| 3 |
|
#define PI 3.14159265359 |
| 4 |
|
|
| 5 |
|
|
| 6 |
< |
GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) { |
| 6 |
> |
GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) { |
| 7 |
|
rbMol = rb; |
| 8 |
< |
bandwidth = bandWidth; |
| 9 |
< |
thetaStep = PI / bandwidth; |
| 8 |
> |
gridwidth = gridWidth; |
| 9 |
> |
thetaStep = PI / gridwidth; |
| 10 |
|
thetaMin = thetaStep / 2.0; |
| 11 |
|
phiStep = thetaStep * 2.0; |
| 12 |
|
} |
| 22 |
|
double startDist; |
| 23 |
|
double phiVal; |
| 24 |
|
double thetaVal; |
| 25 |
+ |
double sigTemp, sTemp, epsTemp, sigProbe; |
| 26 |
|
double minDist = 10.0; //minimum start distance |
| 27 |
|
|
| 28 |
|
sList = sGrid; |
| 29 |
|
sigList = sigmaGrid; |
| 30 |
|
epsList = epsGrid; |
| 31 |
|
forcefield = forceField; |
| 32 |
+ |
|
| 33 |
+ |
//load the probe atom parameters |
| 34 |
+ |
switch(forcefield){ |
| 35 |
+ |
case 1:{ |
| 36 |
+ |
rparHe = 1.4800; |
| 37 |
+ |
epsHe = -0.021270; |
| 38 |
+ |
}; break; |
| 39 |
+ |
case 2:{ |
| 40 |
+ |
rparHe = 1.14; |
| 41 |
+ |
epsHe = 0.0203; |
| 42 |
+ |
}; break; |
| 43 |
+ |
case 3:{ |
| 44 |
+ |
rparHe = 2.28; |
| 45 |
+ |
epsHe = 0.020269601874; |
| 46 |
+ |
}; break; |
| 47 |
+ |
case 4:{ |
| 48 |
+ |
rparHe = 2.5560; |
| 49 |
+ |
epsHe = 0.0200; |
| 50 |
+ |
}; break; |
| 51 |
+ |
case 5:{ |
| 52 |
+ |
rparHe = 1.14; |
| 53 |
+ |
epsHe = 0.0203; |
| 54 |
+ |
}; break; |
| 55 |
+ |
} |
| 56 |
|
|
| 57 |
< |
//first determine the start distance - we always start at least minDist away |
| 57 |
> |
if (rparHe < 2.2) |
| 58 |
> |
sigProbe = 2*rparHe/1.12246204831; |
| 59 |
> |
else |
| 60 |
> |
sigProbe = rparHe; |
| 61 |
> |
|
| 62 |
> |
//determine the start distance - we always start at least minDist away |
| 63 |
|
startDist = rbMol->findMaxExtent() + minDist; |
| 64 |
|
if (startDist < minDist) |
| 65 |
|
startDist = minDist; |
| 66 |
|
|
| 37 |
– |
printf("startDist = %lf\n", startDist); |
| 38 |
– |
|
| 67 |
|
//set the initial orientation of the body and loop over theta values |
| 68 |
|
|
| 69 |
< |
for (k =0; k < bandwidth; k++) { |
| 69 |
> |
for (k =0; k < gridwidth; k++) { |
| 70 |
|
thetaVal = thetaMin + k*thetaStep; |
| 71 |
< |
for (j=0; j < bandwidth; j++) { |
| 71 |
> |
printf("Theta step %i\n", k); |
| 72 |
> |
for (j=0; j < gridwidth; j++) { |
| 73 |
|
phiVal = j*phiStep; |
| 74 |
|
|
| 46 |
– |
printf("setting Euler, phi = %lf\ttheta = %lf\n", phiVal, thetaVal); |
| 47 |
– |
|
| 75 |
|
rbMol->setEuler(0.0, thetaVal, phiVal); |
| 76 |
|
|
| 77 |
|
releaseProbe(startDist); |
| 78 |
|
|
| 79 |
< |
printf("found sigDist = %lf\t sDist = %lf \t epsVal = %lf\n", |
| 80 |
< |
sigDist, sDist, epsVal); |
| 81 |
< |
|
| 82 |
< |
sigList.push_back(sigDist); |
| 83 |
< |
sList.push_back(sDist); |
| 84 |
< |
epsList.push_back(epsVal); |
| 85 |
< |
|
| 79 |
> |
//translate the values to sigma, s, and epsilon of the rigid body |
| 80 |
> |
sigTemp = 2*sigDist - sigProbe; |
| 81 |
> |
sTemp = (2*(sDist - sigDist))/(0.122462048309) - sigProbe; |
| 82 |
> |
epsTemp = pow(epsVal, 2)/fabs(epsHe); |
| 83 |
> |
|
| 84 |
> |
sigList.push_back(sigTemp); |
| 85 |
> |
sList.push_back(sTemp); |
| 86 |
> |
epsList.push_back(epsTemp); |
| 87 |
|
} |
| 88 |
|
} |
| 89 |
|
} |
| 141 |
|
double rXij, rYij, rZij; |
| 142 |
|
double rijSquared; |
| 143 |
|
double rValSquared, rValPowerSix; |
| 116 |
– |
double rparHe, epsHe; |
| 144 |
|
double atomRpar, atomEps; |
| 145 |
|
double rbAtomPos[3]; |
| 146 |
< |
|
| 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 |
< |
|
| 146 |
> |
|
| 147 |
|
potEnergy = 0.0; |
| 148 |
|
|
| 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 |
– |
|
| 149 |
|
for(i=0; i<rbMol->getNumAtoms(); i++){ |
| 150 |
|
rbMol->getAtomPos(rbAtomPos, i); |
| 151 |
|
|
| 155 |
|
|
| 156 |
|
rijSquared = rXij * rXij + rYij * rYij + rZij * rZij; |
| 157 |
|
|
| 158 |
< |
//in the interest of keeping the code more compact, we are being less efficient by placing |
| 159 |
< |
//a switch statement in the calculation loop |
| 158 |
> |
//in the interest of keeping the code more compact, we are being less |
| 159 |
> |
//efficient by placing a switch statement in the calculation loop |
| 160 |
|
switch(forcefield){ |
| 161 |
|
case 1:{ |
| 162 |
|
//we are using the CHARMm force field |
