88 |
|
} |
89 |
|
|
90 |
|
// Build the hydroProp map: |
91 |
< |
std::map<std::string, HydroProp> hydroPropMap; |
91 |
> |
std::map<std::string, HydroProp*> hydroPropMap; |
92 |
|
|
93 |
|
Molecule* mol; |
94 |
|
StuntDouble* integrableObject; |
130 |
|
integrableObject != NULL; |
131 |
|
integrableObject = mol->nextIntegrableObject(j)) { |
132 |
|
|
133 |
< |
std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
133 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
134 |
|
if (iter != hydroPropMap.end()) { |
135 |
|
hydroProps_.push_back(iter->second); |
136 |
|
} else { |
143 |
|
} |
144 |
|
} |
145 |
|
} else { |
146 |
< |
|
147 |
< |
std::map<std::string, HydroProp> hydroPropMap; |
146 |
> |
|
147 |
> |
std::map<std::string, HydroProp*> hydroPropMap; |
148 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
149 |
|
mol = info->nextMolecule(i)) { |
150 |
|
for (integrableObject = mol->beginIntegrableObject(j); |
164 |
|
if (gayBerneData != NULL) { |
165 |
|
GayBerneParam gayBerneParam = gayBerneData->getData(); |
166 |
|
currShape = new Ellipsoid(V3Zero, |
167 |
< |
gayBerneParam.GB_sigma/2.0, |
168 |
< |
gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, |
167 |
> |
gayBerneParam.GB_d / 2.0, |
168 |
> |
gayBerneParam.GB_l / 2.0, |
169 |
|
Mat3x3d::identity()); |
170 |
|
} else { |
171 |
|
sprintf( painCave.errMsg, |
213 |
|
} |
214 |
|
} |
215 |
|
} |
216 |
< |
HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp()); |
217 |
< |
std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
216 |
> |
HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp()); |
217 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
218 |
|
if (iter != hydroPropMap.end()) |
219 |
|
hydroProps_.push_back(iter->second); |
220 |
|
else { |
221 |
< |
HydroProp myProp; |
222 |
< |
myProp.cor = V3Zero; |
223 |
< |
for (int i1 = 0; i1 < 3; i1++) { |
224 |
< |
for (int j1 = 0; j1 < 3; j1++) { |
225 |
< |
myProp.Xirtt(i1,j1) = currHydroProp.Xi(i1,j1); |
226 |
< |
myProp.Xirrt(i1,j1) = currHydroProp.Xi(i1,j1+3); |
227 |
< |
myProp.Xirtr(i1,j1) = currHydroProp.Xi(i1+3,j1); |
228 |
< |
myProp.Xirrr(i1,j1) = currHydroProp.Xi(i1+3,j1+3); |
229 |
< |
} |
230 |
< |
} |
231 |
< |
CholeskyDecomposition(currHydroProp.Xi, myProp.S); |
232 |
< |
hydroPropMap.insert(std::map<std::string, HydroProp>::value_type(integrableObject->getType(), myProp)); |
233 |
< |
hydroProps_.push_back(myProp); |
221 |
> |
currHydroProp->complete(); |
222 |
> |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp)); |
223 |
> |
hydroProps_.push_back(currHydroProp); |
224 |
|
} |
225 |
|
} |
226 |
|
} |
227 |
|
} |
228 |
|
variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
229 |
< |
} |
240 |
< |
|
241 |
< |
|
229 |
> |
} |
230 |
|
|
231 |
< |
|
232 |
< |
|
245 |
< |
std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) { |
246 |
< |
std::map<std::string, HydroProp> props; |
231 |
> |
std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) { |
232 |
> |
std::map<std::string, HydroProp*> props; |
233 |
|
std::ifstream ifs(filename.c_str()); |
234 |
|
if (ifs.is_open()) { |
235 |
|
|
238 |
|
const unsigned int BufferSize = 65535; |
239 |
|
char buffer[BufferSize]; |
240 |
|
while (ifs.getline(buffer, BufferSize)) { |
241 |
< |
StringTokenizer tokenizer(buffer); |
242 |
< |
HydroProp currProp; |
257 |
< |
if (tokenizer.countTokens() >= 40) { |
258 |
< |
std::string atomName = tokenizer.nextToken(); |
259 |
< |
currProp.cor[0] = tokenizer.nextTokenAsDouble(); |
260 |
< |
currProp.cor[1] = tokenizer.nextTokenAsDouble(); |
261 |
< |
currProp.cor[2] = tokenizer.nextTokenAsDouble(); |
262 |
< |
|
263 |
< |
currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble(); |
264 |
< |
currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble(); |
265 |
< |
currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble(); |
266 |
< |
currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble(); |
267 |
< |
currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble(); |
268 |
< |
currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble(); |
269 |
< |
currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble(); |
270 |
< |
currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble(); |
271 |
< |
currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble(); |
272 |
< |
|
273 |
< |
currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble(); |
274 |
< |
currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble(); |
275 |
< |
currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble(); |
276 |
< |
currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble(); |
277 |
< |
currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble(); |
278 |
< |
currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble(); |
279 |
< |
currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble(); |
280 |
< |
currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble(); |
281 |
< |
currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble(); |
282 |
< |
|
283 |
< |
currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble(); |
284 |
< |
currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble(); |
285 |
< |
currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble(); |
286 |
< |
currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble(); |
287 |
< |
currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble(); |
288 |
< |
currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble(); |
289 |
< |
currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble(); |
290 |
< |
currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble(); |
291 |
< |
currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble(); |
292 |
< |
|
293 |
< |
currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble(); |
294 |
< |
currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble(); |
295 |
< |
currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble(); |
296 |
< |
currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble(); |
297 |
< |
currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble(); |
298 |
< |
currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble(); |
299 |
< |
currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble(); |
300 |
< |
currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble(); |
301 |
< |
currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble(); |
302 |
< |
|
303 |
< |
SquareMatrix<RealType, 6> Xir; |
304 |
< |
Xir.setSubMatrix(0, 0, currProp.Xirtt); |
305 |
< |
Xir.setSubMatrix(0, 3, currProp.Xirrt); |
306 |
< |
Xir.setSubMatrix(3, 0, currProp.Xirtr); |
307 |
< |
Xir.setSubMatrix(3, 3, currProp.Xirrr); |
308 |
< |
CholeskyDecomposition(Xir, currProp.S); |
309 |
< |
|
310 |
< |
props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp)); |
311 |
< |
} |
241 |
> |
HydroProp* currProp = new HydroProp(buffer); |
242 |
> |
props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp)); |
243 |
|
} |
244 |
< |
|
244 |
> |
|
245 |
|
return props; |
246 |
|
} |
247 |
< |
|
247 |
> |
|
248 |
|
void LDForceManager::postCalculation() { |
249 |
|
SimInfo::MoleculeIterator i; |
250 |
|
Molecule::IntegrableObjectIterator j; |
316 |
|
//apply friction force and torque at center of resistance |
317 |
|
A = integrableObject->getA(); |
318 |
|
Atrans = A.transpose(); |
319 |
< |
Vector3d rcr = Atrans * hydroProps_[index].cor; |
319 |
> |
Vector3d rcr = Atrans * hydroProps_[index]->getCOR(); |
320 |
|
Vector3d vcdLab = vel + cross(omega, rcr); |
321 |
|
Vector3d vcdBody = A* vcdLab; |
322 |
< |
Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega); |
322 |
> |
Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega); |
323 |
|
Vector3d frictionForceLab = Atrans*frictionForceBody; |
324 |
|
integrableObject->addFrc(frictionForceLab); |
325 |
< |
Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega); |
325 |
> |
Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega); |
326 |
|
Vector3d frictionTorqueLab = Atrans*frictionTorqueBody; |
327 |
|
integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab)); |
328 |
|
|
337 |
|
|
338 |
|
} else { |
339 |
|
//spherical atom |
340 |
< |
Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel); |
340 |
> |
Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel); |
341 |
|
Vector3d randomForce; |
342 |
|
Vector3d randomTorque; |
343 |
|
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
370 |
|
Z[5] = randNumGen_.randNorm(0, variance); |
371 |
|
|
372 |
|
|
373 |
< |
generalForce = hydroProps_[index].S*Z; |
373 |
> |
generalForce = hydroProps_[index]->getS()*Z; |
374 |
|
|
375 |
|
force[0] = generalForce[0]; |
376 |
|
force[1] = generalForce[1]; |