| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* 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, 234107 (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 |
|
#include <algorithm> |
| 43 |
|
#include <math.h> |
| 44 |
|
#include "primitives/RigidBody.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
|
#include "utils/NumericConstant.hpp" |
| 47 |
< |
namespace oopse { |
| 48 |
< |
|
| 49 |
< |
RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){ |
| 50 |
< |
|
| 47 |
> |
namespace OpenMD { |
| 48 |
> |
|
| 49 |
> |
RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), |
| 50 |
> |
inertiaTensor_(0.0){ |
| 51 |
|
} |
| 52 |
< |
|
| 52 |
> |
|
| 53 |
|
void RigidBody::setPrevA(const RotMat3x3d& a) { |
| 54 |
|
((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a; |
| 55 |
< |
//((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
| 56 |
< |
|
| 56 |
< |
for (int i =0 ; i < atoms_.size(); ++i){ |
| 55 |
> |
|
| 56 |
> |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
| 57 |
|
if (atoms_[i]->isDirectional()) { |
| 58 |
< |
atoms_[i]->setPrevA(a * refOrients_[i]); |
| 58 |
> |
atoms_[i]->setPrevA(refOrients_[i].transpose() * a); |
| 59 |
|
} |
| 60 |
|
} |
| 61 |
< |
|
| 61 |
> |
|
| 62 |
|
} |
| 63 |
< |
|
| 64 |
< |
|
| 63 |
> |
|
| 64 |
> |
|
| 65 |
|
void RigidBody::setA(const RotMat3x3d& a) { |
| 66 |
|
((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a; |
| 67 |
– |
//((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
| 67 |
|
|
| 68 |
< |
for (int i =0 ; i < atoms_.size(); ++i){ |
| 68 |
> |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
| 69 |
|
if (atoms_[i]->isDirectional()) { |
| 70 |
< |
atoms_[i]->setA(a * refOrients_[i]); |
| 70 |
> |
atoms_[i]->setA(refOrients_[i].transpose() * a); |
| 71 |
|
} |
| 72 |
|
} |
| 73 |
|
} |
| 74 |
< |
|
| 74 |
> |
|
| 75 |
|
void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) { |
| 76 |
|
((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a; |
| 77 |
< |
//((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_; |
| 78 |
< |
|
| 80 |
< |
for (int i =0 ; i < atoms_.size(); ++i){ |
| 77 |
> |
|
| 78 |
> |
for (unsigned int i = 0 ; i < atoms_.size(); ++i){ |
| 79 |
|
if (atoms_[i]->isDirectional()) { |
| 80 |
< |
atoms_[i]->setA(a * refOrients_[i], snapshotNo); |
| 80 |
> |
atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo); |
| 81 |
|
} |
| 82 |
|
} |
| 83 |
< |
|
| 83 |
> |
|
| 84 |
|
} |
| 85 |
< |
|
| 85 |
> |
|
| 86 |
|
Mat3x3d RigidBody::getI() { |
| 87 |
|
return inertiaTensor_; |
| 88 |
|
} |
| 89 |
< |
|
| 90 |
< |
std::vector<double> RigidBody::getGrad() { |
| 91 |
< |
std::vector<double> grad(6, 0.0); |
| 89 |
> |
|
| 90 |
> |
std::vector<RealType> RigidBody::getGrad() { |
| 91 |
> |
std::vector<RealType> grad(6, 0.0); |
| 92 |
|
Vector3d force; |
| 93 |
|
Vector3d torque; |
| 94 |
|
Vector3d myEuler; |
| 95 |
< |
double phi, theta, psi; |
| 96 |
< |
double cphi, sphi, ctheta, stheta; |
| 95 |
> |
RealType phi, theta; |
| 96 |
> |
// RealType psi; |
| 97 |
> |
RealType cphi, sphi, ctheta, stheta; |
| 98 |
|
Vector3d ephi; |
| 99 |
|
Vector3d etheta; |
| 100 |
|
Vector3d epsi; |
| 101 |
< |
|
| 101 |
> |
|
| 102 |
|
force = getFrc(); |
| 103 |
|
torque =getTrq(); |
| 104 |
|
myEuler = getA().toEulerAngles(); |
| 105 |
< |
|
| 105 |
> |
|
| 106 |
|
phi = myEuler[0]; |
| 107 |
|
theta = myEuler[1]; |
| 108 |
< |
psi = myEuler[2]; |
| 109 |
< |
|
| 108 |
> |
// psi = myEuler[2]; |
| 109 |
> |
|
| 110 |
|
cphi = cos(phi); |
| 111 |
|
sphi = sin(phi); |
| 112 |
|
ctheta = cos(theta); |
| 113 |
|
stheta = sin(theta); |
| 114 |
< |
|
| 114 |
> |
|
| 115 |
|
// get unit vectors along the phi, theta and psi rotation axes |
| 116 |
< |
|
| 116 |
> |
|
| 117 |
|
ephi[0] = 0.0; |
| 118 |
|
ephi[1] = 0.0; |
| 119 |
|
ephi[2] = 1.0; |
| 120 |
< |
|
| 120 |
> |
|
| 121 |
> |
//etheta[0] = -sphi; |
| 122 |
> |
//etheta[1] = cphi; |
| 123 |
> |
//etheta[2] = 0.0; |
| 124 |
> |
|
| 125 |
|
etheta[0] = cphi; |
| 126 |
|
etheta[1] = sphi; |
| 127 |
< |
etheta[2] = 0.0; |
| 128 |
< |
|
| 127 |
> |
etheta[2] = 0.0; |
| 128 |
> |
|
| 129 |
|
epsi[0] = stheta * cphi; |
| 130 |
|
epsi[1] = stheta * sphi; |
| 131 |
|
epsi[2] = ctheta; |
| 132 |
< |
|
| 132 |
> |
|
| 133 |
|
//gradient is equal to -force |
| 134 |
|
for (int j = 0 ; j<3; j++) |
| 135 |
|
grad[j] = -force[j]; |
| 136 |
< |
|
| 136 |
> |
|
| 137 |
|
for (int j = 0; j < 3; j++ ) { |
| 138 |
< |
|
| 138 |
> |
|
| 139 |
|
grad[3] += torque[j]*ephi[j]; |
| 140 |
|
grad[4] += torque[j]*etheta[j]; |
| 141 |
|
grad[5] += torque[j]*epsi[j]; |
| 142 |
< |
|
| 142 |
> |
|
| 143 |
|
} |
| 144 |
|
|
| 145 |
|
return grad; |
| 146 |
|
} |
| 147 |
< |
|
| 147 |
> |
|
| 148 |
|
void RigidBody::accept(BaseVisitor* v) { |
| 149 |
|
v->visit(this); |
| 150 |
|
} |
| 151 |
|
|
| 152 |
|
/**@todo need modification */ |
| 153 |
|
void RigidBody::calcRefCoords() { |
| 154 |
< |
double mtmp; |
| 154 |
> |
RealType mtmp; |
| 155 |
|
Vector3d refCOM(0.0); |
| 156 |
|
mass_ = 0.0; |
| 157 |
|
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 160 |
|
refCOM += refCoords_[i]*mtmp; |
| 161 |
|
} |
| 162 |
|
refCOM /= mass_; |
| 163 |
< |
|
| 163 |
> |
|
| 164 |
|
// Next, move the origin of the reference coordinate system to the COM: |
| 165 |
|
for (std::size_t i = 0; i < atoms_.size(); ++i) { |
| 166 |
|
refCoords_[i] -= refCOM; |
| 172 |
|
Mat3x3d IAtom(0.0); |
| 173 |
|
mtmp = atoms_[i]->getMass(); |
| 174 |
|
IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp; |
| 175 |
< |
double r2 = refCoords_[i].lengthSquare(); |
| 175 |
> |
RealType r2 = refCoords_[i].lengthSquare(); |
| 176 |
|
IAtom(0, 0) += mtmp * r2; |
| 177 |
|
IAtom(1, 1) += mtmp * r2; |
| 178 |
|
IAtom(2, 2) += mtmp * r2; |
| 179 |
< |
|
| 179 |
> |
Itmp += IAtom; |
| 180 |
> |
|
| 181 |
|
//project the inertial moment of directional atoms into this rigid body |
| 182 |
|
if (atoms_[i]->isDirectional()) { |
| 183 |
< |
IAtom += atoms_[i]->getI(); |
| 184 |
< |
Itmp += refOrients_[i].transpose() * IAtom * refOrients_[i]; |
| 181 |
< |
} else { |
| 182 |
< |
Itmp += IAtom; |
| 183 |
< |
} |
| 183 |
> |
Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i]; |
| 184 |
> |
} |
| 185 |
|
} |
| 186 |
|
|
| 187 |
+ |
// std::cout << Itmp << std::endl; |
| 188 |
+ |
|
| 189 |
|
//diagonalize |
| 190 |
|
Vector3d evals; |
| 191 |
|
Mat3x3d::diagonalize(Itmp, evals, sU_); |
| 197 |
|
|
| 198 |
|
int nLinearAxis = 0; |
| 199 |
|
for (int i = 0; i < 3; i++) { |
| 200 |
< |
if (fabs(evals[i]) < oopse::epsilon) { |
| 200 |
> |
if (fabs(evals[i]) < OpenMD::epsilon) { |
| 201 |
|
linear_ = true; |
| 202 |
|
linearAxis_ = i; |
| 203 |
|
++ nLinearAxis; |
| 207 |
|
if (nLinearAxis > 1) { |
| 208 |
|
sprintf( painCave.errMsg, |
| 209 |
|
"RigidBody error.\n" |
| 210 |
< |
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
| 210 |
> |
"\tOpenMD found more than one axis in this rigid body with a vanishing \n" |
| 211 |
|
"\tmoment of inertia. This can happen in one of three ways:\n" |
| 212 |
|
"\t 1) Only one atom was specified, or \n" |
| 213 |
|
"\t 2) All atoms were specified at the same location, or\n" |
| 227 |
|
Vector3d rpos; |
| 228 |
|
Vector3d frc(0.0); |
| 229 |
|
Vector3d trq(0.0); |
| 230 |
+ |
Vector3d ef(0.0); |
| 231 |
|
Vector3d pos = this->getPos(); |
| 232 |
< |
for (int i = 0; i < atoms_.size(); i++) { |
| 232 |
> |
AtomType* atype; |
| 233 |
> |
int eCount = 0; |
| 234 |
> |
|
| 235 |
> |
int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); |
| 236 |
> |
|
| 237 |
> |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 238 |
|
|
| 239 |
+ |
atype = atoms_[i]->getAtomType(); |
| 240 |
+ |
|
| 241 |
|
afrc = atoms_[i]->getFrc(); |
| 242 |
|
apos = atoms_[i]->getPos(); |
| 243 |
|
rpos = apos - pos; |
| 255 |
|
atrq = atoms_[i]->getTrq(); |
| 256 |
|
trq += atrq; |
| 257 |
|
} |
| 258 |
+ |
|
| 259 |
+ |
if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { |
| 260 |
+ |
ef += atoms_[i]->getElectricField(); |
| 261 |
+ |
eCount++; |
| 262 |
+ |
} |
| 263 |
+ |
} |
| 264 |
+ |
addFrc(frc); |
| 265 |
+ |
addTrq(trq); |
| 266 |
+ |
|
| 267 |
+ |
if (sl & DataStorage::dslElectricField) { |
| 268 |
+ |
ef /= eCount; |
| 269 |
+ |
setElectricField(ef); |
| 270 |
+ |
} |
| 271 |
+ |
|
| 272 |
+ |
} |
| 273 |
+ |
|
| 274 |
+ |
Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() { |
| 275 |
+ |
Vector3d afrc; |
| 276 |
+ |
Vector3d atrq; |
| 277 |
+ |
Vector3d apos; |
| 278 |
+ |
Vector3d rpos; |
| 279 |
+ |
Vector3d dfrc; |
| 280 |
+ |
Vector3d frc(0.0); |
| 281 |
+ |
Vector3d trq(0.0); |
| 282 |
+ |
Vector3d ef(0.0); |
| 283 |
+ |
AtomType* atype; |
| 284 |
+ |
int eCount = 0; |
| 285 |
+ |
|
| 286 |
+ |
Vector3d pos = this->getPos(); |
| 287 |
+ |
Mat3x3d tau_(0.0); |
| 288 |
+ |
|
| 289 |
+ |
int sl = ((snapshotMan_->getCurrentSnapshot())->*storage_).getStorageLayout(); |
| 290 |
+ |
|
| 291 |
+ |
for (unsigned int i = 0; i < atoms_.size(); i++) { |
| 292 |
+ |
|
| 293 |
+ |
atype = atoms_[i]->getAtomType(); |
| 294 |
+ |
|
| 295 |
+ |
afrc = atoms_[i]->getFrc(); |
| 296 |
+ |
apos = atoms_[i]->getPos(); |
| 297 |
+ |
rpos = apos - pos; |
| 298 |
|
|
| 299 |
+ |
frc += afrc; |
| 300 |
+ |
|
| 301 |
+ |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
| 302 |
+ |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
| 303 |
+ |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
| 304 |
+ |
|
| 305 |
+ |
// If the atom has a torque associated with it, then we also need to |
| 306 |
+ |
// migrate the torques onto the center of mass: |
| 307 |
+ |
|
| 308 |
+ |
if (atoms_[i]->isDirectional()) { |
| 309 |
+ |
atrq = atoms_[i]->getTrq(); |
| 310 |
+ |
trq += atrq; |
| 311 |
+ |
} |
| 312 |
+ |
|
| 313 |
+ |
if ((sl & DataStorage::dslElectricField) && (atype->isElectrostatic())) { |
| 314 |
+ |
ef += atoms_[i]->getElectricField(); |
| 315 |
+ |
eCount++; |
| 316 |
+ |
} |
| 317 |
+ |
|
| 318 |
+ |
tau_(0,0) -= rpos[0]*afrc[0]; |
| 319 |
+ |
tau_(0,1) -= rpos[0]*afrc[1]; |
| 320 |
+ |
tau_(0,2) -= rpos[0]*afrc[2]; |
| 321 |
+ |
tau_(1,0) -= rpos[1]*afrc[0]; |
| 322 |
+ |
tau_(1,1) -= rpos[1]*afrc[1]; |
| 323 |
+ |
tau_(1,2) -= rpos[1]*afrc[2]; |
| 324 |
+ |
tau_(2,0) -= rpos[2]*afrc[0]; |
| 325 |
+ |
tau_(2,1) -= rpos[2]*afrc[1]; |
| 326 |
+ |
tau_(2,2) -= rpos[2]*afrc[2]; |
| 327 |
+ |
|
| 328 |
|
} |
| 329 |
< |
|
| 330 |
< |
setFrc(frc); |
| 331 |
< |
setTrq(trq); |
| 332 |
< |
|
| 329 |
> |
addFrc(frc); |
| 330 |
> |
addTrq(trq); |
| 331 |
> |
|
| 332 |
> |
if (sl & DataStorage::dslElectricField) { |
| 333 |
> |
ef /= eCount; |
| 334 |
> |
setElectricField(ef); |
| 335 |
> |
} |
| 336 |
> |
|
| 337 |
> |
return tau_; |
| 338 |
|
} |
| 339 |
|
|
| 340 |
|
void RigidBody::updateAtoms() { |
| 356 |
|
if (atoms_[i]->isDirectional()) { |
| 357 |
|
|
| 358 |
|
dAtom = (DirectionalAtom *) atoms_[i]; |
| 359 |
< |
dAtom->setA(refOrients_[i] * a); |
| 359 |
> |
dAtom->setA(refOrients_[i].transpose() * a); |
| 360 |
|
} |
| 361 |
|
|
| 362 |
|
} |
| 383 |
|
if (atoms_[i]->isDirectional()) { |
| 384 |
|
|
| 385 |
|
dAtom = (DirectionalAtom *) atoms_[i]; |
| 386 |
< |
dAtom->setA(refOrients_[i] * a, frame); |
| 386 |
> |
dAtom->setA(refOrients_[i].transpose() * a, frame); |
| 387 |
|
} |
| 388 |
|
|
| 389 |
|
} |
| 413 |
|
|
| 414 |
|
|
| 415 |
|
Vector3d velRot; |
| 416 |
< |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 416 |
> |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 417 |
|
atoms_[i]->setVel(rbVel + mat * refCoords_[i]); |
| 418 |
|
} |
| 419 |
|
|
| 442 |
|
|
| 443 |
|
|
| 444 |
|
Vector3d velRot; |
| 445 |
< |
for (int i =0 ; i < refCoords_.size(); ++i) { |
| 445 |
> |
for (unsigned int i = 0 ; i < refCoords_.size(); ++i) { |
| 446 |
|
atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame); |
| 447 |
|
} |
| 448 |
|
|
| 568 |
|
"RigidBody error.\n" |
| 569 |
|
"\tAtom %s does not have a position specified.\n" |
| 570 |
|
"\tThis means RigidBody cannot set up reference coordinates.\n", |
| 571 |
< |
ats->getType() ); |
| 571 |
> |
ats->getType().c_str() ); |
| 572 |
|
painCave.isFatal = 1; |
| 573 |
|
simError(); |
| 574 |
|
} |
| 588 |
|
"RigidBody error.\n" |
| 589 |
|
"\tAtom %s does not have an orientation specified.\n" |
| 590 |
|
"\tThis means RigidBody cannot set up reference orientations.\n", |
| 591 |
< |
ats->getType() ); |
| 591 |
> |
ats->getType().c_str() ); |
| 592 |
|
painCave.isFatal = 1; |
| 593 |
|
simError(); |
| 594 |
|
} |
