| 42 |
|
#include "primitives/DirectionalAtom.hpp" |
| 43 |
|
#include "utils/simError.h" |
| 44 |
|
namespace oopse { |
| 45 |
< |
|
| 45 |
> |
|
| 46 |
|
DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) |
| 47 |
|
: Atom(dAtomType){ |
| 48 |
< |
objType_= otDAtom; |
| 49 |
< |
if (dAtomType->isMultipole()) { |
| 50 |
< |
electroBodyFrame_ = dAtomType->getElectroBodyFrame(); |
| 48 |
> |
objType_= otDAtom; |
| 49 |
> |
if (dAtomType->isMultipole()) { |
| 50 |
> |
electroBodyFrame_ = dAtomType->getElectroBodyFrame(); |
| 51 |
> |
} |
| 52 |
> |
|
| 53 |
> |
// Check if one of the diagonal inertia tensor of this directional |
| 54 |
> |
// atom is zero: |
| 55 |
> |
int nLinearAxis = 0; |
| 56 |
> |
Mat3x3d inertiaTensor = getI(); |
| 57 |
> |
for (int i = 0; i < 3; i++) { |
| 58 |
> |
if (fabs(inertiaTensor(i, i)) < oopse::epsilon) { |
| 59 |
> |
linear_ = true; |
| 60 |
> |
linearAxis_ = i; |
| 61 |
> |
++ nLinearAxis; |
| 62 |
|
} |
| 52 |
– |
|
| 53 |
– |
//check if one of the diagonal inertia tensor of this directional atom is zero |
| 54 |
– |
int nLinearAxis = 0; |
| 55 |
– |
Mat3x3d inertiaTensor = getI(); |
| 56 |
– |
for (int i = 0; i < 3; i++) { |
| 57 |
– |
if (fabs(inertiaTensor(i, i)) < oopse::epsilon) { |
| 58 |
– |
linear_ = true; |
| 59 |
– |
linearAxis_ = i; |
| 60 |
– |
++ nLinearAxis; |
| 61 |
– |
} |
| 62 |
– |
} |
| 63 |
– |
|
| 64 |
– |
if (nLinearAxis > 1) { |
| 65 |
– |
sprintf( painCave.errMsg, |
| 66 |
– |
"Directional Atom warning.\n" |
| 67 |
– |
"\tOOPSE found more than one axis in this directional atom with a vanishing \n" |
| 68 |
– |
"\tmoment of inertia."); |
| 69 |
– |
painCave.isFatal = 0; |
| 70 |
– |
simError(); |
| 71 |
– |
} |
| 72 |
– |
|
| 63 |
|
} |
| 64 |
|
|
| 65 |
+ |
if (nLinearAxis > 1) { |
| 66 |
+ |
sprintf( painCave.errMsg, |
| 67 |
+ |
"Directional Atom warning.\n" |
| 68 |
+ |
"\tOOPSE found more than one axis in this directional atom with a vanishing \n" |
| 69 |
+ |
"\tmoment of inertia."); |
| 70 |
+ |
painCave.isFatal = 0; |
| 71 |
+ |
simError(); |
| 72 |
+ |
} |
| 73 |
+ |
} |
| 74 |
+ |
|
| 75 |
|
Mat3x3d DirectionalAtom::getI() { |
| 76 |
|
return static_cast<DirectionalAtomType*>(getAtomType())->getI(); |
| 77 |
|
} |
| 78 |
< |
|
| 78 |
> |
|
| 79 |
|
void DirectionalAtom::setPrevA(const RotMat3x3d& a) { |
| 80 |
|
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
| 81 |
|
if (atomType_->isMultipole()) { |
| 82 |
|
((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 83 |
|
} |
| 84 |
|
} |
| 85 |
< |
|
| 86 |
< |
|
| 85 |
> |
|
| 86 |
> |
|
| 87 |
|
void DirectionalAtom::setA(const RotMat3x3d& a) { |
| 88 |
|
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
| 89 |
< |
|
| 89 |
> |
|
| 90 |
|
if (atomType_->isMultipole()) { |
| 91 |
|
((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 92 |
|
} |
| 93 |
|
} |
| 94 |
< |
|
| 94 |
> |
|
| 95 |
|
void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) { |
| 96 |
|
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
| 97 |
< |
|
| 97 |
> |
|
| 98 |
|
if (atomType_->isMultipole()) { |
| 99 |
|
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 100 |
|
} |
| 101 |
|
} |
| 102 |
< |
|
| 102 |
> |
|
| 103 |
|
void DirectionalAtom::rotateBy(const RotMat3x3d& m) { |
| 104 |
|
setA(m *getA()); |
| 105 |
|
} |
| 106 |
< |
|
| 107 |
< |
std::vector<double> DirectionalAtom::getGrad() { |
| 108 |
< |
std::vector<double> grad(6, 0.0); |
| 106 |
> |
|
| 107 |
> |
std::vector<RealType> DirectionalAtom::getGrad() { |
| 108 |
> |
std::vector<RealType> grad(6, 0.0); |
| 109 |
|
Vector3d force; |
| 110 |
|
Vector3d torque; |
| 111 |
|
Vector3d myEuler; |
| 112 |
< |
double phi, theta, psi; |
| 113 |
< |
double cphi, sphi, ctheta, stheta; |
| 112 |
> |
RealType phi, theta, psi; |
| 113 |
> |
RealType cphi, sphi, ctheta, stheta; |
| 114 |
|
Vector3d ephi; |
| 115 |
|
Vector3d etheta; |
| 116 |
|
Vector3d epsi; |
| 117 |
< |
|
| 117 |
> |
|
| 118 |
|
force = getFrc(); |
| 119 |
|
torque =getTrq(); |
| 120 |
|
myEuler = getA().toEulerAngles(); |
| 121 |
< |
|
| 121 |
> |
|
| 122 |
|
phi = myEuler[0]; |
| 123 |
|
theta = myEuler[1]; |
| 124 |
|
psi = myEuler[2]; |
| 125 |
< |
|
| 125 |
> |
|
| 126 |
|
cphi = cos(phi); |
| 127 |
|
sphi = sin(phi); |
| 128 |
|
ctheta = cos(theta); |
| 129 |
|
stheta = sin(theta); |
| 130 |
< |
|
| 130 |
> |
|
| 131 |
|
// get unit vectors along the phi, theta and psi rotation axes |
| 132 |
< |
|
| 132 |
> |
|
| 133 |
|
ephi[0] = 0.0; |
| 134 |
|
ephi[1] = 0.0; |
| 135 |
|
ephi[2] = 1.0; |
| 136 |
< |
|
| 136 |
> |
|
| 137 |
|
etheta[0] = cphi; |
| 138 |
|
etheta[1] = sphi; |
| 139 |
|
etheta[2] = 0.0; |
| 140 |
< |
|
| 140 |
> |
|
| 141 |
|
epsi[0] = stheta * cphi; |
| 142 |
|
epsi[1] = stheta * sphi; |
| 143 |
|
epsi[2] = ctheta; |
| 144 |
< |
|
| 144 |
> |
|
| 145 |
|
//gradient is equal to -force |
| 146 |
|
for (int j = 0 ; j<3; j++) |
| 147 |
|
grad[j] = -force[j]; |
| 148 |
< |
|
| 149 |
< |
for (int j = 0; j < 3; j++ ) { |
| 150 |
< |
|
| 148 |
> |
|
| 149 |
> |
for (int j = 0; j < 3; j++ ) { |
| 150 |
|
grad[3] -= torque[j]*ephi[j]; |
| 151 |
|
grad[4] -= torque[j]*etheta[j]; |
| 152 |
< |
grad[5] -= torque[j]*epsi[j]; |
| 154 |
< |
|
| 152 |
> |
grad[5] -= torque[j]*epsi[j]; |
| 153 |
|
} |
| 154 |
|
|
| 155 |
|
return grad; |
| 156 |
|
} |
| 157 |
< |
|
| 157 |
> |
|
| 158 |
|
void DirectionalAtom::accept(BaseVisitor* v) { |
| 159 |
|
v->visit(this); |
| 160 |
< |
} |
| 163 |
< |
|
| 160 |
> |
} |
| 161 |
|
} |
| 162 |
|
|
