| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
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|
#include "primitives/DirectionalAtom.hpp" |
| 44 |
+ |
#include "types/DirectionalAdapter.hpp" |
| 45 |
+ |
#include "types/MultipoleAdapter.hpp" |
| 46 |
|
#include "utils/simError.h" |
| 47 |
< |
namespace oopse { |
| 47 |
> |
namespace OpenMD { |
| 48 |
> |
|
| 49 |
> |
DirectionalAtom::DirectionalAtom(AtomType* dAtomType) |
| 50 |
> |
: Atom(dAtomType) { |
| 51 |
> |
objType_= otDAtom; |
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|
|
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< |
DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) |
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< |
: Atom(dAtomType){ |
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< |
objType_= otDAtom; |
| 49 |
< |
if (dAtomType->isMultipole()) { |
| 50 |
< |
electroBodyFrame_ = dAtomType->getElectroBodyFrame(); |
| 51 |
< |
} |
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> |
DirectionalAdapter da = DirectionalAdapter(dAtomType); |
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> |
I_ = da.getI(); |
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|
|
| 56 |
< |
//check if one of the diagonal inertia tensor of this directional atom is zero |
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< |
int nLinearAxis = 0; |
| 58 |
< |
Mat3x3d inertiaTensor = getI(); |
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< |
for (int i = 0; i < 3; i++) { |
| 60 |
< |
if (fabs(inertiaTensor(i, i)) < oopse::epsilon) { |
| 61 |
< |
linear_ = true; |
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< |
linearAxis_ = i; |
| 60 |
< |
++ nLinearAxis; |
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< |
} |
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< |
} |
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> |
MultipoleAdapter ma = MultipoleAdapter(dAtomType); |
| 57 |
> |
if (ma.isDipole()) { |
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> |
dipole_ = ma.getDipole(); |
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> |
} |
| 60 |
> |
if (ma.isQuadrupole()) { |
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> |
quadrupole_ = ma.getQuadrupole(); |
| 62 |
> |
} |
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|
|
| 64 |
< |
if (nLinearAxis > 1) { |
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< |
sprintf( painCave.errMsg, |
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< |
"Directional Atom error.\n" |
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< |
"\tOOPSE found more than one axis in this directional atom with a vanishing \n" |
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< |
"\tmoment of inertia."); |
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< |
painCave.isFatal = 1; |
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< |
simError(); |
| 64 |
> |
// Check if one of the diagonal inertia tensor of this directional |
| 65 |
> |
// atom is zero: |
| 66 |
> |
int nLinearAxis = 0; |
| 67 |
> |
Mat3x3d inertiaTensor = getI(); |
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> |
for (int i = 0; i < 3; i++) { |
| 69 |
> |
if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) { |
| 70 |
> |
linear_ = true; |
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> |
linearAxis_ = i; |
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> |
++ nLinearAxis; |
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|
} |
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– |
|
| 74 |
|
} |
| 75 |
|
|
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+ |
if (nLinearAxis > 1) { |
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+ |
sprintf( painCave.errMsg, |
| 78 |
+ |
"Directional Atom warning.\n" |
| 79 |
+ |
"\tOpenMD found more than one axis in this directional atom with a vanishing \n" |
| 80 |
+ |
"\tmoment of inertia."); |
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+ |
painCave.isFatal = 0; |
| 82 |
+ |
simError(); |
| 83 |
+ |
} |
| 84 |
+ |
} |
| 85 |
+ |
|
| 86 |
|
Mat3x3d DirectionalAtom::getI() { |
| 87 |
< |
return static_cast<DirectionalAtomType*>(getAtomType())->getI(); |
| 87 |
> |
return I_; |
| 88 |
|
} |
| 89 |
< |
|
| 89 |
> |
|
| 90 |
|
void DirectionalAtom::setPrevA(const RotMat3x3d& a) { |
| 91 |
|
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
| 92 |
+ |
|
| 93 |
|
if (atomType_->isMultipole()) { |
| 94 |
< |
((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 94 |
> |
RotMat3x3d atrans = a.transpose(); |
| 95 |
> |
|
| 96 |
> |
if (atomType_->isDipole()) { |
| 97 |
> |
((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_; |
| 98 |
> |
} |
| 99 |
> |
|
| 100 |
> |
if (atomType_->isQuadrupole()) { |
| 101 |
> |
((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a; |
| 102 |
> |
} |
| 103 |
|
} |
| 104 |
|
} |
| 105 |
< |
|
| 106 |
< |
|
| 105 |
> |
|
| 106 |
> |
|
| 107 |
|
void DirectionalAtom::setA(const RotMat3x3d& a) { |
| 108 |
|
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
| 109 |
< |
|
| 109 |
> |
|
| 110 |
|
if (atomType_->isMultipole()) { |
| 111 |
< |
((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 111 |
> |
RotMat3x3d atrans = a.transpose(); |
| 112 |
> |
|
| 113 |
> |
if (atomType_->isDipole()) { |
| 114 |
> |
((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_; |
| 115 |
> |
} |
| 116 |
> |
|
| 117 |
> |
if (atomType_->isQuadrupole()) { |
| 118 |
> |
((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a; |
| 119 |
> |
} |
| 120 |
|
} |
| 121 |
+ |
|
| 122 |
|
} |
| 123 |
< |
|
| 123 |
> |
|
| 124 |
|
void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) { |
| 125 |
|
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
| 126 |
|
|
| 127 |
|
if (atomType_->isMultipole()) { |
| 128 |
< |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_; |
| 128 |
> |
RotMat3x3d atrans = a.transpose(); |
| 129 |
> |
|
| 130 |
> |
if (atomType_->isDipole()) { |
| 131 |
> |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_] = atrans * dipole_; |
| 132 |
> |
} |
| 133 |
> |
|
| 134 |
> |
if (atomType_->isQuadrupole()) { |
| 135 |
> |
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a; |
| 136 |
> |
} |
| 137 |
|
} |
| 101 |
– |
} |
| 138 |
|
|
| 139 |
+ |
} |
| 140 |
+ |
|
| 141 |
|
void DirectionalAtom::rotateBy(const RotMat3x3d& m) { |
| 142 |
|
setA(m *getA()); |
| 143 |
|
} |
| 144 |
< |
|
| 145 |
< |
std::vector<double> DirectionalAtom::getGrad() { |
| 146 |
< |
std::vector<double> grad(6, 0.0); |
| 144 |
> |
|
| 145 |
> |
std::vector<RealType> DirectionalAtom::getGrad() { |
| 146 |
> |
std::vector<RealType> grad(6, 0.0); |
| 147 |
|
Vector3d force; |
| 148 |
|
Vector3d torque; |
| 149 |
|
Vector3d myEuler; |
| 150 |
< |
double phi, theta, psi; |
| 151 |
< |
double cphi, sphi, ctheta, stheta; |
| 150 |
> |
RealType phi, theta, psi; |
| 151 |
> |
RealType cphi, sphi, ctheta, stheta; |
| 152 |
|
Vector3d ephi; |
| 153 |
|
Vector3d etheta; |
| 154 |
|
Vector3d epsi; |
| 155 |
< |
|
| 155 |
> |
|
| 156 |
|
force = getFrc(); |
| 157 |
|
torque =getTrq(); |
| 158 |
|
myEuler = getA().toEulerAngles(); |
| 159 |
< |
|
| 159 |
> |
|
| 160 |
|
phi = myEuler[0]; |
| 161 |
|
theta = myEuler[1]; |
| 162 |
|
psi = myEuler[2]; |
| 163 |
< |
|
| 163 |
> |
|
| 164 |
|
cphi = cos(phi); |
| 165 |
|
sphi = sin(phi); |
| 166 |
|
ctheta = cos(theta); |
| 167 |
|
stheta = sin(theta); |
| 168 |
< |
|
| 168 |
> |
|
| 169 |
|
// get unit vectors along the phi, theta and psi rotation axes |
| 170 |
< |
|
| 170 |
> |
|
| 171 |
|
ephi[0] = 0.0; |
| 172 |
|
ephi[1] = 0.0; |
| 173 |
|
ephi[2] = 1.0; |
| 174 |
< |
|
| 174 |
> |
|
| 175 |
> |
//etheta[0] = -sphi; |
| 176 |
> |
//etheta[1] = cphi; |
| 177 |
> |
//etheta[2] = 0.0; |
| 178 |
> |
|
| 179 |
|
etheta[0] = cphi; |
| 180 |
|
etheta[1] = sphi; |
| 181 |
|
etheta[2] = 0.0; |
| 182 |
< |
|
| 182 |
> |
|
| 183 |
|
epsi[0] = stheta * cphi; |
| 184 |
|
epsi[1] = stheta * sphi; |
| 185 |
|
epsi[2] = ctheta; |
| 186 |
< |
|
| 186 |
> |
|
| 187 |
|
//gradient is equal to -force |
| 188 |
|
for (int j = 0 ; j<3; j++) |
| 189 |
|
grad[j] = -force[j]; |
| 190 |
< |
|
| 191 |
< |
for (int j = 0; j < 3; j++ ) { |
| 150 |
< |
|
| 190 |
> |
|
| 191 |
> |
for (int j = 0; j < 3; j++ ) { |
| 192 |
|
grad[3] -= torque[j]*ephi[j]; |
| 193 |
|
grad[4] -= torque[j]*etheta[j]; |
| 194 |
< |
grad[5] -= torque[j]*epsi[j]; |
| 154 |
< |
|
| 194 |
> |
grad[5] -= torque[j]*epsi[j]; |
| 195 |
|
} |
| 196 |
|
|
| 197 |
|
return grad; |
| 198 |
|
} |
| 199 |
< |
|
| 199 |
> |
|
| 200 |
|
void DirectionalAtom::accept(BaseVisitor* v) { |
| 201 |
|
v->visit(this); |
| 202 |
< |
} |
| 163 |
< |
|
| 202 |
> |
} |
| 203 |
|
} |
| 204 |
|
|
