, save the value and position |
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if (potEnergy < epsVal){ |
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epsVal = potEnergy; |
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sDist = probeCoor; |
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} |
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|
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//test if the probe reached the origin - if so, stop stepping closer |
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if (probeCoor < 0){ |
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sigDist = 0.0; |
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tooClose = 1; |
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} |
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|
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//test if the probe beyond the contact point - if not, take a step closer |
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if (potEnergy < 0){ |
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sigDist = probeCoor; |
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tempPotEnergy = potEnergy; |
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probeCoor -= rhoStep; |
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} |
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else { |
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//do a linear interpolation to obtain the sigDist |
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interpRange = potEnergy - tempPotEnergy; |
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interpFrac = potEnergy / interpRange; |
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interpFrac = interpFrac * rhoStep; |
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sigDist = probeCoor + interpFrac; |
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|
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//end the loop |
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tooClose = 1; |
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} |
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} |
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} |
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|
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void GridBuilder::calcEnergy(){ |
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double rXij, rYij, rZij; |
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double rijSquared; |
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double rValSquared, rValPowerSix; |
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double atomRpar, atomEps; |
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double rbAtomPos[3]; |
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|
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potEnergy = 0.0; |
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|
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for(i=0; i<rbMol->getNumAtoms(); i++){ |
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rbMol->getAtomPos(rbAtomPos, i); |
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|
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rXij = rbAtomPos[0]; |
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rYij = rbAtomPos[1]; |
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rZij = rbAtomPos[2] - probeCoor; |
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|
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rijSquared = rXij * rXij + rYij * rYij + rZij * rZij; |
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|
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//in the interest of keeping the code more compact, we are being less |
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//efficient by placing a switch statement in the calculation loop |
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switch(forcefield){ |
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case 1:{ |
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//we are using the CHARMm force field |
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atomRpar = rbMol->getAtomRpar(i); |
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atomEps = rbMol->getAtomEps(i); |
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|
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rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared); |
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rValPowerSix = rValSquared * rValSquared * rValSquared; |
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potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0)); |
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}; break; |
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|
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case 2:{ |
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//we are using the AMBER force field |
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atomRpar = rbMol->getAtomRpar(i); |
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atomEps = rbMol->getAtomEps(i); |
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|
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rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared); |
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rValPowerSix = rValSquared * rValSquared * rValSquared; |
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potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0)); |
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}; break; |
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|
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case 3:{ |
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//we are using Allen-Tildesley LJ parameters |
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atomRpar = rbMol->getAtomRpar(i); |
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atomEps = rbMol->getAtomEps(i); |
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|
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rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (4*rijSquared); |
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rValPowerSix = rValSquared * rValSquared * rValSquared; |
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potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0)); |
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|
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}; break; |
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|
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case 4:{ |
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//we are using the OPLS force field |
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atomRpar = rbMol->getAtomRpar(i); |
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atomEps = rbMol->getAtomEps(i); |
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|
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rValSquared = (pow(sqrt(rparHe+atomRpar),2)) / (rijSquared); |
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rValPowerSix = rValSquared * rValSquared * rValSquared; |
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potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0)); |
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}; break; |
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|
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case 5:{ |
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//we are using the GAFF force field |
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atomRpar = rbMol->getAtomRpar(i); |
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atomEps = rbMol->getAtomEps(i); |
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|
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rValSquared = ((rparHe+atomRpar)*(rparHe+atomRpar)) / (rijSquared); |
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rValPowerSix = rValSquared * rValSquared * rValSquared; |
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potEnergy += sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 2.0)); |
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}; break; |
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} |
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} |
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} |
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|
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void GridBuilder::printGridFiles(){ |
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ofstream sigmaOut("sigma.grid"); |
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ofstream sOut("s.grid"); |
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ofstream epsOut("eps.grid"); |
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|
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for (k=0; k<sigList.size(); k++){ |
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sigmaOut << sigList[k] << "\n0\n"; |
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sOut << sList[k] << "\n0\n"; |
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epsOut << epsList[k] << "\n0\n"; |
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} |
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} |
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