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#include "GridBuilder.hpp" |
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#include "MatVec3.h" |
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#define PI 3.14159265359 |
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GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) { |
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rbMol = rb; |
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bandwidth = bandWidth; |
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thetaStep = PI / bandwidth; |
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thetaMin = thetaStep / 2.0; |
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phiStep = thetaStep * 2.0; |
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|
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//zero out the rot mats |
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for (i=0; i<3; i++) { |
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for (j=0; j<3; j++) { |
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rotX[i][j] = 0.0; |
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rotZ[i][j] = 0.0; |
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rbMatrix[i][j] = 0.0; |
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} |
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} |
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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, vector<double> sGrid, |
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vector<double> epsGrid){ |
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double startDist; |
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double minDist = 10.0; //minimum start distance |
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|
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//first 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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initBody(); |
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for (i=0; i<bandwidth; i++){ |
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for (j=0; j<bandwidth; j++){ |
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releaseProbe(startDist); |
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|
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sigmaGrid.push_back(sigDist); |
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sGrid.push_back(sDist); |
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epsGrid.push_back(epsVal); |
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|
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stepPhi(phiStep); |
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} |
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stepTheta(thetaStep); |
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} |
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|
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} |
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|
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void GridBuilder::initBody(){ |
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//set up the rigid body in the starting configuration |
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stepTheta(thetaMin); |
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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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|
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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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|
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} |
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|
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void GridBuilder::stepTheta(double increment){ |
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//zero out the euler angles |
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for (i=0; i<3; i++) |
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angles[i] = 0.0; |
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|
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//the second euler angle is for rotation about the x-axis (we use the zxz convention) |
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angles[1] = increment; |
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|
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//obtain the rotation matrix through the rigid body class |
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rbMol->doEulerToRotMat(angles, rotX); |
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|
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//rotate the rigid body |
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rbMol->getA(rbMatrix); |
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matMul3(rotX, rbMatrix, rotatedMat); |
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rbMol->setA(rotatedMat); |
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|
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} |
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|
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void GridBuilder::stepPhi(double increment){ |
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//zero out the euler angles |
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for (i=0; i<3; i++) |
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angles[i] = 0.0; |
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|
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//the phi euler angle is for rotation about the z-axis (we use the zxz convention) |
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angles[0] = increment; |
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|
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//obtain the rotation matrix through the rigid body class |
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rbMol->doEulerToRotMat(angles, rotZ); |
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|
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//rotate the rigid body |
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rbMol->getA(rbMatrix); |
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matMul3(rotZ, rbMatrix, rotatedMat); |
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rbMol->setA(rotatedMat); |
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|
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} |
