| 86 |
|
} |
| 87 |
|
|
| 88 |
|
void RNEMDZ::processFrame(int istep) { |
| 89 |
+ |
RealType z; |
| 90 |
+ |
|
| 91 |
+ |
hmat_ = currentSnapshot_->getHmat(); |
| 92 |
+ |
for (int i = 0; i < nBins_; i++) { |
| 93 |
+ |
z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2); |
| 94 |
+ |
dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z); |
| 95 |
+ |
} |
| 96 |
+ |
volume_ = currentSnapshot_->getVolume(); |
| 97 |
+ |
|
| 98 |
+ |
|
| 99 |
|
Molecule* mol; |
| 100 |
|
RigidBody* rb; |
| 101 |
|
StuntDouble* sd; |
| 104 |
|
int i; |
| 105 |
|
|
| 106 |
|
vector<RealType> binMass(nBins_, 0.0); |
| 107 |
< |
vector<Vector3d> binVel(nBins_, V3Zero); |
| 107 |
> |
vector<Vector3d> binP(nBins_, V3Zero); |
| 108 |
|
vector<RealType> binKE(nBins_, 0.0); |
| 109 |
|
vector<unsigned int> binDof(nBins_, 0); |
| 100 |
– |
vector<unsigned int> binCount(nBins_, 0); |
| 110 |
|
|
| 102 |
– |
|
| 111 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 112 |
|
mol = info_->nextMolecule(mi)) { |
| 113 |
|
|
| 115 |
|
|
| 116 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 117 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 118 |
< |
rb->updateAtoms(); |
| 118 |
> |
rb->updateAtomVel(); |
| 119 |
|
} |
| 120 |
|
} |
| 121 |
< |
|
| 121 |
> |
|
| 122 |
|
if (evaluator_.isDynamic()) { |
| 123 |
|
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 124 |
|
} |
| 133 |
|
Vector3d vel = sd->getVel(); |
| 134 |
|
RealType m = sd->getMass(); |
| 135 |
|
|
| 128 |
– |
currentSnapshot_->wrapVector(pos); |
| 136 |
|
int bin = getBin(pos); |
| 130 |
– |
binCount[bin] += 1; |
| 137 |
|
|
| 138 |
|
binMass[bin] += m; |
| 139 |
< |
binVel[bin] += vel; |
| 139 |
> |
binP[bin] += m * vel; |
| 140 |
|
binKE[bin] += 0.5 * (m * vel.lengthSquare()); |
| 141 |
|
binDof[bin] += 3; |
| 142 |
|
|
| 160 |
|
} |
| 161 |
|
|
| 162 |
|
for (unsigned int i = 0; i < nBins_; i++) { |
| 163 |
+ |
|
| 164 |
|
if (binDof[i] > 0) { |
| 165 |
|
RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb * |
| 166 |
|
PhysicalConstants::energyConvert); |
| 167 |
|
RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert |
| 168 |
|
/ volume_; |
| 169 |
< |
Vector3d vel = binVel[i] / RealType(binCount[i]); |
| 169 |
> |
Vector3d vel = binP[i] / binMass[i]; |
| 170 |
> |
|
| 171 |
|
dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp); |
| 172 |
|
dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel); |
| 173 |
|
dynamic_cast<Accumulator *>(density->accumulator[i])->add(den); |
| 217 |
|
data_.push_back(density); |
| 218 |
|
} |
| 219 |
|
|
| 212 |
– |
void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) { |
| 213 |
– |
RealType mass = sd->getMass(); |
| 214 |
– |
Vector3d vel = sd->getVel(); |
| 215 |
– |
Vector3d rPos = sd->getPos() - coordinateOrigin_; |
| 216 |
– |
Vector3d aVel = cross(rPos, vel); |
| 220 |
|
|
| 221 |
< |
RealType KE = 0.5 * (mass * vel.lengthSquare()); |
| 219 |
< |
int dof = 3; |
| 221 |
> |
void RNEMDR::processFrame(int istep) { |
| 222 |
|
|
| 223 |
< |
if (sd->isDirectional()) { |
| 224 |
< |
Vector3d angMom = sd->getJ(); |
| 225 |
< |
Mat3x3d I = sd->getI(); |
| 226 |
< |
if (sd->isLinear()) { |
| 227 |
< |
int i = sd->linearAxis(); |
| 228 |
< |
int j = (i + 1) % 3; |
| 229 |
< |
int k = (i + 2) % 3; |
| 230 |
< |
KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) + |
| 231 |
< |
angMom[k] * angMom[k] / I(k, k)); |
| 232 |
< |
dof += 2; |
| 233 |
< |
} else { |
| 234 |
< |
KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) + |
| 235 |
< |
angMom[1] * angMom[1] / I(1, 1) + |
| 236 |
< |
angMom[2] * angMom[2] / I(2, 2)); |
| 237 |
< |
dof += 3; |
| 223 |
> |
Molecule* mol; |
| 224 |
> |
RigidBody* rb; |
| 225 |
> |
StuntDouble* sd; |
| 226 |
> |
SimInfo::MoleculeIterator mi; |
| 227 |
> |
Molecule::RigidBodyIterator rbIter; |
| 228 |
> |
int i; |
| 229 |
> |
|
| 230 |
> |
vector<RealType> binMass(nBins_, 0.0); |
| 231 |
> |
vector<Mat3x3d> binI(nBins_); |
| 232 |
> |
vector<Vector3d> binL(nBins_, V3Zero); |
| 233 |
> |
vector<RealType> binKE(nBins_, 0.0); |
| 234 |
> |
vector<int> binDof(nBins_, 0); |
| 235 |
> |
|
| 236 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 237 |
> |
mol = info_->nextMolecule(mi)) { |
| 238 |
> |
|
| 239 |
> |
// change the positions of atoms which belong to the rigidbodies |
| 240 |
> |
|
| 241 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 242 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 243 |
> |
rb->updateAtomVel(); |
| 244 |
|
} |
| 245 |
|
} |
| 246 |
+ |
|
| 247 |
+ |
if (evaluator_.isDynamic()) { |
| 248 |
+ |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
| 249 |
+ |
} |
| 250 |
|
|
| 251 |
< |
RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb * |
| 252 |
< |
PhysicalConstants::energyConvert); |
| 251 |
> |
// loop over the selected atoms: |
| 252 |
> |
|
| 253 |
> |
for (sd = seleMan_.beginSelected(i); sd != NULL; |
| 254 |
> |
sd = seleMan_.nextSelected(i)) { |
| 255 |
|
|
| 256 |
< |
RealType rinner = (RealType)bin * binWidth_; |
| 257 |
< |
RealType router = (RealType)(bin+1) * binWidth_; |
| 258 |
< |
RealType den = mass * 3.0 * PhysicalConstants::densityConvert |
| 259 |
< |
/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3))); |
| 256 |
> |
// figure out where that object is: |
| 257 |
> |
int bin = getBin( sd->getPos() ); |
| 258 |
> |
|
| 259 |
> |
if (bin >= 0 && bin < nBins_) { |
| 260 |
> |
|
| 261 |
> |
Vector3d rPos = sd->getPos() - coordinateOrigin_; |
| 262 |
> |
Vector3d vel = sd->getVel(); |
| 263 |
> |
RealType m = sd->getMass(); |
| 264 |
> |
Vector3d L = m * cross(rPos, vel); |
| 265 |
> |
Mat3x3d I(0.0); |
| 266 |
> |
I = outProduct(rPos, rPos) * m; |
| 267 |
> |
RealType r2 = rPos.lengthSquare(); |
| 268 |
> |
I(0, 0) += m * r2; |
| 269 |
> |
I(1, 1) += m * r2; |
| 270 |
> |
I(2, 2) += m * r2; |
| 271 |
> |
|
| 272 |
> |
binMass[bin] += m; |
| 273 |
> |
binI[bin] += I; |
| 274 |
> |
binL[bin] += L; |
| 275 |
> |
binKE[bin] += 0.5 * (m * vel.lengthSquare()); |
| 276 |
> |
binDof[bin] += 3; |
| 277 |
> |
|
| 278 |
> |
if (sd->isDirectional()) { |
| 279 |
> |
Vector3d angMom = sd->getJ(); |
| 280 |
> |
Mat3x3d Ia = sd->getI(); |
| 281 |
> |
if (sd->isLinear()) { |
| 282 |
> |
int i = sd->linearAxis(); |
| 283 |
> |
int j = (i + 1) % 3; |
| 284 |
> |
int k = (i + 2) % 3; |
| 285 |
> |
binKE[bin] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) + |
| 286 |
> |
angMom[k] * angMom[k] / Ia(k, k)); |
| 287 |
> |
binDof[bin] += 2; |
| 288 |
> |
} else { |
| 289 |
> |
binKE[bin] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) + |
| 290 |
> |
angMom[1] * angMom[1] / Ia(1, 1) + |
| 291 |
> |
angMom[2] * angMom[2] / Ia(2, 2)); |
| 292 |
> |
binDof[bin] += 3; |
| 293 |
> |
} |
| 294 |
> |
} |
| 295 |
> |
} |
| 296 |
> |
} |
| 297 |
|
|
| 298 |
< |
dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp); |
| 299 |
< |
dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[bin])->add(aVel); |
| 300 |
< |
dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den); |
| 298 |
> |
for (unsigned int i = 0; i < nBins_; i++) { |
| 299 |
> |
RealType rinner = (RealType)i * binWidth_; |
| 300 |
> |
RealType router = (RealType)(i+1) * binWidth_; |
| 301 |
> |
if (binDof[i] > 0) { |
| 302 |
> |
RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb * |
| 303 |
> |
PhysicalConstants::energyConvert); |
| 304 |
> |
RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert |
| 305 |
> |
/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3))); |
| 306 |
|
|
| 307 |
+ |
Vector3d omega = binI[i].inverse() * binL[i]; |
| 308 |
+ |
|
| 309 |
+ |
dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp); |
| 310 |
+ |
dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(omega); |
| 311 |
+ |
dynamic_cast<Accumulator *>(density->accumulator[i])->add(den); |
| 312 |
+ |
dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1); |
| 313 |
+ |
} |
| 314 |
+ |
} |
| 315 |
|
} |
| 316 |
+ |
|
| 317 |
+ |
|
| 318 |
+ |
void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) { |
| 319 |
+ |
} |
| 320 |
|
} |
| 321 |
|
|
