| 45 |
|
|
| 46 |
|
namespace oopse { |
| 47 |
|
|
| 48 |
< |
Ellipsoid::Ellipsoid(Vector3d origin, double rMajor, double rMinor,Mat3x3d rotMat) |
| 48 |
> |
Ellipsoid::Ellipsoid(Vector3d origin, RealType rMajor, RealType rMinor,Mat3x3d rotMat) |
| 49 |
|
: origin_(origin), rMajor_(rMajor), rMinor_(rMinor), rotMat_(rotMat) { |
| 50 |
|
|
| 51 |
|
} |
| 52 |
|
bool Ellipsoid::isInterior(Vector3d pos) { |
| 53 |
|
Vector3d r = pos - origin_; |
| 54 |
|
Vector3d rbody = rotMat_ * r; |
| 55 |
< |
double xovera = rbody[0]/rMajor_; |
| 56 |
< |
double yovera = rbody[1]/rMajor_; |
| 57 |
< |
double zoverb = rbody[2]/rMinor_; |
| 55 |
> |
RealType xovera = rbody[0]/rMajor_; |
| 56 |
> |
RealType yovera = rbody[1]/rMajor_; |
| 57 |
> |
RealType zoverb = rbody[2]/rMinor_; |
| 58 |
|
|
| 59 |
|
bool result; |
| 60 |
|
if (xovera*xovera + yovera*yovera + zoverb*zoverb < 1) |
| 69 |
|
|
| 70 |
|
std::pair<Vector3d, Vector3d> boundary; |
| 71 |
|
//make a cubic box |
| 72 |
< |
double rad = rMajor_ > rMinor_ ? rMajor_ : rMinor_; |
| 72 |
> |
RealType rad = rMajor_ > rMinor_ ? rMajor_ : rMinor_; |
| 73 |
|
Vector3d r(rad, rad, rad); |
| 74 |
|
boundary.first = origin_ - r; |
| 75 |
|
boundary.second = origin_ + r; |
| 76 |
|
return boundary; |
| 77 |
|
} |
| 78 |
|
|
| 79 |
< |
HydroProps Ellipsoid::getHydroProps(double viscosity, double temperature) { |
| 79 |
> |
HydroProps Ellipsoid::getHydroProps(RealType viscosity, RealType temperature) { |
| 80 |
|
|
| 81 |
< |
double a = rMinor_; |
| 82 |
< |
double b = rMajor_; |
| 83 |
< |
double a2 = a * a; |
| 84 |
< |
double b2 = b* b; |
| 81 |
> |
RealType a = rMinor_; |
| 82 |
> |
RealType b = rMajor_; |
| 83 |
> |
RealType a2 = a * a; |
| 84 |
> |
RealType b2 = b* b; |
| 85 |
|
|
| 86 |
< |
double p = a /b; |
| 87 |
< |
double S; |
| 86 |
> |
RealType p = a /b; |
| 87 |
> |
RealType S; |
| 88 |
|
if (p > 1.0) { //prolate |
| 89 |
|
S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b); |
| 90 |
|
} else { //oblate |
| 91 |
|
S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a); |
| 92 |
|
} |
| 93 |
|
|
| 94 |
< |
double P = 1.0/(a2 - b2) * (S - 2.0/a); |
| 95 |
< |
double Q = 0.5/(a2-b2) * (2.0*a/b2 - S); |
| 94 |
> |
RealType P = 1.0/(a2 - b2) * (S - 2.0/a); |
| 95 |
> |
RealType Q = 0.5/(a2-b2) * (2.0*a/b2 - S); |
| 96 |
|
|
| 97 |
< |
double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
| 98 |
< |
double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
| 99 |
< |
double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
| 100 |
< |
double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
| 97 |
> |
RealType transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
| 98 |
> |
RealType transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
| 99 |
> |
RealType rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
| 100 |
> |
RealType rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
| 101 |
|
|
| 102 |
|
|
| 103 |
|
HydroProps props; |
| 109 |
|
props.Xi(4,4) = rotMajor; |
| 110 |
|
props.Xi(5,5) = rotMinor; |
| 111 |
|
|
| 112 |
< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 112 |
> |
const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 113 |
|
props.Xi *= convertConstant; |
| 114 |
|
|
| 115 |
|
Mat6x6d XiCopy = props.Xi; |
| 116 |
|
invertMatrix(XiCopy, props.D); |
| 117 |
< |
double kt = OOPSEConstant::kB * temperature; |
| 117 |
> |
RealType kt = OOPSEConstant::kB * temperature; |
| 118 |
|
props.D *= kt; |
| 119 |
|
props.Xi *= OOPSEConstant::kb * temperature; |
| 120 |
|
|
